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PTL2/Scripts/guidance.py
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212
PTL2/Scripts/guidance.py
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# Last updated Apr 2 2024
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# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
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# This script runs Guidance in an iterative fashion for more both MSA construction
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# and more rigorous homology assessment than what is offered in EukPhylo part 1.
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# Guidance runs until the input number of iterations (--guidance_iters, default = 5)
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# has been reached, or until there are no sequences below the sequence score cutoff.
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# All sequences below the score cutoff (--seq_cutoff, default = 0.3) are removed at
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# each iteration. By default, EukPhylo does not remove residues that fall below the
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# given residue cutoff (--res_cutoff) and columns that fall below the given column
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# cutoff (--col_cutoff, defaults are 0), though this can be turned on by adjusting
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# these parameters. Outputs at this point are found in the “Guidance_NotGapTrimmed”
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# output folder. We then run MSAs through TrimAl to remove all sites in the alignment
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# that are at least 95% gaps (or --gap_trim_cutoff) generating files in the “Guidance”
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# output folder.
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# This step is either intended to be run starting with --start = unaligned (but not raw)
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# inputs, meaning one amino acid alignment per OG. It can also be run directly after the
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# preguidance step. The run() function is called in two places: in eukphylo.py generally,
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# and in contamination.py if the contamination loop is using Guidance as the re-alignment
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# method.
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#Dependencies
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import os, sys, re
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from Bio import SeqIO
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#Called in eukphylo.py and contamination.py
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def run(params):
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if params.start == 'raw' or params.start == 'unaligned':
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#Checking that pre-Guidance has been run or that unaligned files per OG are provided.
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if params.start == 'raw':
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preguidance_path = params.output + '/Output/Pre-Guidance'
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else:
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preguidance_path = params.data
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if not os.path.isdir(preguidance_path):
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print('\nERROR: The path ' + preguidance_path + ' could not be found when trying to locate pre-Guidance (unaligned) files. Make sure that the --start and --data parameters are correct and/or that the pre-Guidance step ran successfully.\n')
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exit()
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if len([f for f in os.listdir(preguidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]) == 0:
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print('\nERROR: No pre-Guidance (unaligned) files could be found at the path ' + preguidance_path + '. Make sure that the --start and --data parameters are correct, that the pre-Guidance step ran successfully, and that the unaligned files are formatted correctly (they must have the file extension .faa, .fa, or .fasta).\n')
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exit()
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#Creating intermedate folders that will later be deleted unless running with --keep_temp
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os.mkdir(params.output + '/Output/Intermediate/Guidance')
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os.mkdir(params.output + '/Output/Intermediate/Guidance/Input')
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os.mkdir(params.output + '/Output/Intermediate/Guidance/Output')
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guidance_input = params.output + '/Output/Intermediate/Guidance/Input/'
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os.system('cp -r ' + preguidance_path + '/* ' + guidance_input)
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guidance_removed_file = open(params.output + '/Output/GuidanceRemovedSeqs.txt', 'w')
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guidance_removed_file.write('Sequence\tScore\n')
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too_many_seqs = False
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#For each unaligned AA fasta file
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for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
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nseqs = len([rec for rec in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
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if nseqs > 2000:
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too_many_seqs = True
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break
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if too_many_seqs and not params.allow_large_files:
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return False
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#For each unaligned AA fasta file
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for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
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tax_guidance_outdir = params.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
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os.mkdir(tax_guidance_outdir)
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fail = False
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#For each iteration
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for i in range(params.guidance_iters):
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n_recs = len([r for r in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
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#Guidance can't handle inputs with fewer than 4 sequences
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if n_recs < 4:
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print('\nWARNING: Gene famiily ' + file.split('.')[0].split('_preguidance')[0] + ' contains fewer than 4 sequences after ' + str(i) + ' Guidance iterations, therefore no alignment will be produced for this gene family.\n')
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os.system('rm -rf ' + tax_guidance_outdir)
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if i == 0:
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fail = True
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break
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#Determining MAFFT algorithm based on the number of input sequences
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if n_recs < 200:
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mafft_alg = 'genafpair'
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else:
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mafft_alg = 'auto'
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#Running Guidance (one per OG per iteration)
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#for katzlab/Smith College HPC (Grid):
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os.system('python /gridapps/software/Guidance_mid/2.1b-foss-2023a/bin/script/guidance_main.py --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType aa --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(params.seq_cutoff) + ' --colCutoff ' + str(params.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(params.guidance_threads) + " --bl 62 --anysymbol' > " + params.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt')
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#Example:
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#os.system('Scripts/guidance.v2.02/www/Guidance/guidance.pl --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType aa --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(params.seq_cutoff) + ' --colCutoff ' + str(params.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(params.guidance_threads) + " --bl 62 --anysymbol' > " + params.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt')
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#Checking for a sequence score file; if not available, Guidance failed.
