# Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for SearchIO BlastIO parsers."""

import os
import sys
import unittest
import warnings

from Bio import BiopythonParserWarning
from Bio.SearchIO import parse


# test case files are in the Blast directory
TEST_DIR = "Blast"
FMT = "blast-xml"

REFERENCE = (
    "Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, "
    "Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "
    '"Gapped BLAST and PSI-BLAST: a new generation of protein database '
    'search programs", Nucleic Acids Res. 25:3389-3402.'
)


def get_file(filename):
    """Return the path of a test file."""
    return os.path.join(TEST_DIR, filename)


class BlastnXmlCases(unittest.TestCase):
    def test_xml_2212L_blastn_001(self):
        xml_file = get_file("xml_2212L_blastn_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.12", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual(1, qresult.param_score_match)
        self.assertEqual(-3, qresult.param_score_mismatch)
        self.assertEqual(5, qresult.param_gap_open)
        self.assertEqual(2, qresult.param_gap_extend)

        # test parsed values of qresult
        self.assertEqual("gi|1348916|gb|G26684.1|G26684", qresult.id)
        self.assertEqual(
            "human STS STS_D11570, sequence tagged site", qresult.description
        )
        self.assertEqual(285, qresult.seq_len)
        self.assertEqual(371021, qresult.stat_db_num)
        self.assertEqual(1233631384, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.710603, qresult.stat_kappa)
        self.assertEqual(1.37406, qresult.stat_lambda)
        self.assertEqual(1.30725, qresult.stat_entropy)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|9950606|gb|AE004854.1|", hit.id)
        self.assertEqual(
            "Pseudomonas aeruginosa PAO1, section 415 of 529 of the complete genome",
            hit.description,
        )
        self.assertEqual(11884, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(38.1576, hsp.bitscore)
        self.assertEqual(19, hsp.bitscore_raw)
        self.assertEqual(1.0598, hsp.evalue)
        self.assertEqual(67, hsp.query_start)
        self.assertEqual(86, hsp.query_end)
        self.assertEqual(6011, hsp.hit_start)
        self.assertEqual(6030, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(19, hsp.ident_num)
        self.assertEqual(19, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(19, hsp.aln_span)
        self.assertEqual("CAGGCCAGCGACTTCTGGG", str(hsp.query.seq))
        self.assertEqual("CAGGCCAGCGACTTCTGGG", str(hsp.hit.seq))
        self.assertEqual("|||||||||||||||||||", hsp.aln_annotation["similarity"])
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # parse last hit
        hit = qresult[-1]
        self.assertEqual("gi|15073988|emb|AL591786.1|SME591786", hit.id)
        self.assertEqual(
            "Sinorhizobium meliloti 1021 complete chromosome; segment 5/12",
            hit.description,
        )
        self.assertEqual(299350, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(36.1753, hsp.bitscore)
        self.assertEqual(18, hsp.bitscore_raw)
        self.assertEqual(4.18768, hsp.evalue)
        self.assertEqual(203, hsp.query_start)
        self.assertEqual(224, hsp.query_end)
        self.assertEqual(83627, hsp.hit_start)
        self.assertEqual(83648, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(-1, hsp.hit_frame)
        self.assertEqual(20, hsp.ident_num)
        self.assertEqual(20, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(21, hsp.aln_span)
        self.assertEqual("TGAAAGGAAATNAAAATGGAA", str(hsp.query.seq))
        self.assertEqual("TGAAAGGAAATCAAAATGGAA", str(hsp.hit.seq))
        self.assertEqual("||||||||||| |||||||||", hsp.aln_annotation["similarity"])
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastn_001(self):
        xml_file = get_file("xml_2226_blastn_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Zheng Zhang, Scott Schwartz, Lukas Wagner, and "
            'Webb Miller (2000), "A greedy algorithm for '
            'aligning DNA sequences", J Comput Biol 2000; '
            "7(1-2):203-14.",
            qresult.reference,
        )
        self.assertEqual(1.0, qresult.param_score_match)
        self.assertEqual(-2.0, qresult.param_score_mismatch)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;m;", qresult.param_filter)
        self.assertEqual(0.0, qresult.param_gap_open)
        self.assertEqual(0.0, qresult.param_gap_extend)
        self.assertEqual("blastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(7616765.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|356995852:1-490", qresult.id)
        self.assertEqual(
            "Mus musculus POU domain, class 5, transcription factor 1 (Pou5f1), transcript variant 1, mRNA",
            qresult.description,
        )
        self.assertEqual(490, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(31860807.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|356995852|ref|NM_013633.3|", hit.id)
        self.assertEqual(
            "Mus musculus POU "
            "domain, class 5, transcription factor 1 (Pou5f1), "
            "transcript variant 1, mRNA",
            hit.description,
        )
        self.assertEqual(1353, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(905.979, hsp.bitscore)
        self.assertEqual(490, hsp.bitscore_raw)
        self.assertEqual(0, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(490, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(490, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(490, hsp.ident_num)
        self.assertEqual(490, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(490, hsp.aln_span)
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207307-1207372 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(66, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(3506256.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|94721341|ref|NM_001040441.1|", hit.id)
        self.assertEqual(
            "Homo sapiens zinc finger and BTB domain containing 8A (ZBTB8A), mRNA",
            hit.description,
        )
        self.assertEqual(7333, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(115.613, hsp.bitscore)
        self.assertEqual(62, hsp.bitscore_raw)
        self.assertEqual(5.52066e-29, hsp.evalue)
        self.assertEqual(4, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(3676, hsp.hit_start)
        self.assertEqual(3738, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(62, hsp.ident_num)
        self.assertEqual(62, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(62, hsp.aln_span)
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(98.9927, hsp.bitscore)
        self.assertEqual(53, hsp.bitscore_raw)
        self.assertEqual(5.55986e-24, hsp.evalue)
        self.assertEqual(5, hsp.query_start)
        self.assertEqual(58, hsp.query_end)
        self.assertEqual(2823, hsp.hit_start)
        self.assertEqual(2876, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(53, hsp.ident_num)
        self.assertEqual(53, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(53, hsp.aln_span)
        self.assertEqual(
            "CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA", str(hsp.query.seq)
        )
        self.assertEqual(
            "CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA", str(hsp.hit.seq)
        )
        self.assertEqual(
            "|||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|332865372|ref|XM_003318468.1|", hit.id)
        self.assertEqual(
            "PREDICTED: Pan "
            "troglodytes zinc finger protein 273, transcript "
            "variant 1 (ZNF273), mRNA",
            hit.description,
        )
        self.assertEqual(4430, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(111.919, hsp.bitscore)
        self.assertEqual(60, hsp.bitscore_raw)
        self.assertEqual(7.14143e-28, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(2734, hsp.hit_start)
        self.assertEqual(2800, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(-1, hsp.hit_frame)
        self.assertEqual(64, hsp.ident_num)
        self.assertEqual(64, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(66, hsp.aln_span)
        self.assertEqual(
            "TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_xml_2226_blastn_002(self):
        xml_file = get_file("xml_2226_blastn_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Zheng Zhang, Scott Schwartz, Lukas Wagner, and "
            'Webb Miller (2000), "A greedy algorithm for '
            'aligning DNA sequences", J Comput Biol 2000; '
            "7(1-2):203-14.",
            qresult.reference,
        )
        self.assertEqual(1.0, qresult.param_score_match)
        self.assertEqual(-2.0, qresult.param_score_mismatch)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;m;", qresult.param_filter)
        self.assertEqual(0.0, qresult.param_gap_open)
        self.assertEqual(0.0, qresult.param_gap_extend)
        self.assertEqual("blastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(7616765.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))
        self.assertEqual([], list(qresult.hits))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastn_003(self):
        xml_file = get_file("xml_2226_blastn_003.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Zheng Zhang, Scott Schwartz, Lukas Wagner, and "
            'Webb Miller (2000), "A greedy algorithm for '
            'aligning DNA sequences", J Comput Biol 2000; '
            "7(1-2):203-14.",
            qresult.reference,
        )
        self.assertEqual(1.0, qresult.param_score_match)
        self.assertEqual(-2.0, qresult.param_score_mismatch)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;m;", qresult.param_filter)
        self.assertEqual(0.0, qresult.param_gap_open)
        self.assertEqual(0.0, qresult.param_gap_extend)
        self.assertEqual("blastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("gi|356995852:1-490", qresult.id)
        self.assertEqual(
            "Mus musculus POU domain, class 5, transcription "
            "factor 1 (Pou5f1), transcript variant 1, mRNA",
            qresult.description,
        )
        self.assertEqual(490, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(31860807.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|356995852|ref|NM_013633.3|", hit.id)
        self.assertEqual(
            "Mus musculus POU "
            "domain, class 5, transcription factor 1 (Pou5f1), "
            "transcript variant 1, mRNA",
            hit.description,
        )
        self.assertEqual(1353, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(905.979, hsp.bitscore)
        self.assertEqual(490, hsp.bitscore_raw)
        self.assertEqual(0, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(490, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(490, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(490, hsp.ident_num)
        self.assertEqual(490, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(490, hsp.aln_span)
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastn_004(self):
        xml_file = get_file("xml_2226_blastn_004.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1
        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207307-1207372 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(66, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(3506256.0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|94721341|ref|NM_001040441.1|", hit.id)
        self.assertEqual(
            "Homo sapiens zinc finger and BTB domain containing 8A (ZBTB8A), mRNA",
            hit.description,
        )
        self.assertEqual(7333, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(115.613, hsp.bitscore)
        self.assertEqual(62, hsp.bitscore_raw)
        self.assertEqual(5.52066e-29, hsp.evalue)
        self.assertEqual(4, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(3676, hsp.hit_start)
        self.assertEqual(3738, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(62, hsp.ident_num)
        self.assertEqual(62, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(62, hsp.aln_span)
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(98.9927, hsp.bitscore)
        self.assertEqual(53, hsp.bitscore_raw)
        self.assertEqual(5.55986e-24, hsp.evalue)
        self.assertEqual(5, hsp.query_start)
        self.assertEqual(58, hsp.query_end)
        self.assertEqual(2823, hsp.hit_start)
        self.assertEqual(2876, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(53, hsp.ident_num)
        self.assertEqual(53, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(53, hsp.aln_span)
        self.assertEqual(
            "CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA", str(hsp.query.seq)
        )
        self.assertEqual(
            "CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA", str(hsp.hit.seq)
        )
        self.assertEqual(
            "|||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|332865372|ref|XM_003318468.1|", hit.id)
        self.assertEqual(
            "PREDICTED: Pan "
            "troglodytes zinc finger protein 273, transcript "
            "variant 1 (ZNF273), mRNA",
            hit.description,
        )
        self.assertEqual(4430, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(111.919, hsp.bitscore)
        self.assertEqual(60, hsp.bitscore_raw)
        self.assertEqual(7.14143e-28, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(2734, hsp.hit_start)
        self.assertEqual(2800, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(-1, hsp.hit_frame)
        self.assertEqual(64, hsp.ident_num)
        self.assertEqual(64, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(66, hsp.aln_span)
        self.assertEqual(
            "TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastn_005(self):
        xml_file = get_file("xml_2226_blastn_005.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Zheng Zhang, Scott Schwartz, Lukas Wagner, and "
            'Webb Miller (2000), "A greedy algorithm for '
            'aligning DNA sequences", J Comput Biol 2000; '
            "7(1-2):203-14.",
            qresult.reference,
        )
        self.assertEqual(1.0, qresult.param_score_match)
        self.assertEqual(-2.0, qresult.param_score_mismatch)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;m;", qresult.param_filter)
        self.assertEqual(0.0, qresult.param_gap_open)
        self.assertEqual(0.0, qresult.param_gap_extend)
        self.assertEqual("blastn", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|356995852:1-490", qresult.id)
        self.assertEqual(
            "Mus musculus POU domain, class 5, transcription "
            "factor 1 (Pou5f1), transcript variant 1, mRNA",
            qresult.description,
        )
        self.assertEqual(490, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|356995852|ref|NM_013633.3|", hit.id)
        self.assertEqual(
            "Mus musculus POU "
            "domain, class 5, transcription factor 1 (Pou5f1), "
            "transcript variant 1, mRNA",
            hit.description,
        )
        self.assertEqual(1353, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(905.979, hsp.bitscore)
        self.assertEqual(490, hsp.bitscore_raw)
        self.assertEqual(0, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(490, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(490, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(490, hsp.ident_num)
        self.assertEqual(490, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(490, hsp.aln_span)
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207307-1207372 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(66, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.46, qresult.stat_kappa)
        self.assertEqual(1.28, qresult.stat_lambda)
        self.assertEqual(0.85, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|332237160|ref|XM_003267724.1|", hit.id)
        self.assertEqual(
            "PREDICTED: Nomascus leucogenys ATG14 autophagy "
            "related 14 homolog (S. cerevisiae) (ATG14), mRNA",
            hit.description,
        )
        self.assertEqual(4771, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(115.613, hsp.bitscore)
        self.assertEqual(62, hsp.bitscore_raw)
        self.assertEqual(3.35972e-23, hsp.evalue)
        self.assertEqual(4, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(2864, hsp.hit_start)
        self.assertEqual(2926, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(62, hsp.ident_num)
        self.assertEqual(62, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(62, hsp.aln_span)
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|332254616|ref|XM_003276378.1|", hit.id)
        self.assertEqual(
            "PREDICTED: Nomascus leucogenys S100P binding "
            "protein, transcript variant 2 (S100PBP), mRNA",
            hit.description,
        )
        self.assertEqual(4345, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(111.919, hsp.bitscore)
        self.assertEqual(60, hsp.bitscore_raw)
        self.assertEqual(4.34607e-22, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(66, hsp.query_end)
        self.assertEqual(2791, hsp.hit_start)
        self.assertEqual(2857, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(-1, hsp.hit_frame)
        self.assertEqual(64, hsp.ident_num)
        self.assertEqual(64, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(66, hsp.aln_span)
        self.assertEqual(
            "TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "TCATGCCACTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)


