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translationSimple.py
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translationSimple.py
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#!/usr/bin/python
'''translate RNA file to protein string'''
import os
import sys
from Bio import Seq
def translationDict(data):
## define protein dictionary
map = {"UUU":"F", "UUC":"F", "UUA":"L", "UUG":"L",
"UCU":"S", "UCC":"L", "UCA":"S", "UCG":"S",
"UAU":"Y", "UAC":"Y", "UAA":"STOP", "UAG":"STOP",
"UGU":"C", "UGC":"C", "UGA":"STOP", "UGG":"W",
"CUU":"L", "CUC":"L", "CUA":"L", "CUG":"L",
"CCU":"P", "CCC":"P", "CCA":"P", "CCG":"P",
"CAU":"H", "CAC":"H", "CAA":"Q", "CAG":"Q",
"CGU":"R", "CGC":"R", "CGA":"R", "CGG":"R",
"AUU":"I", "AUC":"I", "AUA":"I", "AUG":"M",
"ACU":"T", "ACC":"T", "ACA":"T", "ACG":"T",
"AAU":"N", "AAC":"N", "AAA":"K", "AAG":"K",
"AGU":"S", "AGC":"S", "AGA":"R", "AGG":"R",
"GUU":"V", "GUC":"V", "GUA":"V", "GUG":"V",
"GCU":"A", "GCC":"A", "GCA":"A", "GCG":"A",
"GAU":"D", "GAC":"D", "GAA":"E", "GAG":"E",
"GGU":"G", "GGC":"G", "GGA":"G", "GGG":"G",}
proteinSeq =''
for line in data:
for index in xrange(0,len(line)-3,3):
frame = line[index:index+3]
#print "frame", frame
if frame in map:
if map[frame]!="STOP":
proteinSeq += map[frame]
print proteinSeq
def translationBio(data):
'''Uses Biopython translate '''
proteinSeq = ''
for line in data:
proteinSeq += Seq.translate(line, table='Standard', stop_symbol='', to_stop=False)
#proteinSeq += Seq.translate(line)
print proteinSeq
if __name__=="__main__":
filename = sys.argv[1]
fileh = open(filename, 'r')
data = fileh.readlines()
#translationDict(data)
translationBio(data)