mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 05:10:28 +08:00
Minor changes to PTL2
This commit is contained in:
Auden Cote-L'Heureux
GitHub
parent
480cf3b9d6
commit
cfd582f6ee
@ -27,12 +27,15 @@ def run(params):
|
||||
tax_guidance_outdir = params.output + '/Output/Temp/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
|
||||
os.mkdir(tax_guidance_outdir)
|
||||
|
||||
fail = False
|
||||
for i in range(params.guidance_iters):
|
||||
n_recs = len([r for r in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
|
||||
|
||||
if n_recs < 4:
|
||||
Logger.Warning('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.')
|
||||
os.system('rm -rf ' + tax_guidance_outdir)
|
||||
if i == 0:
|
||||
fail = True
|
||||
break
|
||||
|
||||
if n_recs < 200:
|
||||
@ -42,51 +45,60 @@ def run(params):
|
||||
|
||||
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/Temp/Guidance/Output/' + file[:10] + '/log.txt')
|
||||
|
||||
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 os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
|
||||
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 n_recs - seqs_below < 4:
|
||||
Logger.Warning('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.')
|
||||
os.system('rm -rf ' + tax_guidance_outdir)
|
||||
if n_recs - seqs_below < 4:
|
||||
Logger.Warning('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.')
|
||||
os.system('rm -rf ' + tax_guidance_outdir)
|
||||
break
|
||||
|
||||
if seqs_below == 0 or i == params.guidance_iters - 1:
|
||||
Logger.Message('Guidance complete after ' + str(i + 1) + ' iterations for gene family ' + file.split('.')[0].split('_preguidance')[0])
|
||||
break
|
||||
|
||||
os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
|
||||
|
||||
os.system('rm -r ' + tax_guidance_outdir + '/*')
|
||||
else:
|
||||
fail = True
|
||||
break
|
||||
|
||||
if seqs_below == 0 or i == params.guidance_iters - 1:
|
||||
Logger.Message('Guidance complete after ' + str(i + 1) + ' iterations for gene family ' + file.split('.')[0].split('_preguidance')[0])
|
||||
break
|
||||
if not fail:
|
||||
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 }
|
||||
|
||||
os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
|
||||
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]:
|
||||
if(orig_seqs[site[0]] in seqs2keep):
|
||||
running_aln[orig_seqs[site[0]]][site[1]] = 'X'
|
||||
|
||||
os.system('rm -r ' + tax_guidance_outdir + '/*')
|
||||
|
||||
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 }
|
||||
|
||||
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]:
|
||||
if(orig_seqs[site[0]] in seqs2keep):
|
||||
running_aln[orig_seqs[site[0]]][site[1]] = 'X'
|
||||
|
||||
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 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])
|
||||
|
||||
with open(tax_guidance_outdir + '/postGuidance_preTrimAl.fasta', 'w') as o:
|
||||
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 seq in running_aln:
|
||||
o.write('>' + seq + '\n' + str(running_aln[seq]) + '\n\n')
|
||||
running_aln[seq] = ''.join([running_aln[seq][i] for i in range(len(running_aln[seq])) if i not in cols2remove])
|
||||
|
||||
os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/postGuidance_preTrimAl.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fas -gapthreshold 0.05 -fasta')
|
||||
os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/postGuidance_preTrimAl.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.phy -gapthreshold 0.05 -phylip')
|
||||
with open(tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta', 'w') as o:
|
||||
for seq in running_aln:
|
||||
o.write('>' + seq + '\n' + str(running_aln[seq]).replace('-', '') + '\n\n')
|
||||
|
||||
os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fas ' + params.output + '/Output/Guidance/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fas')
|
||||
|
||||
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'):
|
||||
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')
|
||||
print('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_postGuidance_preTrimAl_aligned.fasta')
|
||||
os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta')
|
||||
|
||||
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')
|
||||
|
||||
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')
|
||||
|
||||
|
||||
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:
|
||||
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
|
||||
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)
