YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 07:10:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Small update to backtranslating script to account for sequence mismatch

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2023-08-10 10:33:34 -04:00 committed by GitHub
parent 6324cabb71
commit 29daa4932b
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 17 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

27
Utilities/for_fastas/BacktranslateAlignment.py
View File

@ -33,7 +33,10 @@ universal_6fold = {
'TGG': ['W', 'one', 0], 'TAT': ['Y', 'two', 0], 'TAC': ['Y', 'two', 0],
'GTT': ['V', 'four', 0], 'GTC': ['V', 'four', 0], 'GTA': ['V', 'four', 0],
'GTG': ['V', 'four', 0], 'TAA': ['*', 'none', 0], 'TGA': ['*', 'none', 0],
'TAG': ['*', 'none', 0], 'XXX': ['_missing', 'none', 0]}
'TAG': ['*', 'none', 0]}
aas = list(dict.fromkeys([universal_6fold[codon][0] for codon in universal_6fold]))
codons_per_aa = { aa : [codon for codon in universal_6fold if universal_6fold[codon][0] == aa] for aa in aas }
def get_args():
@ -56,19 +59,23 @@ def backtranslate(aa, nucls, output):
for rec in aa:
if(rec.id in nucls):
if len(nucls[rec.id]) == len(str(rec.seq).replace('-', '')) * 3:
o.write('>' + rec.id + '\n')
c = 0
running_seq = ''; c = 0; fail = False
for i, char in enumerate(str(rec.seq)):
if(char == '-'):
o.write('---')
running_seq += '---'
else:
o.write(nucls[rec.id][c:c+3])
c += 3
o.write('\n\n')
codon = nucls[rec.id][c:c+3]
if char == 'X' or codon in codons_per_aa[char]:
running_seq += codon
c += 3
else:
fail = True
if fail:
print('\nWARNING: The nucleotide sequence ' + rec.id + ' does not match the corresponding amino acid sequence. This sequence will be missing from the alignment.\n')
else:
o.write('>' + rec.id + '\n')
o.write(running_seq + '\n\n')
else:
print('\nWARNING: The nucleotide sequence ' + rec.id + ' is not 3x the length of the corresponding amino acid sequence. This sequence will be missing from the alignment.\n')
else: