Package core :: Module prep
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Module prep

Created on Nov 11, 2011

Contains various help functions which initialize / translate /preprocess the data


Author: Sven Giese

Functions [hide private]
dictionary
createdic(AAsequence)
Creates the dictionary for the AA triplets and searches the starting indices of the triplets in the given aminoacid sequence.
bool
isvalidtriplet(codon, dictentry)
Function which checks if a given triplet has max hamming distance of 1 to a other triplet.
dictionary
loadpickle(inputname)
basic pickle functions.
 
savepickle(dictionary, outputname)
basic pickle functions.
prot,rest
trans_seq(DNA)
Funtion which translates DNA to AA
Variables [hide private]
  __package__ = 'core'
  genetic_code = {'AAA': 'K', 'AAC': 'N', 'AAG': 'K', 'AAT': 'N'...
Function Details [hide private]

createdic(AAsequence)

 

Creates the dictionary for the AA triplets and searches the starting indices of the triplets in the given aminoacid sequence.

Parameters:
  • AAsequence (string) - aminoacid sequence
Returns: dictionary
A dictionary with starting positions of each triplet in the given AA sequence

isvalidtriplet(codon, dictentry)

 

Function which checks if a given triplet has max hamming distance of 1 to a other triplet. Used for generation of possible substitutions triplets

Parameters:
  • codon (string) - nucleotide triplet
  • dictentry (string) - nucleotide triplet
Returns: bool
Boolean value. True if max hamming distance 1,else False .

loadpickle(inputname)

 

basic pickle functions. actually for debugging and to speed up multiple simulations ( possible to load orf lists)

Parameters:
  • inputname (string) - Filename for loading.
Returns: dictionary
Dictionary containing start and end positions of ORFs.

savepickle(dictionary, outputname)

 

basic pickle functions. actually for debugging and to speed up multiple simulations ( possible to load orf lists)

Parameters:
  • dictionary (dictionary) - Dictionary containg start and end positions of ORFs.
  • outputname (string) - Filename for saving.

trans_seq(DNA)

 

Funtion which translates DNA to AA

Parameters:
  • DNA (list) - nucleotide sequence
Returns: prot,rest
Translated aminoacid sequence,untranslated nucleotide sequence

Variables Details [hide private]

genetic_code

Value:
{'AAA': 'K',
 'AAC': 'N',
 'AAG': 'K',
 'AAT': 'N',
 'ACA': 'T',
 'ACC': 'T',
 'ACG': 'T',
 'ACT': 'T',
...