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Annotating wrapper.py

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Auden Cote-L'Heureux 2024-01-26 11:17:11 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/wrapper.py
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@ -1,3 +1,15 @@
# Last updated Sept 2023
# Author: Auden Cote-L'Heureux
# This script is a WRAPPER for the PhyloToL Part 1 TRANSCRIPTOMES pipeline. Users should
# use this script to run the pipeline, rather than running any of the sub-scripts (number 1a through 7b)
# independently. To run an individual step in the pipeline, use --script X where X is the number (1 through 7).
# To run multiple sets (usually all of them), use --first script 1 --last_script 7, or whichever first
# and last scripts are desired. Run "python wrapper.py --help" for details on how to run this script. Before
# running this script ensure that the databases are correctly located and named, and that input assembled
# transcripts are named in the format Op_me_Hsap_assembledTranscripts.fasta, where Op_me_Hsap can be replaced
# with any 10-digit sample identifier.
#Dependencies
import os, sys, re
import shutil
@ -5,6 +17,7 @@ import argparse
import CheckSetup
#Reading in the arguments
def get_args():
parser = argparse.ArgumentParser(
@ -32,10 +45,12 @@ def script_one(args, ten_digit_codes):
CheckSetup.run(args)
#Running script 1a on all files
for file in os.listdir(args.assembled_transcripts):
if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes:
os.system('python 1a_TranscriptLengthFilter.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT??
#Run script 1b if the XPC step is being run
if args.xplate_contam:
if not os.path.isfile(args.conspecific_names):
print('\nERROR: If you are running cross-plate contamination, a file designating species assignments is required for the --conspecific_names argument\n')
@ -46,6 +61,7 @@ def script_one(args, ten_digit_codes):
def script_two(args):
#Run scripts 2a and 2b on all files.
for folder in os.listdir(args.output + '/Output/'):
if os.path.isfile(args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta'):
os.system('python 2a_Identify_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases)
@ -55,7 +71,7 @@ def script_two(args):
#NEED TO SORT OUT FILE NAMES ETC. BELOW HERE
#running the third script
#running the third script on all files
def script_three(args):
for folder in os.listdir(args.output + '/Output'):
@ -79,8 +95,10 @@ def script_four(args):
if line_sep[0] == 'Summary':
gcode_info.append([folder, line_sep[6], line_sep[7], line_sep[8][:-1]])
#Available genetic codes
valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
#Reading the input genetic codes file if given (should be tab-separated)
stop = False
gcode_file = { }
if args.genetic_code.endswith('.txt') or args.genetic_code.endswith('.tsv'):
@ -98,6 +116,8 @@ def script_four(args):
print('\nGenetic code ERROR -- it looks like you tried to enter a .txt/.tsv file, but it could not be found. Stopping after script 4; you may fill out the file gcode_output.tsv and continue with script 5.\n')
stop = True
#Writing the gcode_output.tsv file with in-frame stop codon frequencies. If you didn't input genetic codes originally,
#edit the last column in this file to contain your desired genetic codes for each sample.
with open(args.output + '/Output/gcode_output.tsv', 'w') as g:
g.writelines('10 Digit Code\tIn-frame TAG Density\tIn-frame TGA Density\tIn-frame TAA Density\tGenetic Code\n')
for row in gcode_info:
@ -121,6 +141,7 @@ def script_four(args):
exit()
#Running script 5 on all taxa
def script_five(args):
valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
@ -132,10 +153,11 @@ def script_five(args):
for line in lines:
if line[0] == folder and line[-1].lower() in valid_codes:
os.system('python 5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + line[-1])
elif line[-1].lower() not in valid_codes and line[-1] != 'Genetic Code':
#Taxa without valid genetic codes will be skipped.
elif line[-1].lower() not in valid_codes and 'Genetic Code' not in line:
print('\n' + line[-1] + ' is not a valid genetic code. Skipping taxon ' + folder + '.\n')
#Run script 6 on all files
def script_six(args):
prefixes = []
@ -145,6 +167,7 @@ def script_six(args):
unique_prefixes = list(dict.fromkeys(prefixes))
#Checking to make sure there is only one fasta file for the OG reference database, and recording its name.
hook_fasta = ''
for file in os.listdir(args.databases + '/db_OG'):
if file.split('.')[-1] in ('fasta', 'fas', 'fa', 'faa'):
@ -152,11 +175,12 @@ def script_six(args):
if hook_fasta == '':
print('\nNo .fasta file could be found containing Hook sequences. This should be supplied along with the .dmnd-formatted database file in the Databases/db_OG folder. Quitting before script 6.\n')
exit()
for prefix in unique_prefixes:
os.system('python 6_FilterPartials.py --file_prefix ' + args.output + '/Output/' + prefix + ' --hook_fasta ' + hook_fasta)
#Running scripts 7a and 7b on all taxa
def script_seven(args):
for file in os.listdir(args.output + '/Output/ToRename'):
@ -176,6 +200,7 @@ if __name__ == "__main__":
args = get_args()
#The following code checks to make sure combinations of input arguments are compatible
if (args.first_script == 1 or args.script == 1) and (args.assembled_transcripts == None or not os.path.isdir(args.assembled_transcripts)):
print('\nERROR: If starting at the first script, a valid path to a folder of assembled transcript files (which must end in .fasta, .fa, or .fna) should be input using the --assembled_transcripts argument')
quit()