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Fixed error with blast hits

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Godwin Ani 2024-04-26 14:24:36 -04:00 committed by GitHub
parent bbe97c5888
commit a70558b880
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1 changed files with 14 additions and 2 deletions
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PTL1/Transcriptomes/Scripts/wrapper.py
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@ -35,7 +35,10 @@ def get_args():
parser.add_argument('-g', '--genetic_code', type = str, help = 'If all of your taxa use the same genetic code, you may enter it here (to be used in script 5). Alternatively, if you need to use a variety of genetic codes but know which codes to use, you may fill give here the path to a .txt or .tsv with two tab-separated columns, the first with the ten-digit codes and the second column with the corresponding genetics codes. Otherwise, stop at script 4 and fill in "gcode_output.tsv" before running script 5')
parser.add_argument('-min', '--minlen', type = int, default = 200, help = 'Minimum transcript length')
parser.add_argument('-max', '--maxlen', type = int, default = 12000, help = 'Maximum transcript length')
parser.add_argument('-c', '--seq_count', type = int, default = 50, help = 'minimum number of sequences after assigning OGs')
parser.add_argument('-d', '--databases', type = str, default = '../Databases', help = 'Path to databases folder')
return parser.parse_args()
@ -77,14 +80,23 @@ def script_three(args):
for folder in os.listdir(args.output + '/Output'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta'):
os.system('python 3_AssignOGs.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta --evalue 1e-15 --databases ' + args.databases)
#running the fourth script
def script_four(args):
for folder in os.listdir(args.output + '/Output'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'):
os.system('python 4_InFrameStopCodonEstimator.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --databases ' + args.databases)
os.system('python 4_InFrameStopCodonEstimator.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --databases ' + args.databases + ' --seq_count ' + str(args.seq_count))
#Checking to see if there are taxa with less than the required number of sequences.
if os.path.exists(args.databases + '/Taxa_with_few_sequences.txt'):
with open(args.databases + '/Taxa_with_few_sequences.txt', 'r') as f:
content = f.read()
print(f'These samples do not run through PTL6p1, perhaps because they has no good hits to the hook. We suggest you remove them and restart.')
print(content)
print('Stopping Run.')
os.remove(args.databases + '/Taxa_with_few_sequences.txt')
sys.exit()
#putting all of the gcode summaries produced by fourth script into a spreadsheet
gcode_info = []
for folder in os.listdir(args.output + '/Output'):