class BlastpXmlCases(unittest.TestCase):
    def test_xml_2212L_blastp_001(self):
        xml_file = get_file("xml_2212L_blastp_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.12", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("nr", qresult.target)

        self.assertEqual("gi|49176427|ref|NP_418280.3|", qresult.id)
        self.assertEqual(
            "component of Sec-independent translocase [Escherichia coli K12]",
            qresult.description,
        )
        self.assertEqual(103, qresult.seq_len)
        self.assertEqual(2934173, qresult.stat_db_num)
        self.assertEqual(1011751523, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(212, len(qresult))
        # check for alternative ID results
        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|26250604|ref|NP_756644.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|30064867|ref|NP_839038.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|24115132|ref|NP_709642.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|24054404|gb|AAN45349.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|2367310|gb|AAC76839.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|30043127|gb|AAP18849.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|26111035|gb|AAN83218.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"],
            qresult["gi|3193217|gb|AAC19240.1|"],
        )

        self.assertEqual(
            qresult["gi|49176427|ref|NP_418280.3|"], qresult["gi|7444818|pir||E65188"]
        )

        hit = qresult[0]
        self.assertEqual("gi|49176427|ref|NP_418280.3|", hit.id)
        self.assertEqual(
            "component of Sec-independent translocase [Escherichia coli K12]",
            hit.description,
        )
        self.assertEqual(10, len(hit.id_all))
        self.assertEqual(10, len(hit.description_all))
        self.assertEqual(103, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(185.267, hsp.bitscore)
        self.assertEqual(469, hsp.bitscore_raw)
        self.assertEqual(4.20576e-46, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(103, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(103, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(103, hsp.ident_num)
        self.assertEqual(103, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(103, hsp.aln_span)
        self.assertEqual(
            "MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # parse last hit
        hit = qresult[-1]
        self.assertEqual("gi|39593039|emb|CAE64508.1|", hit.id)
        self.assertEqual(
            "Hypothetical protein CBG09238 [Caenorhabditis briggsae]", hit.description
        )
        self.assertEqual(960, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(31.5722, hsp.bitscore)
        self.assertEqual(70, hsp.bitscore_raw)
        self.assertEqual(7.7721, hsp.evalue)
        self.assertEqual(54, hsp.query_start)
        self.assertEqual(102, hsp.query_end)
        self.assertEqual(409, hsp.hit_start)
        self.assertEqual(459, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(19, hsp.ident_num)
        self.assertEqual(33, hsp.pos_num)
        self.assertEqual(4, hsp.gap_num)
        self.assertEqual(51, hsp.aln_span)
        self.assertEqual(
            "KAMSDDEPKQD---KTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ", str(hsp.query.seq)
        )
        self.assertEqual(
            "KKEADDKAKKDLEAKTKKEADEKAKKEADEKA-KKEAEAKTKEAEAKTKKE", str(hsp.hit.seq)
        )
        self.assertEqual(
            "K  +DD+ K+D   KT ++AD  AK  AD++A   + +AKT++A+   K++",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2218_blastp_001(self):
        xml_file = get_file("xml_2218_blastp_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.18+", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("nr", qresult.target)

        self.assertEqual("31493", qresult.id)
        self.assertEqual("unnamed protein product", qresult.description)
        self.assertEqual(70, qresult.seq_len)
        self.assertEqual(15287, qresult.stat_db_num)
        self.assertEqual(7033566, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(10, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|151942244|gb|EDN60600.1|", hit.id)
        self.assertEqual(
            "cytosolic iron-sulfur protein assembly protein [Saccharomyces cerevisiae YJM789]",
            hit.description,
        )
        self.assertEqual(330, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(33.113, hsp.bitscore)
        self.assertEqual(74, hsp.bitscore_raw)
        self.assertEqual(0.0185319, hsp.evalue)
        self.assertEqual(14, hsp.query_start)
        self.assertEqual(62, hsp.query_end)
        self.assertEqual(113, hsp.hit_start)
        self.assertEqual(163, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(16, hsp.ident_num)
        self.assertEqual(27, hsp.pos_num)
        self.assertEqual(2, hsp.gap_num)
        self.assertEqual(50, hsp.aln_span)
        self.assertEqual(
            "AWNKDRTQIAICPNNHEVHIYE--KSGAKWNKVHELKEHNGQVTGIDWAP", str(hsp.query.seq)
        )
        self.assertEqual(
            "AWSNDGYYLATCSRDKSVWIWETDESGEEYECISVLQEHSQDVKHVIWHP", str(hsp.hit.seq)
        )
        self.assertEqual(
            "AW+ D   +A C  +  V I+E  +SG ++  +  L+EH+  V  + W P",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # parse last hit
        hit = qresult[-1]
        self.assertEqual("gi|151567870|pdb|2PM9|B", hit.id)
        self.assertEqual(
            "Chain B, Crystal Structure Of Yeast Sec1331 VERTEX ELEMENT OF THE Copii Vesicular Coat",
            hit.description,
        )
        self.assertEqual(297, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(30.8018, hsp.bitscore)
        self.assertEqual(68, hsp.bitscore_raw)
        self.assertEqual(0.0919731, hsp.evalue)
        self.assertEqual(20, hsp.query_start)
        self.assertEqual(62, hsp.query_end)
        self.assertEqual(67, hsp.hit_start)
        self.assertEqual(109, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(11, hsp.ident_num)
        self.assertEqual(23, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(42, hsp.aln_span)
        self.assertEqual(
            "TQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAP", str(hsp.query.seq)
        )
        self.assertEqual("TILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAP", str(hsp.hit.seq))
        self.assertEqual(
            "T +A C  + +V I+++   +W+++     H+  V  + WAP",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2218_blastp_002(self):
        xml_file = get_file("xml_2218_blastp_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.18+", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(0.01, qresult.param_evalue_threshold)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("m L; R -d repeat/repeat_9606;", qresult.param_filter)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("gpipe/9606/Previous/protein", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("gi|585505|sp|Q08386|MOPB_RHOCA", qresult.id)
        self.assertEqual(
            "Molybdenum-pterin-binding protein mopB >gi|310278|gb|AAA71913.1| molybdenum-pterin-binding protein",
            qresult.description,
        )
        self.assertEqual(270, qresult.seq_len)
        self.assertEqual(27252, qresult.stat_db_num)
        self.assertEqual(13958303, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual("gi|129628|sp|P07175.1|PARA_AGRTU", qresult.id)
        self.assertEqual("Protein parA", qresult.description)
        self.assertEqual(222, qresult.seq_len)
        self.assertEqual(27252, qresult.stat_db_num)
        self.assertEqual(13958303, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)

