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Iterations parameter added
This commit is contained in:
Godwin Ani
GitHub
parent
b8a68098f3
commit
b91cf0fb63
@ -1,14 +1,10 @@
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#Author, date: Auden Cote-L'Heureux, July 17 2023
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#Motivation: Run Guidance on multiple files
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#Intent: To be used in place of PhyloToL part 2 if there is a good reason not to use the guidance-only mode of PhyloToL
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#Dependencies: Python3, BioPython
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#Inputs: A folder of unaligned fasta files
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#Outputs: Folder for each input file with selected Guidance output files, renamed with the original file name at the front
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#Example: python3 GuidanceWrapper_v2.1.py -i FastaFiles
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# Last updated Sept 2023
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# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
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########### new code
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#Dependencies
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import os, sys
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import os, sys, re
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import argparse
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from Bio import SeqIO
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@ -18,7 +14,7 @@ parser = argparse.ArgumentParser(
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description = "Updated July 21, 2023 by Auden Cote-L'Heureux"
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)
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parser.add_argument('--input', '-i', required = True, type = str, help = 'Path to folder of unaligned amino acid fasta files to align. File extensions must be fasta, fa, fas, or faa. Try using the absolute rather than relative path if working on the Grid and having trouble')
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parser.add_argument('--output', '-o', default = '.', type = str, help = 'Path to folder where a folder named "GuidanceOutput" will be created')
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parser.add_argument('--output', '-o', default = '.', type = str, help = 'Path to folder where files will be created')
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parser.add_argument('--codon', action = 'store_true', help = 'Run on nucleotide files by translating codons')
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parser.add_argument('--iterations', '-n', default = 5, type = int, help = 'Number of Guidance iterations (default = 5)')
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parser.add_argument('--guidance_path', '-p', default = 'guidance.v2.02', type = str, help = 'Path to the guidance_v2.02 folder')
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@ -28,133 +24,135 @@ parser.add_argument('--res_cutoff', '-r', default = 0.0, type = float, help = 'D
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parser.add_argument('--force', '-f', action = 'store_true', help = 'Delete existing output folder at given output path')
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parser.add_argument('--keep_temp', '-k', action = 'store_true', help = 'Keep all Guidance intermediate files (beware, some can be very large)')
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parser.add_argument('--guidance_threads', '-t', default = 20, type = int, help = 'Number of threads to allocate to Guidance')
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parser.add_argument('--keep_iter', '-z', action = 'store_true', help = 'Keep all Guidance intermediate files (beware, some can be very large)')
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args = parser.parse_args()
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#Creating an output folder
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if not os.path.isdir(args.output + '/GuidanceOutput'):
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os.mkdir(args.output + '/GuidanceOutput')
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elif not args.force:
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print('\nERROR: An output folder already exists at the given path. Delete it or run in --force mode\n')
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quit()
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#Creating intermedate folders that will later be deleted unless running with --keep_temp
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#For each file in the input folder
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for file in os.listdir(args.input):
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#If it has an appropriate extension for an amino acid fasta file
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if file.split('.')[-1] in ('fasta', 'fa', 'fas', 'faa'):
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#Create the output folder
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tax_guidance_outdir = args.output + '/GuidanceOutput/' + file.split('.')[0]
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if(not os.path.isdir(tax_guidance_outdir)):
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os.makedirs(args.output + '/Output/Intermediate/Guidance')
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os.mkdir(args.output + '/Output/Intermediate/Guidance/Input')
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os.mkdir(args.output + '/Output/Intermediate/Guidance/Output')
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#new
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os.mkdir(args.output + '/Output/Guidance')
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os.mkdir(args.output + '/Output/NotGapTrimmed')
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#new
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guidance_input = args.output + 'Output/Intermediate/Guidance/Input/'
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os.system('cp -r ' + args.input + '/* ' + guidance_input)
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guidance_removed_file = open(args.output + '/Output/GuidanceRemovedSeqs.txt', 'w')
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guidance_removed_file.write('Sequence\tScore\n')
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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 = args.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
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os.mkdir(tax_guidance_outdir)
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#Read in the sequence data and replace any * and U characters with 'X'
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recs = [r for r in SeqIO.parse(args.input + '/' + file, 'fasta')]
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with open(args.input + '/' + file, 'w') as o:
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for rec in recs:
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o.write('>' + rec.description + '\n' + str(rec.seq).replace('*', 'X').replace('U', 'X') + '\n\n')
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fail = False
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#For each Guidance iteration (default = 5)
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#For each iteration
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for i in range(args.iterations):
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#Get the number sequences in the unaligned file
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n_recs = len([r for r in SeqIO.parse(args.input + '/' + file, 'fasta')])
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#Cancel the Guidance run if there are fewer than 4 sequences
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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('\nGene 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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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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#MAFFT parameters depend on sequence count
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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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#Determining if its nucleotide or AA
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if args.codon:
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seqtype = 'codon'
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else:
