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121 lines
3.7 KiB
Python
121 lines
3.7 KiB
Python
import os, sys, re
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from logger import Logger
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from Bio import SeqIO
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def run(params):
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try:
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ogs = list(dict.fromkeys([line.strip() for line in open(params.gf_list)]))
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except (FileNotFoundError, TypeError) as e:
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Logger.Error('Unable to read GF list file. Please make sure that the path is correct and that the file is formatted correctly.\n\n' + str(e))
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try:
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taxa = list(dict.fromkeys([line.strip() for line in open(params.taxon_list)]))
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except (FileNotFoundError, TypeError) as e:
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Logger.Error('Unable to read taxon list file. Please make sure that the path is correct and that the file is formatted correctly.\n\n' + str(e))
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if not os.path.isdir(params.data):
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Logger.Error(Logger.Error('Input amino-acid data files not found. Please make sure that the given path (--data) is correct.'))
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aa_files = [f for f in os.listdir(params.data) if f[:10] in taxa if f.endswith('.faa') or f.endswith('.fa') or f.endswith('.fasta')]
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missing_taxa = [tax for tax in taxa if tax not in [f[:10] for f in aa_files]]
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if(len(missing_taxa) > 0):
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Logger.Warning('The following taxa in the taxon list are missing amino-acid files in ' + params.data + ':\n' + '\n'.join(['\t' + t for t in missing_taxa]))
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os.mkdir(params.output + '/Output/Temp/SF_Diamond')
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for og in ogs:
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Logger.Message('Processing ' + og)
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with open(params.output + '/Output/Pre-Guidance/' + og + '_preguidance.faa', 'w') as preguidance_file:
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for taxon_file in aa_files:
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recs = []
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for rec in sorted([rec for rec in SeqIO.parse(params.data + '/' + taxon_file, 'fasta') if rec.id[-10:] == og], key=lambda x: -len(x.seq)):
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if(rec.id == rec.description):
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recs.append(rec)
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else:
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Logger.Warning('\tThe sequence ID ' + rec.description + ' is invalid. Please make sure that sequence IDs contain no spaces, tabs, etc. This sequence is being excluded.')
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masters = []; removed = 0; flag = 0; cycle = 0
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if params.similarity_filter:
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if len(recs) > 1:
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while flag == 0:
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master_file_name = params.output + '/Output/Temp/SF_Diamond/' + og + '_' + taxon_file[:10] + '_master_' + str(cycle)
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query_file_name = params.output + '/Output/Temp/SF_Diamond/' + og + '_' + taxon_file[:10] + '_queries_' + str(cycle) + '.faa'
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diamond_out_name = params.output + '/Output/Temp/SF_Diamond/' + og + '_' + taxon_file[:10] + '_diamond_results_' + str(cycle) + '.tsv'
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open(master_file_name + '.faa', 'w').write('>' + recs[0].id + '\n' + str(recs[0].seq) + '\n\n')
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masters.append(recs[0])
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with open(query_file_name, 'w') as queries:
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for rec in recs[1:]:
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queries.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
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os.system('diamond makedb --in ' + master_file_name + '.faa -d ' + master_file_name)
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os.system('diamond blastp -d ' + master_file_name + '.dmnd -q ' + query_file_name + ' --outfmt 6 -o ' + diamond_out_name)
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diamond_out = open(diamond_out_name).readlines()
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recs_to_remove = []
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for line in diamond_out:
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line = line.strip().split('\t')
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if float(line[2])/100 >= params.sim_cutoff:
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recs_to_remove.append(seq); removed =+ 1
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if len([rec for rec in recs[1:] if rec.id not in recs_to_remove]) < 2:
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recs = [rec for rec in recs[1:] if rec.id not in recs_to_remove]
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flag = 1
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else:
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recs = [rec for rec in recs[1:] if rec.id not in recs_to_remove]
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cycle += 1
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Logger.Message('\t' + str(removed) + ' sequence(s) removed by the similarity filter (' + str(cycle + 1) + ' iterations) from ' + taxon_file[:10])
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for rec in recs + masters:
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preguidance_file.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
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if(not params.keep_temp):
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os.system('rm -r ' + params.output + '/Output/Temp/SF_Diamond')
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