    def test_xml_2218L_blastp_001(self):
        xml_file = get_file("xml_2218L_blastp_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.18", qresult.version)
        self.assertEqual(
            "~Reference: Altschul, Stephen F., "
            "Thomas L. Madden, Alejandro A. Schaffer, "
            "~Jinghui Zhang, Zheng Zhang, Webb Miller, "
            'and David J. Lipman (1997), ~"Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search~programs",  '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(1e-05, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual(
            "/Users/pjcock/Downloads/Software/blast-2.2.18/data/nr", qresult.target
        )

        # test parsed values of the first qresult
        self.assertEqual("Fake", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(9, qresult.seq_len)
        self.assertEqual(6589360, qresult.stat_db_num)
        self.assertEqual(2253133281, qresult.stat_db_len)
        self.assertEqual(2.02782e10, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2222_blastp_001(self):
        xml_file = get_file("xml_2222_blastp_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.22+", qresult.version)
        self.assertEqual(
            'Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.',
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(1e-06, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("nr", qresult.target)

        self.assertEqual("1", qresult.id)
        self.assertEqual("gi|3298468|dbj|BAA31520.1| SAMIPF", qresult.description)
        self.assertEqual(107, qresult.seq_len)
        self.assertEqual(8994603, qresult.stat_db_num)
        self.assertEqual(-1216159329, qresult.stat_db_len)
        self.assertEqual(76934807744, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(10, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|3298468|dbj|BAA31520.1|", hit.id)
        self.assertEqual("SAMIPF [Aster tripolium]", hit.description)
        self.assertEqual(107, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(204.912011757068, hsp.bitscore)
        self.assertEqual(520, hsp.bitscore_raw)
        self.assertEqual(1.77242652875017e-51, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(107, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(107, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(107, hsp.ident_num)
        self.assertEqual(107, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(107, hsp.aln_span)
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # parse last hit
        hit = qresult[-1]
        self.assertEqual("gi|162809290|dbj|BAF95576.1|", hit.id)
        self.assertEqual(
            "tonoplast intrinsic protein [Nicotiana tabacum]", hit.description
        )
        self.assertEqual(251, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(177.948041442853, hsp.bitscore)
        self.assertEqual(450, hsp.bitscore_raw)
        self.assertEqual(2.0302699895292e-43, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(107, hsp.query_end)
        self.assertEqual(80, hsp.hit_start)
        self.assertEqual(187, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(91, hsp.ident_num)
        self.assertEqual(95, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(107, hsp.aln_span)
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITLFRGILYIIAQLLGSTVACFLLEFATGGMSTGAFALSAGVSVWNAFVFEIVMTFGLVYTVYATAIDPKKGDLGVIAPIAIGFIVGANI",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "GGHVNPAVTFGAFVGGNITL RGI+YIIAQLLGSTVAC LL+F T  M+ G F+LSAGV V NA VFEIVMTFGLVYTVYATAIDPKKG LG IAPIAIGFIVGANI",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

    # def test_xml_2218L_rpsblast_001(self):
    # PSI-blast, handle later

    def test_xml_2226_blastp_001(self):
        xml_file = get_file("xml_2226_blastp_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(156650.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis "
            "subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(361344, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|308175296|ref|YP_003922001.1|", hit.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus amyloliquefaciens DSM 7]",
            hit.description,
        )
        self.assertEqual(100, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(139.428, hsp.bitscore)
        self.assertEqual(350, hsp.bitscore_raw)
        self.assertEqual(1.99275e-46, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(102, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(100, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(69, hsp.ident_num)
        self.assertEqual(81, hsp.pos_num)
        self.assertEqual(2, hsp.gap_num)
        self.assertEqual(102, hsp.aln_span)
        self.assertEqual(
            "MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "MKKIFGCLFFILLLAGCGVTNEKSQGEDAG--EKLVTKEGTYVGLADTHTIEVTVDHEPVSFDITEESADDVKNLNNGEKVTVKYQKNSKGQLVLKDIEPAN",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "MKK    LFFILLL+GCGV ++KSQGED      + TKEGTYVGLADTHTIEVTVD+EPVS DITEES  D+   N+G+KVT+ Y+KN +GQL+LKDIE AN",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(345626, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|11464971|ref|NP_062422.1|", hit.id)
        self.assertEqual("pleckstrin [Mus musculus]", hit.description)
        self.assertEqual(350, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(205.682, hsp.bitscore)
        self.assertEqual(522, hsp.bitscore_raw)
        self.assertEqual(2.24956e-69, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(98, hsp.ident_num)
        self.assertEqual(98, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(43.5134, hsp.bitscore)
        self.assertEqual(101, hsp.bitscore_raw)
        self.assertEqual(2.90061e-09, hsp.evalue)
        self.assertEqual(2, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(245, hsp.hit_start)
        self.assertEqual(345, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(29, hsp.ident_num)
        self.assertEqual(48, hsp.pos_num)
        self.assertEqual(6, hsp.gap_num)
        self.assertEqual(100, hsp.aln_span)
        self.assertEqual(
            "IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "I++G L+K+G     WK    +L ED   + +Y       P G + L+G  +TS     D  K     + +I T  +  ++ QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|350596020|ref|XP_003360649.2|", hit.id)
        self.assertEqual("PREDICTED: pleckstrin-like [Sus scrofa]", hit.description)
        self.assertEqual(228, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(199.519, hsp.bitscore)
        self.assertEqual(506, hsp.bitscore_raw)
        self.assertEqual(1.97058e-68, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_xml_2226_blastp_002(self):
        xml_file = get_file("xml_2226_blastp_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(156650.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastp_003(self):
        xml_file = get_file("xml_2226_blastp_003.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis "
            "subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(361344, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|308175296|ref|YP_003922001.1|", hit.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus amyloliquefaciens DSM 7]",
            hit.description,
        )
        self.assertEqual(100, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(139.428, hsp.bitscore)
        self.assertEqual(350, hsp.bitscore_raw)
        self.assertEqual(1.99275e-46, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(102, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(100, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(69, hsp.ident_num)
        self.assertEqual(81, hsp.pos_num)
        self.assertEqual(2, hsp.gap_num)
        self.assertEqual(102, hsp.aln_span)
        self.assertEqual(
            "MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "MKKIFGCLFFILLLAGCGVTNEKSQGEDAG--EKLVTKEGTYVGLADTHTIEVTVDHEPVSFDITEESADDVKNLNNGEKVTVKYQKNSKGQLVLKDIEPAN",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "MKK    LFFILLL+GCGV ++KSQGED      + TKEGTYVGLADTHTIEVTVD+EPVS DITEES  D+   N+G+KVT+ Y+KN +GQL+LKDIE AN",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastp_004(self):
        xml_file = get_file("xml_2226_blastp_004.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(345626, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|11464971|ref|NP_062422.1|", hit.id)
        self.assertEqual("pleckstrin [Mus musculus]", hit.description)
        self.assertEqual(350, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(205.682, hsp.bitscore)
        self.assertEqual(522, hsp.bitscore_raw)
        self.assertEqual(2.24956e-69, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(98, hsp.ident_num)
        self.assertEqual(98, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(43.5134, hsp.bitscore)
        self.assertEqual(101, hsp.bitscore_raw)
        self.assertEqual(2.90061e-09, hsp.evalue)
        self.assertEqual(2, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(245, hsp.hit_start)
        self.assertEqual(345, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(29, hsp.ident_num)
        self.assertEqual(48, hsp.pos_num)
        self.assertEqual(6, hsp.gap_num)
        self.assertEqual(100, hsp.aln_span)
        self.assertEqual(
            "IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "I++G L+K+G     WK    +L ED   + +Y       P G + L+G  +TS     D  K     + +I T  +  ++ QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|350596020|ref|XP_003360649.2|", hit.id)
        self.assertEqual("PREDICTED: pleckstrin-like [Sus scrofa]", hit.description)
        self.assertEqual(228, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(199.519, hsp.bitscore)
        self.assertEqual(506, hsp.bitscore_raw)
        self.assertEqual(1.97058e-68, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastp_005(self):
        xml_file = get_file("xml_2226_blastp_005.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("F", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastp", qresult.program)
        self.assertEqual("refseq_protein", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(12646943, qresult.stat_db_num)
        self.assertEqual(4397139428, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(12646943, qresult.stat_db_num)
        self.assertEqual(4397139428, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))
        # check for alternative ID results
        self.assertEqual(
            qresult["gi|16080617|ref|NP_391444.1|"],
            qresult["gi|221311516|ref|ZP_03593363.1|"],
        )

