YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 05:10:28 +08:00
Code Issues Packages Projects Releases Wiki Activity

annotating trees.py

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2024-02-07 12:30:22 -05:00 committed by GitHub
parent 7220b81402
commit 23b81f83f7
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 28 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
PTL2/Scripts/trees.py
View File

@ -1,14 +1,27 @@
# Last updated Sept 2023
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
# This is a relatively simple script that only runs trees, using either IQ-Tree
# or RAxML. The run() function is called in two places: both in phylotol.py, and
# in contamination.py, where it is used to re-build trees. When starting at this
# step, users must input one aligned amino acid fasta file per OG. Otherwise, if
# starting at the pre-Guidance or Guidance steps, this step will be run if --end = trees.
#Dependencies
import os, sys, re
from Bio import SeqIO
from color import color
#Called in phylotol.py and contamination.py
def run(params):
#Checking whether aligned files were input, or it should just start with the Guidance outputs from the previous step.
if params.start == 'aligned':
guidance_path = params.data
else:
guidance_path = params.output + '/Output/Guidance'
#Looking for input files
if not os.path.isdir(guidance_path):
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')
exit()
@ -16,36 +29,45 @@ def run(params):
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:
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')
exit()
#For each input alignment
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')]:
#Run IQ-Tree
if params.tree_method == 'iqtree':
#Make intermediate folders
if not os.path.isdir(params.output + '/Output/Intermediate/IQTree'):
os.mkdir(params.output + '/Output/Intermediate/IQTree')
tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_iqtree_outdir)
#Run IQ-Tree
os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T AUTO --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree')
#Copy over the final output
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:
print('\nWARNING: No tree file created by IQ-Tree for OG ' + file[:10] + '\n')
#If not IQ-Tree, then run RAxML
elif params.tree_method == 'raxml':
#Make intermediate folders
if not os.path.isdir(params.output + '/Output/Intermediate/RAxML'):
os.mkdir(params.output + '/Output/Intermediate/RAxML')
tax_raxml_outdir = params.output + '/Output/Intermediate/RAxML/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_raxml_outdir)
#Reformat the alignment as phylip
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))
#Run RAxML
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))
#Copy over final output
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')