core.readandwrite

Package core :: Module readandwrite |
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# Module readandwrite

Created on Nov 11, 2011

Contains various help functions which read or produce an input/ output

Author: Sven Giese

Functions | [hide private]
aa_dist_seq(seq, txt_file, shallwrite) Writes the AA distribution in a file and returns the dictionary. |
gethammingdistance(original, artificial) Calculates the hamming distances between two sequences. |
nucleotide_dist_file(file_fasta, txt_file) Writes the DNA distribution in a file and returns the dictionary. |
nucleotide_dist_seq(seq, txt_file, shallwrite) Writes the nucleotide distribution in a file and returns the dictionary. |
HTSeq Sequence object |
readdna(filename) Reads in the dna sequence of the given fasta |
writefile(sequenceObject, filename) Writes a given sequence object to a fasta file. |
writeoverview(Ndic_G, aadic_G, Ndic_AR, aadic_AR, filename) Creates the "delta" file for the comparison of the two chromosoms. |

Variables | [hide private]
| __package__ = ``'``core``'``

Function Details | [hide private]

### aa_dist_seq(seq, txt_file, shallwrite) |
Writes the AA distribution in a file and returns the dictionary. adjust s for % results. Parameters: `seq` (string) - Nucleotide sequence. `txt_file` (string) - Output compare file. `shallwrite` (Bool) - Write output in percentages..

### gethammingdistance(original, artificial) |
Calculates the hamming distances between two sequences. Parameters: `original` (list) - Nucleotide sequence from the reference. `artificial` (list) - Nucleotide sequence from the artificial reference.

### nucleotide_dist_file(file_fasta, txt_file) |
Writes the DNA distribution in a file and returns the dictionary. adjust n for % results Parameters: `file_fasta` (string) - DNA Sequence `txt_file` (string) - Filename for output.

### nucleotide_dist_seq(seq, txt_file, shallwrite) |
Writes the nucleotide distribution in a file and returns the dictionary. adjust s for % results. Parameters: `seq` (string) - Nucleotide sequence. `txt_file` (string) - Output compare file. `shallwrite` (Bool) - Decides if percentages values are written to the output.

### readdna(filename) |
Reads in the dna sequence of the given fasta Parameters: `filename` (string) - Fasta-file used as input. Returns: HTSeq Sequence object Reference Fasta.

### writefile(sequenceObject, filename) |
Writes a given sequence object to a fasta file. Parameters: `sequenceObject` (HTSeq Sequence object) - Reference sequence as fasta.

### writeoverview(Ndic_G, aadic_G, Ndic_AR, aadic_AR, filename) |
Creates the "delta" file for the comparison of the two chromosoms. This file contains the differences in nucleotide distribution between reference and artificial. input: nucleotid dictionary genom, aa dictionary genome, nucleotid dictionary artificial chromosom, aa dictionary, filename Parameters: `Ndic_G` (dictionary) - Nucleotid dictionary genom. `aadic_G` (dictionary) - AA dictionary genome. `Ndic_AR` (dictionary) - Nucleotid dictionary artificial. `aadic_AR` (dictionary) - AA dictionary artificial `filename` (string) - Output filename.