        self.assertEqual(
            qresult["gi|16080617|ref|NP_391444.1|"],
            qresult["gi|221315843|ref|ZP_03597648.1|"],
        )

        self.assertEqual(
            qresult["gi|16080617|ref|NP_391444.1|"],
            qresult["gi|221320757|ref|ZP_03602051.1|"],
        )

        self.assertEqual(
            qresult["gi|16080617|ref|NP_391444.1|"],
            qresult["gi|221325043|ref|ZP_03606337.1|"],
        )

        self.assertEqual(
            qresult["gi|16080617|ref|NP_391444.1|"],
            qresult["gi|321313111|ref|YP_004205398.1|"],
        )

        hit = qresult[0]
        self.assertEqual("gi|16080617|ref|NP_391444.1|", hit.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus "
            "subtilis subsp. subtilis str. 168]",
            hit.description,
        )
        self.assertEqual(6, len(hit.id_all))
        self.assertEqual(6, len(hit.description_all))
        self.assertEqual(102, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(205.297, hsp.bitscore)
        self.assertEqual(521, hsp.bitscore_raw)
        self.assertEqual(1.45285e-66, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(102, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(102, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(102, hsp.ident_num)
        self.assertEqual(102, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(102, hsp.aln_span)
        self.assertEqual(
            "MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(12646943, qresult.stat_db_num)
        self.assertEqual(4397139428, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|11464971|ref|NP_062422.1|", hit.id)
        self.assertEqual("pleckstrin [Mus musculus]", hit.description)
        self.assertEqual(350, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(205.682, hsp.bitscore)
        self.assertEqual(522, hsp.bitscore_raw)
        self.assertEqual(1.54412e-63, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(98, hsp.ident_num)
        self.assertEqual(98, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(43.5134, hsp.bitscore)
        self.assertEqual(101, hsp.bitscore_raw)
        self.assertEqual(0.00199101, hsp.evalue)
        self.assertEqual(2, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(245, hsp.hit_start)
        self.assertEqual(345, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(29, hsp.ident_num)
        self.assertEqual(48, hsp.pos_num)
        self.assertEqual(6, hsp.gap_num)
        self.assertEqual(100, hsp.aln_span)
        self.assertEqual(
            "IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "I++G L+K+G     WK    +L ED   + +Y       P G + L+G  +TS     D  K     + +I T  +  ++ QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|350596020|ref|XP_003360649.2|", hit.id)
        self.assertEqual("PREDICTED: pleckstrin-like [Sus scrofa]", hit.description)
        self.assertEqual(228, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(199.519, hsp.bitscore)
        self.assertEqual(506, hsp.bitscore_raw)
        self.assertEqual(1.35263e-62, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)


class BlastxXmlCases(unittest.TestCase):
    def test_xml_2212L_blastx_001(self):
        xml_file = get_file("xml_2212L_blastx_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.12", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("nr", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("gi|1347369|gb|G25137.1|G25137", qresult.id)
        self.assertEqual(
            "human STS EST48004, sequence tagged site", qresult.description
        )
        self.assertEqual(556, qresult.seq_len)
        self.assertEqual(2934173, qresult.stat_db_num)
        self.assertEqual(1011751523, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)

        # test parsed values of the first hit
        hit = qresult[0]
        self.assertEqual("gi|12654095|gb|AAH00859.1|", hit.id)
        self.assertEqual(
            "Unknown (protein for IMAGE:3459481) [Homo sapiens]", hit.description
        )
        self.assertEqual(319, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(247.284, hsp.bitscore)
        self.assertEqual(630, hsp.bitscore_raw)
        self.assertEqual(1.69599e-64, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(399, hsp.query_end)
        self.assertEqual(155, hsp.hit_start)
        self.assertEqual(288, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(122, hsp.ident_num)
        self.assertEqual(123, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(133, hsp.aln_span)
        self.assertEqual(
            "DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW  IA AVPGR K+",
            hsp.aln_annotation["similarity"],
        )

        # test parsed values of last hit
        hit = qresult[-1]
        self.assertEqual("gi|72081091|ref|XP_800619.1|", hit.id)
        self.assertEqual(
            "PREDICTED: hypothetical protein XP_795526 [Strongylocentrotus purpuratus]",
            hit.description,
        )
        self.assertEqual(337, hit.seq_len)

        hsp = hit.hsps[0]
        self.assertEqual(32.3426, hsp.bitscore)
        self.assertEqual(72, hsp.bitscore_raw)
        self.assertEqual(8.57476, hsp.evalue)
        self.assertEqual(39, hsp.query_start)
        self.assertEqual(231, hsp.query_end)
        self.assertEqual(105, hsp.hit_start)
        self.assertEqual(172, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(21, hsp.ident_num)
        self.assertEqual(37, hsp.pos_num)
        self.assertEqual(3, hsp.gap_num)
        self.assertEqual(
            "AGTNSRWEVIANYMNI--HSSSGVKRT-AKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "SSSNSSSKASASSSNVGASSSSGTKKSDSKSSNESSKSKRDKEDHKEGSINRSKDEKVSKEHRVVKE",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "+ +NS  +  A+  N+   SSSG K++ +K     +KS +  + H++  IN+   +K  KEH VV +",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2222_blastx_001(self):
        xml_file = get_file("xml_2222_blastx_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.22+", qresult.version)
        self.assertEqual(
            'Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.',
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(0.0001, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("nr", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("1", qresult.id)
        self.assertEqual(
            "gi|4104054|gb|AH007193.1|SEG_CVIGS Centaurea vallesiaca 18S ribosomal RNA gene, partial sequence",
            qresult.description,
        )
        self.assertEqual(1002, qresult.seq_len)
        self.assertEqual(8994603, qresult.stat_db_num)
        self.assertEqual(-1216159329, qresult.stat_db_len)
        self.assertEqual(367397307882, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)

        # test parsed values of the first hit
        hit = qresult[0]
        self.assertEqual("gi|149390769|gb|ABR25402.1|", hit.id)
        self.assertEqual(
            "unknown [Oryza sativa (indica cultivar-group)]", hit.description
        )
        self.assertEqual(26, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(54.2989775733826, hsp.bitscore)
        self.assertEqual(129, hsp.bitscore_raw)
        self.assertEqual(1.83262460293058e-05, hsp.evalue)
        self.assertEqual(910, hsp.query_start)
        self.assertEqual(988, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(26, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(24, hsp.ident_num)
        self.assertEqual(25, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(26, hsp.aln_span)
        self.assertEqual("HMLVSKIKPCMCKYEQIQTVKLRMAH", str(hsp.query.seq))
        self.assertEqual("HMLVSKIKPCMCKYELIRTVKLRMAH", str(hsp.hit.seq))
        self.assertEqual("HMLVSKIKPCMCKYE I+TVKLRMAH", hsp.aln_annotation["similarity"])

    def test_xml_2226_blastx_001(self):
        xml_file = get_file("xml_2226_blastx_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein "
            'database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207057-1207541 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(485, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(662354, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|332258565|ref|XP_003278367.1|", hit.id)
        self.assertEqual(
            "PREDICTED: UPF0764 protein C16orf89-like [Nomascus leucogenys]",
            hit.description,
        )
        self.assertEqual(132, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(121.709, hsp.bitscore)
        self.assertEqual(304, hsp.bitscore_raw)
        self.assertEqual(2.9522e-38, hsp.evalue)
        self.assertEqual(15, hsp.query_start)
        self.assertEqual(300, hsp.query_end)
        self.assertEqual(24, hsp.hit_start)
        self.assertEqual(119, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(69, hsp.ident_num)
        self.assertEqual(74, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(95, hsp.aln_span)
        self.assertEqual(
            "LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "LRRSFALVAQ  VQW +LG PQPPPPGFK FSCLS  SSW+YRH+PP L NF+FLVE GF HVGQAGLE   SG+ P   SQS GI GVSH AQP",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(51.6026, hsp.bitscore)
        self.assertEqual(122, hsp.bitscore_raw)
        self.assertEqual(2.73605e-12, hsp.evalue)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(459, hsp.query_end)
        self.assertEqual(31, hsp.hit_start)
        self.assertEqual(98, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(34, hsp.ident_num)
        self.assertEqual(41, hsp.pos_num)
        self.assertEqual(5, hsp.gap_num)
        self.assertEqual(72, hsp.aln_span)
        self.assertEqual(
            "VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "V   RVQ ++L S QPP P FK FS LSL SSW+ R  PPH AN     F F +   F  V QAG++ +  G",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|33188429|ref|NP_872601.1|", hit.id)
        self.assertEqual(
            "histone demethylase UTY isoform 1 [Homo sapiens]", hit.description
        )
        self.assertEqual(1079, hit.seq_len)
        self.assertEqual(6, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(104.375, hsp.bitscore)
        self.assertEqual(259, hsp.bitscore_raw)
        self.assertEqual(6.31914e-29, hsp.evalue)
        self.assertEqual(18, hsp.query_start)
        self.assertEqual(291, hsp.query_end)
        self.assertEqual(988, hsp.hit_start)
        self.assertEqual(1079, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(59, hsp.ident_num)
        self.assertEqual(66, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(91, hsp.aln_span)
        self.assertEqual(
            "SFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQ",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "SFQESLRAGMQWCDLSSLQPPPPGFKRFSHLSLPNSWNYRHLPSCPTNFCIFVETGFHHVGQACLELLTSGGLLASASQSAGITGVSHHAR",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "SF    +AG+QW DL   QPPPPGFK FS LS P+SW+YRH+P C  NF   VETGF+HVGQA LE   SG L A ASQS GITGVSHHA+",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)

    def test_xml_2226_blastx_002(self):
        xml_file = get_file("xml_2226_blastx_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein database "
            'search programs", Nucleic Acids Res. 25:3389-3402.',
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastx_003(self):
        xml_file = get_file("xml_2226_blastx_003.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein database "
            'search programs", Nucleic Acids Res. 25:3389-3402.',
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("db/minirefseq_prot", qresult.target)

