mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 07:40:25 +08:00
Add files via upload
This commit is contained in:
Godwin Ani
GitHub
parent
8b35b8a64d
commit
2f67243515
@ -1,175 +1,195 @@
|
|||||||
# Last updated Sept 2023
|
# Last updated Apr 2 2024
|
||||||
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
|
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
|
||||||
|
|
||||||
# This script runs Guidance in an iterative fashion for more both MSA construction
|
# This script runs Guidance in an iterative fashion for more both MSA construction
|
||||||
# and more rigorous homology assessment than what is offered in PhyloToL 6 part 1.
|
# and more rigorous homology assessment than what is offered in PhyloToL 6 part 1.
|
||||||
# Guidance runs until the input number of iterations (--guidance_iters, default = 5)
|
# Guidance runs until the input number of iterations (--guidance_iters, default = 5)
|
||||||
# has been reached, or until there are no sequences below the sequence score cutoff.
|
# has been reached, or until there are no sequences below the sequence score cutoff.
|
||||||
# All sequences below the score cutoff (--seq_cutoff, default = 0.3) are removed at
|
# All sequences below the score cutoff (--seq_cutoff, default = 0.3) are removed at
|
||||||
# each iteration. By default, PhyloToL does not remove residues that fall below the
|
# each iteration. By default, PhyloToL does not remove residues that fall below the
|
||||||
# given residue cutoff (--res_cutoff) and columns that fall below the given column
|
# given residue cutoff (--res_cutoff) and columns that fall below the given column
|
||||||
# cutoff (--col_cutoff, defaults are 0), though this can be turned on by adjusting
|
# cutoff (--col_cutoff, defaults are 0), though this can be turned on by adjusting
|
||||||
# these parameters. Outputs at this point are found in the “Guidance_NotGapTrimmed”
|
# these parameters. Outputs at this point are found in the “Guidance_NotGapTrimmed”
|
||||||
# output folder. We then run MSAs through TrimAl to remove all sites in the alignment
|
# output folder. We then run MSAs through TrimAl to remove all sites in the alignment
|
||||||
# that are at least 95% gaps (or --gap_trim_cutoff) generating files in the “Guidance”
|
# that are at least 95% gaps (or --gap_trim_cutoff) generating files in the “Guidance”
|
||||||
# output folder.
|
# output folder.
|
||||||
|
|
||||||
# This step is either intended to be run starting with --start = unaligned (but not raw)
|
# This step is either intended to be run starting with --start = unaligned (but not raw)
|
||||||
# inputs, meaning one amino acid alignment per OG. It can also be run directly after the
|
# inputs, meaning one amino acid alignment per OG. It can also be run directly after the
|
||||||
# preguidance step. The run() function is called in two places: in phylotol.py generally,
|
# preguidance step. The run() function is called in two places: in phylotol.py generally,
|
||||||
# and in contamination.py if the contamination loop is using Guidance as the re-alignment
|
# and in contamination.py if the contamination loop is using Guidance as the re-alignment
|
||||||
# method.
|
# method.
|
||||||
|
|
||||||
#Dependencies
|
#Dependencies
|
||||||
import os, sys, re
|
import os, sys, re
|
||||||
from Bio import SeqIO
|
from Bio import SeqIO
|
||||||
|
|
||||||
#Called in phylotol.py and contamination.py
|
#Called in phylotol.py and contamination.py
|
||||||
def run(params):
|
def run(params):
|
||||||
|
|
||||||
if params.start == 'raw' or params.start == 'unaligned':
|
if params.start == 'raw' or params.start == 'unaligned':
|
||||||
#Checking that pre-Guidance has been run or that unaligned files per OG are provided.
|
#Checking that pre-Guidance has been run or that unaligned files per OG are provided.
