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Translate.py
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Translate.py
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import os
import re
path = '/home/tannerv1/single_copy_orthologs/S_ciliatus_267108'
for files in os.listdir(path):
if re.search(r'.*faa', files):
break
else:
writing_path = f'/home/tannerv1/single_copy_orthologs/S_ciliatus_267108/{files}.faa'
with open(writing_path, 'a') as Protein:
inputfile = files
f = open(inputfile, "r")
seq = f.read()
line = re.findall(r'>.*', seq)
Protein.write(f'{line[0]}\n')
seq = seq.replace(line[0], "")
seq = seq.replace("\n", "")
seq = seq.replace("\r", "")
table = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'', 'TAG':'',
'TGC':'C', 'TGT':'C', 'TGA':'', 'TGG':'W',
}
z = 0
for i in range(0, len(seq), 3):
codon = seq[i:i + 3]
if codon in table:
if table[codon] == '':
Protein.write("")
break
else:
amino_acid = table[codon]
Protein.write(amino_acid)
else:
break