        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207057-1207541 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(485, qresult.seq_len)
        self.assertEqual(20, qresult.stat_db_num)
        self.assertEqual(6406, qresult.stat_db_len)
        self.assertEqual(662354, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|332258565|ref|XP_003278367.1|", hit.id)
        self.assertEqual(
            "PREDICTED: UPF0764 protein C16orf89-like [Nomascus leucogenys]",
            hit.description,
        )
        self.assertEqual(132, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(121.709, hsp.bitscore)
        self.assertEqual(304, hsp.bitscore_raw)
        self.assertEqual(2.9522e-38, hsp.evalue)
        self.assertEqual(15, hsp.query_start)
        self.assertEqual(300, hsp.query_end)
        self.assertEqual(24, hsp.hit_start)
        self.assertEqual(119, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(69, hsp.ident_num)
        self.assertEqual(74, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(95, hsp.aln_span)
        self.assertEqual(
            "LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "LRRSFALVAQ  VQW +LG PQPPPPGFK FSCLS  SSW+YRH+PP L NF+FLVE GF HVGQAGLE   SG+ P   SQS GI GVSH AQP",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(51.6026, hsp.bitscore)
        self.assertEqual(122, hsp.bitscore_raw)
        self.assertEqual(2.73605e-12, hsp.evalue)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(459, hsp.query_end)
        self.assertEqual(31, hsp.hit_start)
        self.assertEqual(98, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(34, hsp.ident_num)
        self.assertEqual(41, hsp.pos_num)
        self.assertEqual(5, hsp.gap_num)
        self.assertEqual(72, hsp.aln_span)
        self.assertEqual(
            "VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "V   RVQ ++L S QPP P FK FS LSL SSW+ R  PPH AN     F F +   F  V QAG++ +  G",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|33188429|ref|NP_872601.1|", hit.id)
        self.assertEqual(
            "histone demethylase UTY isoform 1 [Homo sapiens]", hit.description
        )
        self.assertEqual(1079, hit.seq_len)
        self.assertEqual(6, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(104.375, hsp.bitscore)
        self.assertEqual(259, hsp.bitscore_raw)
        self.assertEqual(6.31914e-29, hsp.evalue)
        self.assertEqual(18, hsp.query_start)
        self.assertEqual(291, hsp.query_end)
        self.assertEqual(988, hsp.hit_start)
        self.assertEqual(1079, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(59, hsp.ident_num)
        self.assertEqual(66, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(91, hsp.aln_span)
        self.assertEqual(
            "SFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQ",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "SFQESLRAGMQWCDLSSLQPPPPGFKRFSHLSLPNSWNYRHLPSCPTNFCIFVETGFHHVGQACLELLTSGGLLASASQSAGITGVSHHAR",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "SF    +AG+QW DL   QPPPPGFK FS LS P+SW+YRH+P C  NF   VETGF+HVGQA LE   SG L A ASQS GITGVSHHA+",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_blastx_004(self):
        xml_file = get_file("xml_2226_blastx_004.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb "
            'Miller, and David J. Lipman (1997), "Gapped BLAST '
            "and PSI-BLAST: a new generation of protein database "
            'search programs", Nucleic Acids Res. 25:3389-3402.',
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("blastx", qresult.program)
        self.assertEqual("refseq_protein", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(12646943, qresult.stat_db_num)
        self.assertEqual(4397139428, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("hg19_dna", qresult.id)
        self.assertEqual(
            "range=chr1:1207057-1207541 5'pad=0 3'pad=0 strand=+ repeatMasking=none",
            qresult.description,
        )
        self.assertEqual(485, qresult.seq_len)
        self.assertEqual(12646943, qresult.stat_db_num)
        self.assertEqual(4397139428, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|332258565|ref|XP_003278367.1|", hit.id)
        self.assertEqual(
            "PREDICTED: UPF0764 protein C16orf89-like [Nomascus leucogenys]",
            hit.description,
        )
        self.assertEqual(132, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(121.709, hsp.bitscore)
        self.assertEqual(304, hsp.bitscore_raw)
        self.assertEqual(2.02642e-32, hsp.evalue)
        self.assertEqual(15, hsp.query_start)
        self.assertEqual(300, hsp.query_end)
        self.assertEqual(24, hsp.hit_start)
        self.assertEqual(119, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(69, hsp.ident_num)
        self.assertEqual(74, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(95, hsp.aln_span)
        self.assertEqual(
            "LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "LRRSFALVAQ  VQW +LG PQPPPPGFK FSCLS  SSW+YRH+PP L NF+FLVE GF HVGQAGLE   SG+ P   SQS GI GVSH AQP",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(51.6026, hsp.bitscore)
        self.assertEqual(122, hsp.bitscore_raw)
        self.assertEqual(1.87805e-06, hsp.evalue)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(459, hsp.query_end)
        self.assertEqual(31, hsp.hit_start)
        self.assertEqual(98, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(34, hsp.ident_num)
        self.assertEqual(41, hsp.pos_num)
        self.assertEqual(5, hsp.gap_num)
        self.assertEqual(72, hsp.aln_span)
        self.assertEqual(
            "VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "V   RVQ ++L S QPP P FK FS LSL SSW+ R  PPH AN     F F +   F  V QAG++ +  G",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|332815399|ref|XP_003309509.1|", hit.id)
        self.assertEqual(
            "PREDICTED: histone demethylase UTY-like [Pan troglodytes]", hit.description
        )
        self.assertEqual(101, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(97.0561, hsp.bitscore)
        self.assertEqual(240, hsp.bitscore_raw)
        self.assertEqual(2.76414e-23, hsp.evalue)
        self.assertEqual(6, hsp.query_start)
        self.assertEqual(279, hsp.query_end)
        self.assertEqual(9, hsp.hit_start)
        self.assertEqual(100, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(0, hsp.hit_frame)
        self.assertEqual(56, hsp.ident_num)
        self.assertEqual(62, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(91, hsp.aln_span)
        self.assertEqual(
            "VAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQPLCE",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "VPHAGVQWHNLSSLQPPPSRFKPFSYLSLLSSWDQRRPPPCLVTFVFLIETGFRHVGQAGLKLLTSGDPSASASQSAGIRGVSHCTWPECQ",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "V  AGVQW +L   QPPP  FK FS LS  SSWD R  PPCL+ FVFL+ETGF HVGQAGL+   SG+  A ASQS GI GVSH   P C+",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)


class TblastnXmlCases(unittest.TestCase):
    def test_xml_2212L_tblastn_001(self):
        xml_file = get_file("xml_2212L_tblastn_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.12", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(0.001, qresult.param_evalue_threshold)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("nr", qresult.target)

        # test parsed values of qresult
        self.assertEqual("gi|729325|sp|P39483|DHG2_BACME", qresult.id)
        self.assertEqual("Glucose 1-dehydrogenase II (GLCDH-II)", qresult.description)
        self.assertEqual(261, qresult.seq_len)
        self.assertEqual(251887, qresult.stat_db_num)
        self.assertEqual(438542399, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(100, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|58264321|ref|XM_569317.1|", hit.id)
        self.assertEqual(
            "Filobasidiella neoformans glucose 1-dehydrogenase, putative (CNB05760) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(904, hit.seq_len)
        self.assertEqual(1, len(hit))
        self.assertRaises(IndexError, hit.__getitem__, 1)

        hsp = hit.hsps[0]
        self.assertEqual(148.288, hsp.bitscore)
        self.assertEqual(373, hsp.bitscore_raw)
        self.assertEqual(1.46834e-35, hsp.evalue)
        self.assertEqual(4, hsp.query_start)
        self.assertEqual(250, hsp.query_end)
        self.assertEqual(15, hsp.hit_start)
        self.assertEqual(762, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(84, hsp.ident_num)
        self.assertEqual(143, hsp.pos_num)
        self.assertEqual(9, hsp.gap_num)
        self.assertEqual(252, hsp.aln_span)
        self.assertEqual(
            "LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH---ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKG-NVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LQGKVVAITGCSTGIGRAIAIGAAKNGANVVLHHLGDSTASDIAQVQEECKQAGAKTVVVPGDIAEAKTANEIVSAAVSSFSRIDVLISNAGI---CPFHSFLDLPHPLWKRVQDVNLNGSFYVVQAVANQMAKQEPKGGSIVAVSSISALMGGGEQCHYTPTKAGIKSLMESCAIALGPMGIRCNSVLPGTIETNINKEDLSNPEKRADQIRRVPLGRLGKPEDLVGPTLFFASDLSNYCTGASVLVDGGM",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "L+ KVV +TG S G+GRA+A+   +  + VV+++  +   +   + + E  +AG + ++V GD+ + +    +V  AV  F  +DV+I+NAG+    P H   +L    W +V D NL G+F   +       + + KG +++ +SS+  ++      HY  +K G+K + E+ A+   P GIR N++ PG I+T IN E  ++PE+RAD    +P+G +GKPE++     F AS  ++Y TG ++  DGGM",
            hsp.aln_annotation["similarity"],
        )

        # parse last hit
        hit = qresult[-1]
        self.assertEqual("gi|450259|gb|L27825.1|EMEVERA1AA", hit.id)
        self.assertEqual(
            "Emericella nidulans (verA) gene, complete cds, ORF 1 gene, complete cds, and ORF 2 gene, 5' end",
            hit.description,
        )
        self.assertEqual(4310, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(91.2781, hsp.bitscore)
        self.assertEqual(225, hsp.bitscore_raw)
        self.assertEqual(1.31998e-20, hsp.evalue)
        self.assertEqual(4, hsp.query_start)
        self.assertEqual(204, hsp.query_end)
        self.assertEqual(578, hsp.hit_start)
        self.assertEqual(1253, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(3, hsp.hit_frame)
        self.assertEqual(76, hsp.ident_num)
        self.assertEqual(113, hsp.pos_num)
        self.assertEqual(31, hsp.gap_num)
        self.assertEqual(228, hsp.aln_span)
        self.assertEqual(
            "LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-----------ENPVPS-HELSLE-----NWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LDGKVALVTGAGRGIGAAIAVALGQPGAKVVVNYANSREAAEKVVDEIKSNAQSAISIQADVGDPDAVTKLMDQAVEHFGYLDIVSSNAGIVSFGHVKDVTPDVCVPSPYESPVEL*PQQEFDRVFRVNTRGQFFVAREAYRHLREG---GRIILTSSNTASVKGVPRHAVYSGSKGAIDTFVRCLAIDCGDKKITVNAVAPGAIKTDMFLSVSREYIPNGETFTDEQ",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "L  KV +VTG  +G+G A+AV  GQ  +KVVVNY ++ E A +V  EI+     AI ++ DV   + V  L++ AV+ FG LD++ +NAG+           +  VPS +E  +E      +++V   N  G F  +REA ++  E    G +I  SS    +   P    Y+ SKG +      LA++   K I VN + PGAI T +          N E F D +",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastn_001(self):
        xml_file = get_file("xml_2226_tblastn_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis "
            "subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1205400.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual(
            "Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA",
            hit.description,
        )
        self.assertEqual(4632, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(34.6538, hsp.bitscore)
        self.assertEqual(78, hsp.bitscore_raw)
        self.assertEqual(1.08241e-05, hsp.evalue)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(15, hsp.ident_num)
        self.assertEqual(26, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(
            "PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", str(hsp.query.seq)
        )
        self.assertEqual(
            "PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID", str(hsp.hit.seq)
        )
        self.assertEqual(
            "P +   TK+GT +GL   HTI   + +  +SL++ E++  D+D",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1119300.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual(
            "PREDICTED: Sus scrofa pleckstrin-like (LOC100626968), mRNA",
            hit.description,
        )
        self.assertEqual(772, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(199.519, hsp.bitscore)
        self.assertEqual(506, hsp.bitscore_raw)
        self.assertEqual(1.57249e-67, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(32.7278, hsp.bitscore)
        self.assertEqual(73, hsp.bitscore_raw)
        self.assertEqual(4.07518e-05, hsp.evalue)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(21, hsp.ident_num)
        self.assertEqual(33, hsp.pos_num)
        self.assertEqual(4, hsp.gap_num)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(
            "IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "+ +Y       P G I L+G  +TS      GK  F+ +     T  +  +F QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|365982352|ref|XM_003667962.1|", hit.id)
        self.assertEqual(
            "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA",
            hit.description,
        )
        self.assertEqual(4932, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(19.631, hsp.bitscore)
        self.assertEqual(39, hsp.bitscore_raw)
        self.assertEqual(1.65923, hsp.evalue)
        self.assertEqual(11, hsp.query_start)
        self.assertEqual(54, hsp.query_end)
        self.assertEqual(3180, hsp.hit_start)
        self.assertEqual(3336, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(16, hsp.ident_num)
        self.assertEqual(23, hsp.pos_num)
        self.assertEqual(9, hsp.gap_num)
        self.assertEqual(52, hsp.aln_span)
        self.assertEqual(
            "GSVFNTWKPMWVVLL---------EDGIEFYKKKSDNSPKGMIPLKGSTLTS", str(hsp.query.seq)
        )
        self.assertEqual(
            "GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS", str(hsp.hit.seq)
        )
        self.assertEqual(
            "GS F TW  +++ +L         E   E   K  D + KG++ L  S  TS",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)

    def test_xml_2226_tblastn_002(self):
        xml_file = get_file("xml_2226_tblastn_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastn_003(self):
        xml_file = get_file("xml_2226_tblastn_003.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1205400.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual(
            "Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA",
            hit.description,
        )
        self.assertEqual(4632, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(34.6538, hsp.bitscore)
        self.assertEqual(78, hsp.bitscore_raw)
        self.assertEqual(1.08241e-05, hsp.evalue)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(15, hsp.ident_num)
        self.assertEqual(26, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(
            "PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", str(hsp.query.seq)
        )
        self.assertEqual(
            "PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID", str(hsp.hit.seq)
        )
        self.assertEqual(
            "P +   TK+GT +GL   HTI   + +  +SL++ E++  D+D",
            hsp.aln_annotation["similarity"],
        )

        self.assertRaises(IndexError, hit.__getitem__, 1)

        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastn_004(self):
        xml_file = get_file("xml_2226_tblastn_004.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1119300.0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|350596019|ref|XM_003360601.2|", hit.id)
        self.assertEqual(
            "PREDICTED: Sus scrofa pleckstrin-like (LOC100626968), mRNA",
            hit.description,
        )
        self.assertEqual(772, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(199.519, hsp.bitscore)
        self.assertEqual(506, hsp.bitscore_raw)
        self.assertEqual(1.57249e-67, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(94, hsp.hit_start)
        self.assertEqual(388, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(94, hsp.ident_num)
        self.assertEqual(96, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(32.7278, hsp.bitscore)
        self.assertEqual(73, hsp.bitscore_raw)
        self.assertEqual(4.07518e-05, hsp.evalue)
        self.assertEqual(29, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(541, hsp.hit_start)
        self.assertEqual(754, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(21, hsp.ident_num)
        self.assertEqual(33, hsp.pos_num)
        self.assertEqual(4, hsp.gap_num)
        self.assertEqual(71, hsp.aln_span)
        self.assertEqual(
            "IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "+ +Y       P G I L+G  +TS      GK  F+ +     T  +  +F QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|365982352|ref|XM_003667962.1|", hit.id)
        self.assertEqual(
            "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA",
            hit.description,
        )
        self.assertEqual(4932, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(19.631, hsp.bitscore)
        self.assertEqual(39, hsp.bitscore_raw)
        self.assertEqual(1.65923, hsp.evalue)
        self.assertEqual(11, hsp.query_start)
        self.assertEqual(54, hsp.query_end)
        self.assertEqual(3180, hsp.hit_start)
        self.assertEqual(3336, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(16, hsp.ident_num)
        self.assertEqual(23, hsp.pos_num)
        self.assertEqual(9, hsp.gap_num)
        self.assertEqual(52, hsp.aln_span)
        self.assertEqual(
            "GSVFNTWKPMWVVLL---------EDGIEFYKKKSDNSPKGMIPLKGSTLTS", str(hsp.query.seq)
        )
        self.assertEqual(
            "GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS", str(hsp.hit.seq)
        )
        self.assertEqual(
            "GS F TW  +++ +L         E   E   K  D + KG++ L  S  TS",
            hsp.aln_annotation["similarity"],
        )

        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastn_005(self):
        xml_file = get_file("xml_2226_tblastn_005.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastn", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|16080617|ref|NP_391444.1|", qresult.id)
        self.assertEqual(
            "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]",
            qresult.description,
        )
        self.assertEqual(102, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(3, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|145479850|ref|XM_001425911.1|", hit.id)
        self.assertEqual(
            "Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA",
            hit.description,
        )
        self.assertEqual(4632, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(34.6538, hsp.bitscore)
        self.assertEqual(78, hsp.bitscore_raw)
        self.assertEqual(0.755176, hsp.evalue)
        self.assertEqual(30, hsp.query_start)
        self.assertEqual(73, hsp.query_end)
        self.assertEqual(1743, hsp.hit_start)
        self.assertEqual(1872, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(15, hsp.ident_num)
        self.assertEqual(26, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(43, hsp.aln_span)
        self.assertEqual(
            "PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", str(hsp.query.seq)
        )
        self.assertEqual(
            "PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID", str(hsp.hit.seq)
        )
        self.assertEqual(
            "P +   TK+GT +GL   HTI   + +  +SL++ E++  D+D",
            hsp.aln_annotation["similarity"],
        )
        self.assertRaises(IndexError, hit.__getitem__, 1)

