core.FindOrfs

Package core :: Module FindOrfs |
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# Module FindOrfs

source code

FindOrfs, Created 2012

Script to detect start and stop codon of open reading frames in a dna sequence. Note that the algorithm is only rudimentary and does not respect intron-exon structures.

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

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

Function Details | [hide private]

### build_ORF(sequence, file_ORF, pdic) | source code
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

### findstop_help(posLastStop, sequence, codon) | source code
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.

### find_orfs(genomeSequence, pdic) | source code
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.