|
||||||
if params.start == 'raw':
|
if params.start == 'raw':
|
||||||
preguidance_path = params.output + '/Output/Pre-Guidance'
|
preguidance_path = params.output + '/Output/Pre-Guidance'
|
||||||
else:
|
else:
|
||||||
preguidance_path = params.data
|
preguidance_path = params.data
|
||||||
|
|
||||||
if not os.path.isdir(preguidance_path):
|
if not os.path.isdir(preguidance_path):
|
||||||
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')
|
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')
|
||||||
exit()
|
exit()
|
||||||
|
|
||||||
if len([f for f in os.listdir(preguidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]) == 0:
|
if len([f for f in os.listdir(preguidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]) == 0:
|
||||||
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')
|
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')
|
||||||
exit()
|
exit()
|
||||||
|
|
||||||
#Creating intermedate folders that will later be deleted unless running with --keep_temp
|
#Creating intermedate folders that will later be deleted unless running with --keep_temp
|
||||||
os.mkdir(params.output + '/Output/Intermediate/Guidance')
|
os.mkdir(params.output + '/Output/Intermediate/Guidance')
|
||||||
os.mkdir(params.output + '/Output/Intermediate/Guidance/Input')
|
os.mkdir(params.output + '/Output/Intermediate/Guidance/Input')
|
||||||
os.mkdir(params.output + '/Output/Intermediate/Guidance/Output')
|
os.mkdir(params.output + '/Output/Intermediate/Guidance/Output')
|
||||||
|
|
||||||
guidance_input = params.output + '/Output/Intermediate/Guidance/Input/'
|
guidance_input = params.output + '/Output/Intermediate/Guidance/Input/'
|
||||||
os.system('cp -r ' + preguidance_path + '/* ' + guidance_input)
|
os.system('cp -r ' + preguidance_path + '/* ' + guidance_input)
|
||||||
|
|
||||||
guidance_removed_file = open(params.output + '/Output/GuidanceRemovedSeqs.txt', 'w')
|
guidance_removed_file = open(params.output + '/Output/GuidanceRemovedSeqs.txt', 'w')
|
||||||
guidance_removed_file.write('Sequence\tScore\n')
|
guidance_removed_file.write('Sequence\tScore\n')
|
||||||
|
|
||||||
#For each unaligned AA fasta file
|
#For each unaligned AA fasta file
|
||||||
for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
|
for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
|
||||||
tax_guidance_outdir = params.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
|
tax_guidance_outdir = params.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
|
||||||
os.mkdir(tax_guidance_outdir)
|
os.mkdir(tax_guidance_outdir)
|
||||||
|
|
||||||
fail = False
|
fail = False
|
||||||
#For each iteration
|
#For each iteration
|
||||||
for i in range(params.guidance_iters):
|
for i in range(params.guidance_iters):
|
||||||
n_recs = len([r for r in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
|
n_recs = len([r for r in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
|
||||||
|
|
||||||
#Guidance can't handle inputs with fewer than 4 sequences
|
#Guidance can't handle inputs with fewer than 4 sequences
|
||||||
if n_recs < 4:
|
if n_recs < 4:
|
||||||
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')
|
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')
|
||||||
os.system('rm -rf ' + tax_guidance_outdir)
|
os.system('rm -rf ' + tax_guidance_outdir)
|
||||||
if i == 0:
|
if i == 0:
|
||||||
fail = True
|
fail = True
|
||||||
break
|
break
|
||||||
|
|
||||||
#Determining MAFFT algorithm based on the number of input sequences
|
#Determining MAFFT algorithm based on the number of input sequences
|
||||||
if n_recs < 200:
|
if n_recs < 200:
|
||||||
mafft_alg = 'genafpair'
|
mafft_alg = 'genafpair'
|
||||||
else:
|
else:
|
||||||
mafft_alg = 'auto'
|
mafft_alg = 'auto'
|
||||||
|
|
||||||
#Running Guidance (one per OG per iteration)
|
#Running Guidance (one per OG per iteration)
|
||||||
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')
|
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')
|
||||||
|
|
||||||
#Checking for a sequence score file; if not available, Guidance failed.
|
#Checking for a sequence score file; if not available, Guidance failed.
|
||||||
if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
|
if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
|
||||||
#All sequences below score cutoff
|
#All sequences below score cutoff
|
||||||
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])
|
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])
|
||||||
#If fewer than four were above the cutoff, this OG is done iterating.
|
#If fewer than four were above the cutoff, this OG is done iterating.
|
||||||
if n_recs - seqs_below < 4:
|
if n_recs - seqs_below < 4:
|
||||||
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')
|
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')
|
||||||
os.system('rm -rf ' + tax_guidance_outdir)
|
os.system('rm -rf ' + tax_guidance_outdir)
|
||||||
break
|
break
|
||||||
#If all sequences were above the cutoff, this OG is done iterating.
|
#If all sequences were above the cutoff, this OG is done iterating.
|
||||||
if seqs_below == 0 or i == params.guidance_iters - 1:
|
if seqs_below == 0 or i == params.guidance_iters - 1:
|
||||||
print('\nGuidance complete after ' + str(i + 1) + ' iterations for gene family ' + file.split('.')[0].split('_preguidance')[0] + '\n')
|
print('\nGuidance complete after ' + str(i + 1) + ' iterations for gene family ' + file.split('.')[0].split('_preguidance')[0] + '\n')
|
||||||
break
|
break
|
||||||
#Recording list of sequences removed by Guidance.
|
#Recording list of sequences removed by Guidance.
|
||||||
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]:
|
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]:
|
||||||
guidance_removed_file.write(line)
|
guidance_removed_file.write(line)
|
||||||
#Copying over the old file with the new results
|
#Copying over the old file with the new results
|
||||||
os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
|
os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
|
||||||
#Cleaning up the intermediate files for the iteration.
|
|
||||||
os.system('rm -r ' + tax_guidance_outdir + '/*')
|
#Handling intermediate files for each iteration.
