mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 05:10:28 +08:00
88 lines
3.4 KiB
Python
88 lines
3.4 KiB
Python
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 + ' -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 -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')
|
|
else:
|
|
Logger.Warning('No tree file created by RAxML for OG ' + file[:10])
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|