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seqtype = 'aa'
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#Run Guidance
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os.system(args.guidance_path + '/www/Guidance/guidance.pl --seqFile ' + args.input + '/' + file + ' --msaProgram MAFFT --seqType ' + seqtype + ' --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(args.seq_cutoff) + ' --colCutoff ' + str(args.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(args.guidance_threads) + " --bl 62 --anysymbol' > " + tax_guidance_outdir + '/log.txt')
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#Run Guidance - new
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os.system(args.guidance_path + '/www/Guidance/guidance.pl --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType ' + seqtype + ' --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(args.seq_cutoff) + ' --colCutoff ' + str(args.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(args.guidance_threads) + " --bl 62 --anysymbol' > " + args.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt')
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#If it ran successfully
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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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sep = ' '
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if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1]:
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sep = '\t'
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#Create a record of sequences below the sequence 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(sep)[-1]) < args.seq_cutoff])
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#If the number of remaining sequences is less than 4, then stop iterating
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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]) < args.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('\nGene 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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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 there are no sequences below the cutoff or the number of Guidance iterations has been reached, then stop iterating
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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 == args.iterations - 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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#If another iteration is needed, then replace the original input file with the sequence-filtered run to input to Guidance for the next iteration
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os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + args.input + '/' + file)
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#If another iteration is needed, remove the Guidance output from the last iteration
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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]) < args.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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#new
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#Handling intermediate files for each iteration.
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if args.keep_iter:
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if i +1 < args.iterations:
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os.makedirs(args.output + '/Output/iterations/', exist_ok = True)
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os.makedirs(args.output + '/Output/iterations/' + str(i+1)+'/', exist_ok = True)
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os.makedirs(args.output + '/Output/iterations/' + str(i+1) + '/' + file.split('.')[0].split('_preguidance')[0], exist_ok = True)
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iteration_folder = args.output + '/Output/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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os.system('rm -r ' + tax_guidance_outdir + '/*')
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if not args.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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#new
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else:
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fail = True
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break
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#If Guidance ran successfully
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#After all iterations, THEN apply residue and column cutoffs
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if not fail:
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#Create a record of sequences above the sequence score cutoff
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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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#Put this sequence information in a dictionary and write out the surviving sequences to an unaligned .fasta file
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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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with open(tax_guidance_outdir + '/postGuidance_preMAFFT_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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#Align the file with MAFFT
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os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preMAFFT_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_MAFFT_realigned.fasta')
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#Read in the MAFFT alignment
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running_aln = { rec.description : str(rec.seq) for rec in SeqIO.parse(tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_MAFFT_realigned.fasta', 'fasta') }
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sep = ' '
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if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1]:
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sep = '\t'
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#Apply residue cutoff per site per sequence
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for site in [(int(line.split(sep)[1]), int(line.split(sep)[0]) - 1) for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1:-1] if float(line.split(sep)[-1].strip()) < args.res_cutoff]:
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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()) < args.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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sep = ' '
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if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1]:
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sep = '\t'
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#Apply column cutoff per column
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cols2remove = [int(line.split(sep)[0]) - 1 for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1:-1] if float(line.split(sep)[-1].strip()) < args.col_cutoff]
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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()) < args.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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#Write out the final filtered alignment
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with open(tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_MAFFT_realigned.fasta', 'w') as o:
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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]) + '\n\n')
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o.write('>' + seq + '\n' + str(running_aln[seq]).replace('-', '') + '\n\n')
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#If the user hasn't specified to keep all intermediate files, then delete the extraneous ones and rename the rest per the input file name
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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 0.05 -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 ' + args.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 ' + args.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 args.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', file.split('.')[0].split('_preguidance')[0] + '.postGuidance_MAFFT_realigned.fasta'):
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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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@ -162,11 +160,4 @@ for file in os.listdir(args.input):
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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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