|
||||||
else:
|
if params.keep_iter:
|
||||||
fail = True
|
if i +1 < params.guidance_iters:
|
||||||
break
|
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/', exist_ok = True)
|
||||||
|
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1)+'/', exist_ok = True)
|
||||||
#After all iterations, THEN apply residue and column cutoffs
|
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1) + '/' + file.split('.')[0].split('_preguidance')[0], exist_ok = True)
|
||||||
if not fail:
|
iteration_folder = params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i +1) + '/' + file.split('.')[0].split('_preguidance')[0]
|
||||||
#Getting a list of sequences to keep
|
os.system('cp -r ' + tax_guidance_outdir + '/* ' + iteration_folder)
|
||||||
seqs2keep = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names', 'fasta')]
|
|
||||||
orig_seqs = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/MSA.MAFFT.aln.With_Names', 'fasta')]
|
|
||||||
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 }
|
if not params.keep_temp:
|
||||||
|
for gdir_file in os.listdir(iteration_folder):
|
||||||
#Residues that fall below the confidence cutoff (--res_cutoff) are replaced with 'X'
|
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'):
|
||||||
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]:
|
os.system('rm -r ' + iteration_folder + '/' + gdir_file)
|
||||||
if(orig_seqs[site[0]] in seqs2keep):
|
else:
|
||||||
running_aln[orig_seqs[site[0]]][site[1]] = 'X'
|
if gdir_file == 'MSA.MAFFT.aln.With_Names':
|
||||||
|
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
|
||||||
#Removing columns below the --col_cutoff
|
else:
|
||||||
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]
|
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
|
||||||
for seq in running_aln:
|
|
||||||
running_aln[seq] = ''.join([running_aln[seq][i] for i in range(len(running_aln[seq])) if i not in cols2remove])
|
os.system('rm -r ' + tax_guidance_outdir + '/*')
|
||||||
|
else:
|
||||||
with open(tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta', 'w') as o:
|
fail = True
|
||||||
for seq in running_aln:
|
break
|
||||||
o.write('>' + seq + '\n' + str(running_aln[seq]).replace('-', '') + '\n\n')
|
|
||||||
|
#After all iterations, THEN apply residue and column cutoffs
|
||||||
#Aligning one last time after removing the final set of sequences and applying the res and col cutoffs
|
if not fail:
|
||||||
print('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_postGuidance_preTrimAl_aligned.fasta')
|
#Getting a list of sequences to keep
|
||||||
os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta')
|
seqs2keep = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names', 'fasta')]
|
||||||
|
orig_seqs = [rec.description for rec in SeqIO.parse(tax_guidance_outdir + '/MSA.MAFFT.aln.With_Names', 'fasta')]
|
||||||
#Gap trimming
|
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 }
|
||||||
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')
|
|
||||||
|
#Residues that fall below the confidence cutoff (--res_cutoff) are replaced with 'X'
|
||||||
#Copying over final aligments (pre and post gap trimming) into output folder.
|
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]:
|
||||||
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')
|
if(orig_seqs[site[0]] in seqs2keep):
|
||||||
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')
|
running_aln[orig_seqs[site[0]]][site[1]] = 'X'
|
||||||
|
|
||||||
#Removing intermediate files if not --keep_temp
|
#Removing columns below the --col_cutoff
|
||||||
if not params.keep_temp:
|
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]
|
||||||
for gdir_file in os.listdir(tax_guidance_outdir):
|
for seq in running_aln:
|
||||||
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'):
|
running_aln[seq] = ''.join([running_aln[seq][i] for i in range(len(running_aln[seq])) if i not in cols2remove])
|
||||||
os.system('rm -r ' + tax_guidance_outdir + '/' + gdir_file)
|
|
||||||
else:
|
with open(tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta', 'w') as o:
|
||||||
if gdir_file == 'MSA.MAFFT.aln.With_Names':
|
for seq in running_aln:
|
||||||
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
|
o.write('>' + seq + '\n' + str(running_aln[seq]).replace('-', '') + '\n\n')
|
||||||
else:
|
|
||||||
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
|
#Aligning one last time after removing the final set of sequences and applying the res and col cutoffs
|
||||||
|
print('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_postGuidance_preTrimAl_aligned.fasta')
|
||||||
guidance_removed_file.close()
|
os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta')
|
||||||
|
|
||||||
|
#Gap trimming
|
||||||
|
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')
|
||||||
|
|
||||||
|
#Copying over final aligments (pre and post gap trimming) into output folder.
|
||||||
|
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')
|
||||||
|
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')
|
||||||
|
|
||||||
|
#Removing intermediate files if not --keep_temp
|
||||||
|
if not params.keep_temp:
|
||||||
|
for gdir_file in os.listdir(tax_guidance_outdir):
|
||||||
|
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'):
|
||||||
|
os.system('rm -r ' + tax_guidance_outdir + '/' + gdir_file)
|
||||||
|
else:
|
||||||
|
if gdir_file == 'MSA.MAFFT.aln.With_Names':
|
||||||
|
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
|
||||||
|
else:
|
||||||
|
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
|
||||||
|
|
||||||
|
guidance_removed_file.close()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user