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Update wrapper.py

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Godwin Ani 2025-03-18 15:28:55 -04:00 committed by GitHub
parent b00f272b23
commit ea87b7dcd6
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1 changed files with 10 additions and 10 deletions
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PTL1/Transcriptomes/Scripts/wrapper.py
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@ -51,7 +51,7 @@ def script_one(args, ten_digit_codes):
#Running script 1a on all files #Running script 1a on all files
for file in os.listdir(args.assembled_transcripts): for file in os.listdir(args.assembled_transcripts):
if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes: if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes:
os.system('python 1a_TranscriptLengthFilter.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT?? os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/1a_TranscriptLengthFilter.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT??
#Run script 1b if the XPC step is being run #Run script 1b if the XPC step is being run
if args.xplate_contam: if args.xplate_contam:
@ -59,7 +59,7 @@ def script_one(args, ten_digit_codes):
print('\nERROR: If you are running cross-plate contamination, a file designating species assignments is required for the --conspecific_names argument\n') print('\nERROR: If you are running cross-plate contamination, a file designating species assignments is required for the --conspecific_names argument\n')
exit() exit()
else: else:
os.system('python 1b_CrossPlateContamination.py ' + args.output + '/Output/XlaneBleeding ' + str(args.minlen) + ' ' + args.conspecific_names) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/1b_CrossPlateContamination.py ' + args.output + '/Output/XlaneBleeding ' + str(args.minlen) + ' ' + args.conspecific_names)
def script_two(args): def script_two(args):
@ -67,10 +67,10 @@ def script_two(args):
#Run scripts 2a and 2b on all files. #Run scripts 2a and 2b on all files.
for folder in os.listdir(args.output + '/Output/'): for folder in os.listdir(args.output + '/Output/'):
if os.path.isfile(args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta'): if os.path.isfile(args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta'):
os.system('python 2a_Identify_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/2a_Identify_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases)
fasta_withBact = args.output + '/Output/' + folder + '/' + folder + '_NorRNAseqs.fasta' fasta_withBact = args.output + '/Output/' + folder + '/' + folder + '_NorRNAseqs.fasta'
os.system('python 2b_Identify_Proks.py --input_file ' + fasta_withBact + ' --databases ' + args.databases) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/2b_Identify_Proks.py --input_file ' + fasta_withBact + ' --databases ' + args.databases)
#NEED TO SORT OUT FILE NAMES ETC. BELOW HERE #NEED TO SORT OUT FILE NAMES ETC. BELOW HERE
@ -79,7 +79,7 @@ def script_three(args):
for folder in os.listdir(args.output + '/Output'): for folder in os.listdir(args.output + '/Output'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta'): 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) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/3_AssignOGs.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta --evalue 1e-15 --databases ' + args.databases)
@ -87,7 +87,7 @@ def script_three(args):
def script_four(args): def script_four(args):
for folder in os.listdir(args.output + '/Output'): for folder in os.listdir(args.output + '/Output'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'): 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 + ' --seq_count ' + str(args.seq_count)) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/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. #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'): if os.path.exists(args.databases + '/Taxa_with_few_sequences.txt'):
with open(args.databases + '/Taxa_with_few_sequences.txt', 'r') as f: with open(args.databases + '/Taxa_with_few_sequences.txt', 'r') as f:
@ -164,7 +164,7 @@ def script_five(args):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta') and os.path.isdir(args.output + '/Output/' + folder + '/StopCodonFreq'): if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta') and os.path.isdir(args.output + '/Output/' + folder + '/StopCodonFreq'):
for line in lines: for line in lines:
if line[0] == folder and line[-1].lower() in valid_codes: if line[0] == folder and line[-1].lower() in valid_codes:
os.system('python 5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + line[-1]) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + line[-1])
#Taxa without valid genetic codes will be skipped. #Taxa without valid genetic codes will be skipped.
elif line[-1].lower() not in valid_codes and 'Genetic Code' not in line: elif line[-1].lower() not in valid_codes and 'Genetic Code' not in line:
print('\n' + line[-1] + ' is not a valid genetic code. Skipping taxon ' + folder + '.\n') print('\n' + line[-1] + ' is not a valid genetic code. Skipping taxon ' + folder + '.\n')
@ -190,14 +190,14 @@ def script_six(args):
exit() exit()
for prefix in unique_prefixes: for prefix in unique_prefixes:
os.system('python 6_FilterPartials.py --file_prefix ' + args.output + '/Output/' + prefix + ' --hook_fasta ' + hook_fasta) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/6_FilterPartials.py --file_prefix ' + args.output + '/Output/' + prefix + ' --hook_fasta ' + hook_fasta)
#Running scripts 7a and 7b on all taxa #Running scripts 7a and 7b on all taxa
def script_seven(args): def script_seven(args):
for file in os.listdir(args.output + '/Output/ToRename'): for file in os.listdir(args.output + '/Output/ToRename'):
if '.AA.ORF.fasta' in file: if '.AA.ORF.fasta' in file:
os.system('python 7a_FinalizeName.py --input_file ' + args.output + '/Output/ToRename/' + file + ' --name ' + file[:10]) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/7a_FinalizeName.py --input_file ' + args.output + '/Output/ToRename/' + file + ' --name ' + file[:10])
os.mkdir(args.output + '/Output/Intermediate') os.mkdir(args.output + '/Output/Intermediate')
@ -205,7 +205,7 @@ def script_seven(args):
if file != 'ReadyToGo' and file != 'Intermediate': if file != 'ReadyToGo' and file != 'Intermediate':
os.system('mv ' + args.output + '/Output/' + file + ' ' + args.output + '/Output/Intermediate') os.system('mv ' + args.output + '/Output/' + file + ' ' + args.output + '/Output/Intermediate')
os.system('python 7b_SummaryStats.py -i ' + args.output + '/Output -d ' + args.databases) os.system('python /EukPhylo/PTL1/Transcriptomes/Scripts/7b_SummaryStats.py -i ' + args.output + '/Output -d ' + args.databases)
if __name__ == "__main__": if __name__ == "__main__":