        # test parsed values of the third qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|11464971:4-101", qresult.id)
        self.assertEqual("pleckstrin [Mus musculus]", qresult.description)
        self.assertEqual(98, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.041, qresult.stat_kappa)
        self.assertEqual(0.267, qresult.stat_lambda)
        self.assertEqual(0.14, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|354480463|ref|XM_003502378.1|", hit.id)
        self.assertEqual(
            "PREDICTED: Cricetulus griseus pleckstrin-like (LOC100773128), mRNA",
            hit.description,
        )
        self.assertEqual(1119, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(205.297, hsp.bitscore)
        self.assertEqual(521, hsp.bitscore_raw)
        self.assertEqual(1.46172e-63, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(75, hsp.hit_start)
        self.assertEqual(369, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(98, hsp.ident_num)
        self.assertEqual(98, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(43.8986, hsp.bitscore)
        self.assertEqual(102, hsp.bitscore_raw)
        self.assertEqual(0.00054161, hsp.evalue)
        self.assertEqual(2, hsp.query_start)
        self.assertEqual(96, hsp.query_end)
        self.assertEqual(801, hsp.hit_start)
        self.assertEqual(1101, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(30, hsp.ident_num)
        self.assertEqual(50, hsp.pos_num)
        self.assertEqual(6, hsp.gap_num)
        self.assertEqual(100, hsp.aln_span)
        self.assertEqual(
            "IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTSPCQDF-GKRM---FVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNHDGKKSDDENLFEIITADEVHYYLQAAAPKERTEWIKAIQVA",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "I++G L+K+G     WK    +L ED   + +Y       P G I L+G  +TS   +  GK+     + +I T  +  ++ QAA  +ER  W++ I+ A",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|390474391|ref|XM_002757683.2|", hit.id)
        self.assertEqual(
            "PREDICTED: Callithrix jacchus pleckstrin (PLEK), mRNA", hit.description
        )
        self.assertEqual(1402, hit.seq_len)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(202.986, hsp.bitscore)
        self.assertEqual(515, hsp.bitscore_raw)
        self.assertEqual(1.27031e-61, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual(160, hsp.hit_start)
        self.assertEqual(454, hsp.hit_end)
        self.assertEqual(0, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(96, hsp.ident_num)
        self.assertEqual(97, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(98, hsp.aln_span)
        self.assertEqual(
            "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGSMFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "KRIREGYLVKKGS+FNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERDAWVRDIKKAIK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(3, counter)


class TblastxXmlCases(unittest.TestCase):
    def test_xml_2212L_tblastx_001(self):
        xml_file = get_file("xml_2212L_tblastx_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test the first qresult
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.12", qresult.version)
        self.assertEqual(REFERENCE, qresult.reference)
        self.assertEqual("BLOSUM80", qresult.param_matrix)
        self.assertEqual(1, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(10, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastx", qresult.program)
        self.assertEqual("nr", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("gi|1348853|gb|G26621.1|G26621", qresult.id)
        self.assertEqual(
            "human STS STS_D12006, sequence tagged site", qresult.description
        )
        self.assertEqual(615, qresult.seq_len)
        self.assertEqual(3533718, qresult.stat_db_num)
        # why is the value negative? is this a blast bug?
        self.assertEqual(-1496331888, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0.177051, qresult.stat_kappa)
        self.assertEqual(0.342969, qresult.stat_lambda)
        self.assertEqual(0.656794, qresult.stat_entropy)
        self.assertEqual(10, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|18072170|gb|AC010333.7|", hit.id)
        self.assertEqual(
            "Homo sapiens chromosome 16 clone CTD-3037G24, complete sequence",
            hit.description,
        )
        self.assertEqual(159870, hit.seq_len)
        self.assertEqual(13, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(329.561, hsp.bitscore)
        self.assertEqual(661.0, hsp.bitscore_raw)
        self.assertEqual(5.29552e-90, hsp.evalue)
        self.assertEqual(1, hsp.query_start)
        self.assertEqual(355, hsp.query_end)
        self.assertEqual(44323, hsp.hit_start)
        self.assertEqual(44677, hsp.hit_end)
        self.assertEqual(-3, hsp.query_frame)
        self.assertEqual(-3, hsp.hit_frame)
        self.assertEqual(117, hsp.ident_num)
        self.assertEqual(117, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(118, hsp.aln_span)
        self.assertEqual(
            "ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD",
            hsp.aln_annotation["similarity"],
        )

        hit = qresult[-1]
        self.assertEqual("gi|4309961|gb|AC005993.2|AC005993", hit.id)
        self.assertEqual(
            "Homo sapiens PAC clone RP6-114E22 from 14, complete sequence",
            hit.description,
        )
        self.assertEqual(143943, hit.seq_len)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(41.0922, hsp.bitscore)
        self.assertEqual(78, hsp.bitscore_raw)
        self.assertEqual(0.716571, hsp.evalue)
        self.assertEqual(166, hsp.query_start)
        self.assertEqual(250, hsp.query_end)
        self.assertEqual(43679, hsp.hit_start)
        self.assertEqual(43763, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(3, hsp.hit_frame)
        self.assertEqual(13, hsp.ident_num)
        self.assertEqual(19, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(28, hsp.aln_span)
        self.assertEqual("PLTKAHRLFQTSIVFYVTCFTASSQQLL", str(hsp.query.seq))
        self.assertEqual("PLNKYHTIFQISLCFYLFCYNMAQKQLL", str(hsp.hit.seq))
        self.assertEqual(
            "PL K H +FQ S+ FY+ C+  + +QLL", hsp.aln_annotation["similarity"]
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastx_001(self):
        xml_file = get_file("xml_2226_tblastx_001.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastx", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|296147483:1-350", qresult.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            qresult.description,
        )
        self.assertEqual(350, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1954618.0, qresult.stat_eff_space)
        self.assertEqual(0.133956144488482, qresult.stat_kappa)
        self.assertEqual(0.317605957635731, qresult.stat_lambda)
        self.assertEqual(0.401214524497119, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|296147483|ref|NM_001183135.1|", hit.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(4911, hit.seq_len)
        self.assertEqual(8, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(289.739, hsp.bitscore)
        self.assertEqual(626, hsp.bitscore_raw)
        self.assertEqual(2.35531e-81, hsp.evalue)
        self.assertEqual(1, hsp.query_start)
        self.assertEqual(349, hsp.query_end)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(349, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(116, hsp.ident_num)
        self.assertEqual(116, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(116, hsp.aln_span)
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(18.9375, hsp.bitscore)
        self.assertEqual(35, hsp.bitscore_raw)
        self.assertEqual(7.78658, hsp.evalue)
        self.assertEqual(292, hsp.query_start)
        self.assertEqual(325, hsp.query_end)
        self.assertEqual(340, hsp.hit_start)
        self.assertEqual(373, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(-3, hsp.hit_frame)
        self.assertEqual(6, hsp.ident_num)
        self.assertEqual(9, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(11, hsp.aln_span)
        self.assertEqual("KFWMPSLRLLI", str(hsp.query.seq))
        self.assertEqual("KKWVPPVKLLI", str(hsp.hit.seq))
        self.assertEqual("K W+P ++LLI", hsp.aln_annotation["similarity"])

        hit = qresult[-1]
        self.assertEqual("gi|254579534|ref|XM_002495708.1|", hit.id)
        self.assertEqual(
            "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(4866, hit.seq_len)
        self.assertEqual(6, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(141.279, hsp.bitscore)
        self.assertEqual(302, hsp.bitscore_raw)
        self.assertEqual(1.15566e-36, hsp.evalue)
        self.assertEqual(96, hsp.query_start)
        self.assertEqual(348, hsp.query_end)
        self.assertEqual(96, hsp.hit_start)
        self.assertEqual(348, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(57, hsp.ident_num)
        self.assertEqual(72, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(84, hsp.aln_span)
        self.assertEqual(
            "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP  +LS++LDAFIEA  LAM+I+LK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)

    def test_xml_2226_tblastx_002(self):
        xml_file = get_file("xml_2226_tblastx_002.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastx", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(-1, qresult.stat_kappa)
        self.assertEqual(-1, qresult.stat_lambda)
        self.assertEqual(-1, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastx_003(self):
        xml_file = get_file("xml_2226_tblastx_003.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastx", qresult.program)
        self.assertEqual("db/minirefseq_mrna", qresult.target)

        self.assertEqual("gi|296147483:1-350", qresult.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            qresult.description,
        )
        self.assertEqual(350, qresult.seq_len)
        self.assertEqual(23, qresult.stat_db_num)
        self.assertEqual(67750, qresult.stat_db_len)
        self.assertEqual(1954618.0, qresult.stat_eff_space)
        self.assertEqual(0.133956144488482, qresult.stat_kappa)
        self.assertEqual(0.317605957635731, qresult.stat_lambda)
        self.assertEqual(0.401214524497119, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual("gi|296147483|ref|NM_001183135.1|", hit.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(4911, hit.seq_len)
        self.assertEqual(8, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(289.739, hsp.bitscore)
        self.assertEqual(626, hsp.bitscore_raw)
        self.assertEqual(2.35531e-81, hsp.evalue)
        self.assertEqual(1, hsp.query_start)
        self.assertEqual(349, hsp.query_end)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(349, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(116, hsp.ident_num)
        self.assertEqual(116, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(116, hsp.aln_span)
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(18.9375, hsp.bitscore)
        self.assertEqual(35, hsp.bitscore_raw)
        self.assertEqual(7.78658, hsp.evalue)
        self.assertEqual(292, hsp.query_start)
        self.assertEqual(325, hsp.query_end)
        self.assertEqual(340, hsp.hit_start)
        self.assertEqual(373, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(-3, hsp.hit_frame)
        self.assertEqual(6, hsp.ident_num)
        self.assertEqual(9, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(11, hsp.aln_span)
        self.assertEqual("KFWMPSLRLLI", str(hsp.query.seq))
        self.assertEqual("KKWVPPVKLLI", str(hsp.hit.seq))
        self.assertEqual("K W+P ++LLI", hsp.aln_annotation["similarity"])

        hit = qresult[-1]
        self.assertEqual("gi|254579534|ref|XM_002495708.1|", hit.id)
        self.assertEqual(
            "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(4866, hit.seq_len)
        self.assertEqual(6, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(141.279, hsp.bitscore)
        self.assertEqual(302, hsp.bitscore_raw)
        self.assertEqual(1.15566e-36, hsp.evalue)
        self.assertEqual(96, hsp.query_start)
        self.assertEqual(348, hsp.query_end)
        self.assertEqual(96, hsp.hit_start)
        self.assertEqual(348, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(57, hsp.ident_num)
        self.assertEqual(72, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(84, hsp.aln_span)
        self.assertEqual(
            "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP  +LS++LDAFIEA  LAM+I+LK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_xml_2226_tblastx_004(self):
        xml_file = get_file("xml_2226_tblastx_004.xml")
        qresults = parse(xml_file, FMT)
        counter = 0

