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114 lines
4.6 KiB
Python
114 lines
4.6 KiB
Python
# Last updated Sept 2023
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# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
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# This is a relatively simple script that only runs trees, using either IQ-Tree
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# or RAxML. The run() function is called in two places: both in phylotol.py, and
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# in contamination.py, where it is used to re-build trees. When starting at this
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# step, users must input one aligned amino acid fasta file per OG. Otherwise, if
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# starting at the pre-Guidance or Guidance steps, this step will be run if --end = trees.
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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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from color import color
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#Called in phylotol.py and contamination.py
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def run(params):
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#Checking whether aligned files were input, or it should just start with the Guidance outputs from the previous step.
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if params.start == 'aligned':
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guidance_path = params.data
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else:
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guidance_path = params.output + '/Output/Guidance'
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#Looking for input files
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if not os.path.isdir(guidance_path):
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print('\nERROR: The path ' + guidance_path + ' could not be found when trying to locate Guidance (aligned) files. Make sure that the --start and --data parameters are correct and/or that the Guidance step ran successfully.\n')
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exit()
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if len([f for f in os.listdir(guidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta') or f.endswith('.fas') or f.endswith('.aln')]) == 0:
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print('\nERROR: No Guidance (unaligned) files could be found at the path ' + guidance_path + '. Make sure that the --start and --data parameters are correct, that the Guidance step ran successfully, and that the aligned files are formatted correctly (they must have the file extension .faa, .fa, .aln, .fas, or .fasta).\n')
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exit()
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#For each input alignment
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for file in [f for f in os.listdir(guidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta') or f.endswith('.fas') or f.endswith('.aln')]:
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#Run IQ-Tree
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if params.tree_method == 'iqtree' or params.tree_method == 'iqtree_fast':
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#Make intermediate folders
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if not os.path.isdir(params.output + '/Output/Intermediate/IQTree'):
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os.mkdir(params.output + '/Output/Intermediate/IQTree')
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tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
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os.mkdir(tax_iqtree_outdir)
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#Run IQ-Tree
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if params.tree_method == 'iqtree':
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os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')
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elif params.tree_method == 'iqtree_fast':
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os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T 10 --fast --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')
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#Copy over the final output
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if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
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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')
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#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
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else:
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print('\nWARNING: No tree file created by IQ-Tree for OG ' + file[:10] + '\n')
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#If not IQ-Tree, then run RAxML
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elif params.tree_method == 'raxml':
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#Make intermediate folders
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if not os.path.isdir(params.output + '/Output/Intermediate/RAxML'):
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os.mkdir(params.output + '/Output/Intermediate/RAxML')
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tax_raxml_outdir = params.output + '/Output/Intermediate/RAxML/' + file.split('.')[0].split('_preguidance')[0]
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os.mkdir(tax_raxml_outdir)
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#Reformat the alignment as phylip
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os.system('./Scripts/trimal-trimAl/source/trimal -in ' + guidance_path + '/' + file + ' -phylip -out ' + tax_raxml_outdir + '/aligned.phy')
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#Run RAxML
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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))
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#Copy over final output
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if os.path.isfile(tax_raxml_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
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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')
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#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
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else:
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print('\nWARNING: No tree file created by RAxML for OG ' + file[:10] + '\n')
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