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toolbox_transcription.py
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toolbox_transcription.py
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#!/usr/bin/python
from __future__ import division
from __future__ import with_statement
aa_colors = {'start' : 'c',
'basic' : 'b',
'acidic' : 'r',
'polar' : 'g',
'nonpolar' : 'y',
'stop' : 'k'}
nucleotides = ['a', 'c', 'g', 'u']
start_codon = 'aug'
stop_codons = ['uaa', 'uag', 'uga']
class Codon:
def __init__(self, name, letter, category):
self.name = name
self.letter = letter
self.category = category
self.color = aa_colors[self.category]
codons = {}
alanine = Codon('alanine', 'A', 'nonpolar')
arginine = Codon('arginine', 'R', 'basic')
asparagine = Codon('asparagine', 'N', 'polar')
aspartic = Codon('aspartic', 'D', 'acidic')
cysteine = Codon('cysteine', 'C', 'polar')
glutamic = Codon('glutamic', 'E', 'acidic')
glutamine = Codon('glutamine', 'Q', 'polar')
glycine = Codon('glycine', 'G', 'polar')
histidine = Codon('histidine', 'H', 'basic')
isoleucine = Codon('isoleucine', 'I', 'nonpolar')
leucine = Codon('leucine', 'L', 'nonpolar')
lysine = Codon('lysine', 'K', 'basic')
methionine = Codon('methionine', 'M', 'start')
phenylalanine = Codon('phenylalanine', 'F', 'nonpolar')
proline = Codon('proline', 'P', 'nonpolar')
serine = Codon('serine', 'S', 'polar')
threonine = Codon('threonine', 'T', 'polar')
tryptophan = Codon('tryptophan', 'W', 'nonpolar')
tyrosine = Codon('tyrosine', 'Y', 'polar')
valine = Codon('valine', 'V', 'nonpolar')
codons[start_codon] = methionine
for nt in nucleotides:
codons['ac'+nt] = threonine
codons['aac'] = asparagine
codons['aau'] = asparagine
codons['aag'] = lysine
codons['aaa'] = lysine
codons['agc'] = serine
codons['agu'] = serine
for nt in nucleotides:
codons['uc'+nt] = serine
codons['aga'] = arginine
codons['agg'] = arginine
for nt in nucleotides:
codons['cg'+nt] = arginine
for nt in nucleotides:
codons['gu'+nt] = valine
for nt in nucleotides:
codons['gc'+nt] = alanine
codons['gau'] = aspartic
codons['gac'] = aspartic
codons['gaa'] = glutamic
codons['gag'] = glutamic
for nt in nucleotides:
codons['gg'+nt] = glycine
codons['uuu'] = phenylalanine
codons['uuc'] = phenylalanine
codons['uua'] = leucine
codons['uug'] = leucine
for nt in nucleotides:
codons['cu'+nt] = leucine
codons['uau'] = tyrosine
codons['uac'] = tyrosine
codons['ugu'] = cysteine
codons['ugc'] = cysteine
codons['ugg'] = tryptophan
for nt in nucleotides:
codons['cc'+nt] = proline
codons['cau'] = histidine
codons['cac'] = histidine
codons['caa'] = glutamine
codons['cag'] = glutamine
codons['auu'] = isoleucine
codons['auc'] = isoleucine
codons['aua'] = isoleucine
stop = Codon('stop', '!', 'stop')
for c in stop_codons:
codons[c] = stop