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if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
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#All sequences below score cutoff
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seqs_below = len([line for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1:-1] if float(line.split()[-1]) < params.seq_cutoff])
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#If fewer than four were above the cutoff, this OG is done iterating.
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if n_recs - seqs_below < 4:
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print('\nWARNING: Gene famiily ' + file.split('.')[0].split('_preguidance')[0] + ' contains fewer than 4 sequences after ' + str(i + 1) + ' Guidance iterations, therefore no alignment will be produced for this gene family.\n')
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os.system('rm -rf ' + tax_guidance_outdir)
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break
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#If all sequences were above the cutoff, this OG is done iterating.
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if seqs_below == 0 or i == params.guidance_iters - 1:
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print('\nGuidance complete after ' + str(i + 1) + ' iterations for gene family ' + file.split('.')[0].split('_preguidance')[0] + '\n')
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break
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#Recording list of sequences removed by Guidance.
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for line in [line for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1:-1] if float(line.split()[-1]) < params.seq_cutoff]:
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guidance_removed_file.write(line)
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#Copying over the old file with the new results
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os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
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#Handling intermediate files for each iteration.
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if params.keep_iter:
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if i +1 < params.guidance_iters:
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os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/', exist_ok = True)
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os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1)+'/', exist_ok = True)
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os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1) + '/' + file.split('.')[0].split('_preguidance')[0], exist_ok = True)
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iteration_folder = params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i +1) + '/' + file.split('.')[0].split('_preguidance')[0]
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os.system('cp -r ' + tax_guidance_outdir + '/* ' + iteration_folder)
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if not params.keep_temp:
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for gdir_file in os.listdir(iteration_folder):
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if gdir_file not in ('MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names', 'MSA.MAFFT.aln.With_Names', 'MSA.MAFFT.Guidance2_res_pair_col.scr', 'log', 'postGuidance_preTrimAl_unaligned.fasta'):
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os.system('rm -r ' + iteration_folder + '/' + gdir_file)
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else:
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if gdir_file == 'MSA.MAFFT.aln.With_Names':
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os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
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else:
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os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
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os.system('rm -r ' + tax_guidance_outdir + '/*')
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else:
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fail = True
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break
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#After all iterations, THEN apply residue and column cutoffs
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if not fail:
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#Getting a list of sequences to keep
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seqs2keep = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names', 'fasta')]
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orig_seqs = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/MSA.MAFFT.aln.With_Names', 'fasta')]
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running_aln = { rec.description : str(rec.seq) for rec in SeqIO.parse(tax_guidance_outdir + '/MSA.MAFFT.aln.With_Names', 'fasta') if rec.description in seqs2keep }
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#Residues that fall below the confidence cutoff (--res_cutoff) are replaced with 'X'
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for site in [(int(line.split()[1]), int(line.split()[0]) - 1) for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1:-1] if float(line.split(' ')[-1].strip()) < params.res_cutoff]:
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if(orig_seqs[site[0]] in seqs2keep):
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running_aln[orig_seqs[site[0]]][site[1]] = 'X'
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#Removing columns below the --col_cutoff
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cols2remove = [int(line.split()[0]) - 1 for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1:-1] if float(line.split(' ')[-1].strip()) < params.col_cutoff]
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for seq in running_aln:
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running_aln[seq] = ''.join([running_aln[seq][i] for i in range(len(running_aln[seq])) if i not in cols2remove])
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with open(tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta', 'w') as o:
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for seq in running_aln:
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o.write('>' + seq + '\n' + str(running_aln[seq]).replace('-', '') + '\n\n')
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#Aligning one last time after removing the final set of sequences and applying the res and col cutoffs
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print('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_postGuidance_preTrimAl_aligned.fasta')
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os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta')
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#Gap trimming
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os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta -gapthreshold ' + str(params.trimal_cutoff) + ' -fasta')
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#Copying over final aligments (pre and post gap trimming) into output folder.
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os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta ' + params.output + '/Output/Guidance/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta')
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os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta ' + params.output + '/Output/NotGapTrimmed/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta')
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#Removing intermediate files if not --keep_temp
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if not params.keep_temp:
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for gdir_file in os.listdir(tax_guidance_outdir):
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if gdir_file not in ('MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names', 'MSA.MAFFT.aln.With_Names', 'MSA.MAFFT.Guidance2_res_pair_col.scr', 'log', 'postGuidance_preTrimAl_unaligned.fasta'):
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os.system('rm -r ' + tax_guidance_outdir + '/' + gdir_file)
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else:
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if gdir_file == 'MSA.MAFFT.aln.With_Names':
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os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
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else:
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os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
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guidance_removed_file.close()
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return True
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