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 utils.py

Browse Source
This commit is contained in:
Auden Cote-L'Heureux 2024-02-07 11:52:08 -05:00 committed by GitHub
parent b7a3d1ac12
commit c308864f5c
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 26 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

30
PTL2/Scripts/utils.py
View File

@ -1,13 +1,23 @@
# Last updated: Jan 2024
# Author: Auden Cote-L'Heureux
# This script is a general utility script that does two main things. First, it has
# a function to read in all PhyloToL parameters, which is called in phylotol.py.
# It also has a function that checks for and cleans up existing PhyloToL part 2
# output files from previous runs, and creates a new, empty Output folder structure
# for the new run. This function is also called only in phylotol.py.
#Dependencies
import os, sys, re
import argparse
import shutil
#Reading in all parameters. This function is only called once, in phylotol.py
def get_params():
parser = argparse.ArgumentParser(
prog = 'PhyloToL v6.0',
description = "Updated December 9, 2022 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0"
description = "Updated January, 2022 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0"
)
common = parser.add_argument_group('Commonly adjusted parameters')
@ -62,18 +72,26 @@ def get_params():
return parser.parse_args()
#Cleaning up existing output and creating a new output folder structure. This function is only called once, in phylotol.py
def clean_up(params):
#If an output folder doesn't exist, create one.
if not os.path.isdir(params.output + '/Output'):
os.mkdir(params.output + '/Output')
#If an output folder already exists at the given path and not running in force mode, stop.
elif os.path.isdir(params.output + '/Output') and params.force == False:
print('\nAn "Output" folder already exists at the given path. Please delete or rename this folder and try again.\n')
exit()
#If running in force mode, delete any existing output.
elif params.force and len([d for d in os.listdir(params.output + '/Output') if d != '.DS_Store']) > 0:
print('\nAn "Output" folder already exists at the given path, but all contents were deleted in --force mode.\n')
os.system('rm -r ' + params.output + '/Output/*')
#Create a folder to hold intermediate files.
os.mkdir(params.output + '/Output/Intermediate')
#General function to copy over input data files into the appropriate folder (e.g. if one unaligned amino acid file
#is input per OG, then these files will be put into the Output/Pre-Guidance folder.
def copy_input(dirname):
if os.path.isdir(params.data):
input_files = [f for f in os.listdir(params.data) if f.endswith('.faa') or f.endswith('.fasta') or f.endswith('.fa')]
@ -84,17 +102,21 @@ def clean_up(params):
print('\nThe given path to a folder of ' + params.start.strip('s') + ' files was located, but no ' + params.start.strip('s') + ' files were found. Make sure the file extensions are .fasta, .fa, or .faa.\n')
else:
print('\nInput ' + params.start.strip('s') + ' data files not found. Please make sure that the given path (--data) is correct or set --start to "raw".\n')
#Create the Pre-Guidance folder and copy over any input data files that are
#formatted as Pre-Guidance files
os.mkdir(params.output + '/Output/Pre-Guidance')
if params.start == 'unaligned':
copy_input('Pre-Guidance')
#Do the same for aligned files
if params.start in ('unaligned', 'aligned') or params.end in ('aligned', 'trees', None):
os.mkdir(params.output + '/Output/Guidance')
os.mkdir(params.output + '/Output/NotGapTrimmed')
if params.start == 'aligned':
copy_input('Guidance')
#And for trees
if params.end == 'trees' or params.contamination_loop != None:
os.mkdir(params.output + '/Output/Trees')
os.mkdir(params.output + '/Output/ColoredTrees')