YuuMJ1997/EukPhylo
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Godwin Ani 2024-04-26 14:23:55 -04:00 committed by GitHub
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commit bbe97c5888
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1 changed files with 6 additions and 5 deletions
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PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py
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@ -163,6 +163,8 @@ def check_args():
' Eukaryotic protein coding transcripts'+color.END)
required_arg_group.add_argument('--databases','-d', action='store',
help=color.BOLD+color.GREEN+"Path to databases"+color.END)
required_arg_group.add_argument('--seq_count','-c', action='store',
help=color.BOLD+color.GREEN+"sequence number cutoff"+color.END)
optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
optional_arg_group.add_argument('-author', action='store_true',
@ -293,8 +295,10 @@ def prep_translations(args):
else:
prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])-4)
print(args.seq_count)
if len(list(prot_dict.keys())) < 50:
print('\nStop codon estimation CANCELLED for taxon ' + args.input_file[:10] + ' because its file contains fewer than 50 sequences. This check occurred in script 4.\n')
with open(args.databases +'/Taxa_with_few_sequences.txt', "a") as f:
f.write("\n" +args.input_file.split('/')[-1] )
exit()
@ -752,11 +756,8 @@ def main():
prep_translations(args)
diamond_ProtDB(args, diamond_path)
hunt_for_stops(args)
clean_up(args)
next_script(args)
main()