core.orfs

Package core :: Module orfs |
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# Module orfs

Created 2012

Script which contains the functionality to find start and stop codons in all ORFs in the genome. It is very basic and does not consider intro-exon structure. It is possible to generate the start / stop list extern and give it as input to the main program.

This script is a python port from a java implementation by Franziska Zickmann.

Author: Sven Giese

Functions | [hide private]
dictionary |
build_ORF(sequence, file_ORF, pdic) Get orf positions (forward/backward) and return them in a dictionary |
dictionary |
find_orfs(genomeSequence, pdic) function to identify open reading frames in a dna sequence, careful: intron exon structures are not respected! |
int |
findstop_help(posLastStop, sequence, codon) return the index of the first position of codon in the dna sequence |

Variables | [hide private]
| __package__ = `None`

Function Details | [hide private]

### build_ORF(sequence, file_ORF, pdic) |
Get orf positions (forward/backward) and return them in a dictionary Parameters: `sequence` (string) - nucleotide sequence `file_ORF` (string) - outputfile `pdic` (dictionary) - Used to start start / end positions of ORFs. Returns: dictionary Stored start start / end positions of ORFs

### find_orfs(genomeSequence, pdic) |
function to identify open reading frames in a dna sequence, careful: intron exon structures are not respected! Parameters: `genomeSequence` (string) - Nucleotide sequence. `pdic` (dictionary) - Used to store start / end positions of ORFs. Returns: dictionary Found start / end positions in the sequence consindering only the ORFs.

### findstop_help(posLastStop, sequence, codon) |
return the index of the first position of codon in the dna sequence Parameters: `posLastStop` (int) - Position of the last found stop codon. `sequence` (string) - Nucleotide sequence. `codon` (string) - 3-letter DNA code. Returns: int The position of the stop codon in the nucleotide sequence.