|
||||
|
||||
|
||||
|
||||
|
||||
@ -25,11 +25,11 @@ def run(params):
|
||||
tax_iqtree_outdir = params.output + '/Output/Temp/IQTree/' + file.split('.')[0].split('_preguidance')[0]
|
||||
os.mkdir(tax_iqtree_outdir)
|
||||
|
||||
os.system('iqtree2 -s ' + guidance_path + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fas -m LG+G --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree')
|
||||
os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree')
|
||||
|
||||
if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile'):
|
||||
os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree')
|
||||
color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree')
|
||||
#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree')
|
||||
else:
|
||||
Logger.Warning('No tree file created by IQ-Tree for OG ' + file[:10])
|
||||
|
||||
@ -40,11 +40,14 @@ def run(params):
|
||||
tax_raxml_outdir = params.output + '/Output/Temp/RAxML/' + file.split('.')[0].split('_preguidance')[0]
|
||||
os.mkdir(tax_raxml_outdir)
|
||||
|
||||
os.sytem('raxmlHPC-PTHREADS-AVX2 -s ' + guidance_path + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.phy -m PROTGAMMALG -f d -p 12345 -# 1 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
|
||||
os.system('./Scripts/trimal-trimAl/source/trimal -in ' + guidance_path + '/' + file + ' -phylip -out ' + tax_raxml_outdir + '/aligned.phy')
|
||||
|
||||
print('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
|
||||
os.system('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
|
||||
|
||||
if os.path.isfile(tax_raxml_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile'):
|
||||
os.system('cp ' + tax_raxml_outdir + '/RAxML_bestTree.' + file.split('.')[0].split('_preguidance')[0] + '_RAxML ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
|
||||
color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
|
||||
#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
|
||||
else:
|
||||
Logger.Warning('No tree file created by RAxML for OG ' + file[:10])
|
||||
|
||||
|
||||
@ -19,7 +19,7 @@ def get_params():
|
||||
common.add_argument('--data', help = 'Path to the input dataset. The format of this varies depending on your --start parameter')
|
||||
common.add_argument('--output', default = '../', help = 'Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts.')
|
||||
common.add_argument('--force', action = 'store_true', help = 'Overwrite all existing files in the "Output" folder.')
|
||||
common.add_argument('--tree_method', default = 'iqtree', choices = {'iqtree, raxml, all'}, help = 'Program to use for tree-building')
|
||||
common.add_argument('--tree_method', default = 'iqtree', choices = {'iqtree', 'raxml', 'all'}, help = 'Program to use for tree-building')
|
||||
|
||||
core = parser.add_argument_group('Core parameters (rarely altered from the defaults)')
|
||||
core.add_argument('--blast_cutoff', default = 1e-20, type = float, help = 'Blast e-value cutoff')
|
||||
@ -28,7 +28,7 @@ def get_params():
|
||||
core.add_argument('--overlap_cutoff', default = 0.35, type = float, help = 'A sequence is removed if its alignment length to the longest sequence in its OG & taxon is less than this proportion of the length of the longest sequence')
|
||||
core.add_argument('--guidance_iters', default = 5, type = int, help = 'Number of Guidance iterations for sequence removal')
|
||||
core.add_argument('--seq_cutoff', default = 0.3, type = float, help = 'During guidance, taxa are removed if their score is below this cutoff')
|
||||
core.add_argument('--col_cutoff', default = 0.4, type = float, help = 'During guidance, columns are removed if their score is below this cutoff')
|
||||
core.add_argument('--col_cutoff', default = 0.0, type = float, help = 'During guidance, columns are removed if their score is below this cutoff')
|
||||
core.add_argument('--res_cutoff', default = 0.0, type = float, help = 'During guidance, residues are removed if their score is below this cutoff')
|
||||
core.add_argument('--guidance_threads', default = 20, type = int, help = 'Number of threads to allocate to Guidance')
|
||||
|
||||
@ -93,6 +93,7 @@ def clean_up(params):
|
||||
|
||||
if params.start in ('unaligned', 'aligned') or params.end in ('aligned', 'trees', None):
|
||||
os.mkdir(params.output + '/Output/Guidance')
|
||||
os.mkdir(params.output + '/Output/NotGapTrimmed')
|
||||
if(params.start == 'aligned'):
|
||||
copy_input('Guidance')
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user