        # test each qresult's attributes
        qresult = next(qresults)
        counter += 1

        # test meta variables, only for the first one
        self.assertEqual("2.2.26+", qresult.version)
        self.assertEqual(
            "Stephen F. Altschul, Thomas L. Madden, Alejandro "
            "A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, "
            "Webb Miller, and David J. Lipman (1997), "
            '"Gapped BLAST and PSI-BLAST: a new generation of '
            'protein database search programs", '
            "Nucleic Acids Res. 25:3389-3402.",
            qresult.reference,
        )
        self.assertEqual("BLOSUM62", qresult.param_matrix)
        self.assertEqual(10.0, qresult.param_evalue_threshold)
        self.assertEqual("L;", qresult.param_filter)
        self.assertEqual(11, qresult.param_gap_open)
        self.assertEqual(1, qresult.param_gap_extend)
        self.assertEqual("tblastx", qresult.program)
        self.assertEqual("refseq_rna", qresult.target)

        # test parsed values of the first qresult
        self.assertEqual("random_s00", qresult.id)
        self.assertEqual("", qresult.description)
        self.assertEqual(128, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0, qresult.stat_kappa)
        self.assertEqual(0, qresult.stat_lambda)
        self.assertEqual(0, qresult.stat_entropy)
        self.assertEqual(0, len(qresult))

        # test parsed values of the second qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual("gi|296147483:1-350", qresult.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            qresult.description,
        )
        self.assertEqual(350, qresult.seq_len)
        self.assertEqual(2933984, qresult.stat_db_num)
        self.assertEqual(4726730735, qresult.stat_db_len)
        self.assertEqual(0, qresult.stat_eff_space)
        self.assertEqual(0, qresult.stat_kappa)
        self.assertEqual(0, qresult.stat_lambda)
        self.assertEqual(0, qresult.stat_entropy)
        self.assertEqual(5, len(qresult))
        # check for alternative ID results
        self.assertEqual(
            qresult["gi|296147483|ref|NM_001183135.1|"],
            qresult["gi|116616412|gb|EF059095.1|"],
        )

        hit = qresult[0]
        self.assertEqual("gi|296147483|ref|NM_001183135.1|", hit.id)
        self.assertEqual(
            "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual("gi|116616412|gb|EF059095.1|", hit.id_all[1])
        self.assertEqual(
            "Synthetic construct Saccharomyces cerevisiae "
            "clone FLH203015.01X MON2, complete sequence",
            hit.description_all[1],
        )
        self.assertEqual(4911, hit.seq_len)
        self.assertEqual(7, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(289.739, hsp.bitscore)
        self.assertEqual(626, hsp.bitscore_raw)
        self.assertEqual(1.05874e-76, hsp.evalue)
        self.assertEqual(1, hsp.query_start)
        self.assertEqual(349, hsp.query_end)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(349, hsp.hit_end)
        self.assertEqual(2, hsp.query_frame)
        self.assertEqual(2, hsp.hit_frame)
        self.assertEqual(116, hsp.ident_num)
        self.assertEqual(116, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(116, hsp.aln_span)
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K",
            hsp.aln_annotation["similarity"],
        )

        hsp = hit.hsps[-1]
        self.assertEqual(36.3494, hsp.bitscore)
        self.assertEqual(73, hsp.bitscore_raw)
        self.assertEqual(9.12288e-54, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(42, hsp.query_end)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(42, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(14, hsp.ident_num)
        self.assertEqual(14, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(14, hsp.aln_span)
        self.assertEqual("MAMNTGGFDSMQRQ", str(hsp.query.seq))
        self.assertEqual("MAMNTGGFDSMQRQ", str(hsp.hit.seq))
        self.assertEqual("MAMNTGGFDSMQRQ", hsp.aln_annotation["similarity"])

        hit = qresult[-1]
        self.assertEqual("gi|254579534|ref|XM_002495708.1|", hit.id)
        self.assertEqual(
            "Zygosaccharomyces rouxii hypothetical protein "
            "(ZYRO0C02266g) mRNA, complete cds",
            hit.description,
        )
        self.assertEqual(4866, hit.seq_len)
        self.assertEqual(4, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(141.279, hsp.bitscore)
        self.assertEqual(302, hsp.bitscore_raw)
        self.assertEqual(5.19486e-32, hsp.evalue)
        self.assertEqual(96, hsp.query_start)
        self.assertEqual(348, hsp.query_end)
        self.assertEqual(96, hsp.hit_start)
        self.assertEqual(348, hsp.hit_end)
        self.assertEqual(1, hsp.query_frame)
        self.assertEqual(1, hsp.hit_frame)
        self.assertEqual(57, hsp.ident_num)
        self.assertEqual(72, hsp.pos_num)
        self.assertEqual(0, hsp.gap_num)
        self.assertEqual(84, hsp.aln_span)
        self.assertEqual(
            "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK",
            str(hsp.query.seq),
        )
        self.assertEqual(
            "IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK",
            str(hsp.hit.seq),
        )
        self.assertEqual(
            "IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP  +LS++LDAFIEA  LAM+I+LK",
            hsp.aln_annotation["similarity"],
        )

        # check if we've finished iteration over qresults
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)


class BlastXmlSpecialCases(unittest.TestCase):
    def test_xml_2226_blastn_006(self):
        xml_file = get_file("xml_2226_blastn_006.xml")
        qresults = parse(xml_file, FMT)

        exp_warning = 1
        with warnings.catch_warnings(record=True) as w:
            warnings.simplefilter("always", BiopythonParserWarning)
            qresult = next(qresults)
            self.assertEqual(
                exp_warning,
                len(w),
                "Expected {0} warning(s), got {1}".format(exp_warning, len(w)),
            )

        self.assertEqual(qresult.blast_id, "Query_1")
        hit1 = qresult[0]
        hit2 = qresult[1]
        self.assertEqual("gnl|BL_ORD_ID|18", hit1.blast_id)
        self.assertEqual("gi|347972582|ref|XM_309352.4|", hit1.id)
        self.assertEqual(
            "Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds",
            hit1.description,
        )
        self.assertEqual("gnl|BL_ORD_ID|17", hit2.blast_id)
        self.assertEqual("gnl|BL_ORD_ID|17", hit2.id)
        self.assertEqual(
            "gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds",
            hit2.description,
        )

    def test_xml_2226_blastn_006_use_raw_hit_ids(self):
        xml_file = get_file("xml_2226_blastn_006.xml")
        qresults = parse(xml_file, FMT, use_raw_hit_ids=True)

        exp_warning = 0
        with warnings.catch_warnings(record=True) as w:
            warnings.simplefilter("always", BiopythonParserWarning)
            qresult = next(qresults)
            self.assertEqual(
                exp_warning,
                len(w),
                "Expected {0} warning(s), got {1}".format(exp_warning, len(w)),
            )

        self.assertEqual(qresult.blast_id, "Query_1")
        hit1 = qresult[0]
        hit2 = qresult[1]
        self.assertEqual("gnl|BL_ORD_ID|18", hit1.blast_id)
        self.assertEqual("gnl|BL_ORD_ID|18", hit1.id)
        self.assertEqual(
            "gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds",
            hit1.description,
        )
        self.assertEqual("gnl|BL_ORD_ID|17", hit2.blast_id)
        self.assertEqual("gnl|BL_ORD_ID|17", hit2.id)
        self.assertEqual(
            "gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds",
            hit2.description,
        )

    def test_xml_2226_blastn_006_use_raw_query_ids(self):
        xml_file = get_file("xml_2226_blastn_006.xml")
        qresults = parse(xml_file, FMT, use_raw_query_ids=True)

        exp_warning = 1
        with warnings.catch_warnings(record=True) as w:
            warnings.simplefilter("always", BiopythonParserWarning)
            qresult = next(qresults)
            self.assertEqual(
                exp_warning,
                len(w),
                "Expected {0} warning(s), got {1}".format(exp_warning, len(w)),
            )

        self.assertEqual(qresult.id, "Query_1")
        self.assertEqual(
            qresult.description,
            "gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds",
        )
        self.assertEqual(qresult.blast_id, "Query_1")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
