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removing calls to logger in trees.py

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Auden Cote-L'Heureux 2024-02-07 11:29:55 -05:00 committed by GitHub
parent 556b8646ba
commit b981641f62
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1 changed files with 8 additions and 7 deletions
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15
PTL2/Scripts/trees.py
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@ -1,6 +1,5 @@
import os, sys, re
from Bio import SeqIO
from logger import Logger
from color import color
def run(params):
@ -11,11 +10,13 @@ def run(params):
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.')
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()
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).')
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 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':
@ -31,7 +32,7 @@ def run(params):
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])
print('\nWARNING: No tree file created by IQ-Tree for OG ' + file[:10] + '\n')
elif params.tree_method == 'raxml':
if not os.path.isdir(params.output + '/Output/Intermediate/RAxML'):
@ -49,7 +50,7 @@ def run(params):
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])
print('\nWARNING: No tree file created by RAxML for OG ' + file[:10] + '\n')