From 7af603d7f470121dd017b658ea39bb4b41c14606 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Thu, 31 Aug 2023 13:04:18 -0400 Subject: [PATCH] Delete PTL2/Scripts/trees.py Script with .fas and .fasta issue. --- PTL2/Scripts/trees.py | 87 ------------------------------------------- 1 file changed, 87 deletions(-) delete mode 100644 PTL2/Scripts/trees.py diff --git a/PTL2/Scripts/trees.py b/PTL2/Scripts/trees.py deleted file mode 100644 index 766a46d..0000000 --- a/PTL2/Scripts/trees.py +++ /dev/null @@ -1,87 +0,0 @@ -import os, sys, re -from Bio import SeqIO -from logger import Logger -from color import color - -def run(params): - - if params.start == 'aligned': - guidance_path = params.data - else: - guidance_path = params.output + '/Output/Guidance' - - if not os.path.isdir(guidance_path): - Logger.Error('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.') - - 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: - Logger.Error('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).') - - 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')]: - - if params.tree_method == 'iqtree': - if not os.path.isdir(params.output + '/Output/Temp/IQTree'): - os.mkdir(params.output + '/Output/Temp/IQTree') - - 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') - - 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') - else: - Logger.Warning('No tree file created by IQ-Tree for OG ' + file[:10]) - - elif params.tree_method == 'raxml': - if not os.path.isdir(params.output + '/Output/Temp/RAxML'): - os.mkdir(params.output + '/Output/Temp/RAxML') - - tax_raxml_outdir = params.output + '/Output/Temp/RAxML/' + file.split('.')[0].split('_preguidance')[0] - os.mkdir(tax_raxml_outdir) - - os.system('./Scripts/trimal-trimAl/source/trimal -in ' + guidance_path + '/' + file + ' -phylip -out ' + tax_raxml_outdir + '/aligned.phy') - - print('raxmlHPC-PTHREADS-AVX2 -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 1 -w ' + tax_raxml_outdir + ' -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads)) - os.system('raxmlHPC-PTHREADS-AVX2 -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 1 -w ' + tax_raxml_outdir + ' -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads)) - - if os.path.isfile(tax_raxml_outdir + '/RAxML_bestTree.' + file.split('.')[0].split('_preguidance')[0] + '_RAxML'): - 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') - else: - Logger.Warning('No tree file created by RAxML for OG ' + file[:10]) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -