Package core :: Module orfs

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.