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PEM-Q.py
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PEM-Q.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#Author: Mengzhu
#Date:2019.9.1
#Last Update:2021.6.25
"""PEM-Q
This is a pipeline to analyze PEM-seq data or data similar, help you analyze repair outcome of your DNA library.
Copyright (C) 2019 Mengzhu Liu
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Author: Mengzhu LIU
Contact: liumz@pku.edu.cn/liu.mengzhu128@gmail.com
Usage:
PEM-Q.py <genome> <sample> <cutsite> <primer_chr> <primer_start> <primer_end> <primer_strand> <primer>
Options:
-h --help Show this screen.
-v --version Show version.
<genome> reference genome(hg19/hg38/mm9/mm10).
<sample> sample name of input file(Note: your input file must look like <sample>_R1/2.fq.gz).
<cutsite> position of cutsite(3' break end of positive strand).
<primer_chr> chromosome of red primer(eg:chr1).
<primer_start> start of red primer.
<primer_end> end of red primer.
<primer_strand> strand of red primer(+/-).
<primer> sequence of red primer.
In this program is for PEM-seq data analysis. Pair end target sequencing data is also compatible with this program.
Input file: fastq file
Output directory: results
Last Update:2021.1.12
"""
import os
import sys
import threading
from time import time
from docopt import docopt
def run_script(sample=None, cutsite=None, genome=None, primer=None, primer_chr=None, primer_start=None, primer_end=None, primer_strand=None):
start_time = time()
# basename = "LY015B_100"
# cutsite = "36573328"
# genome = "hg38"
# primer = "AGGATCTCACCCGGAACAGC"
basename = sample
os.system("mkdir log")
print("######## 01 Reads alignment... ########")
cmd = "align_make_v5.1.py {} {}_R1.fq.gz {}_R2.fq.gz -a CCACGCGTGCTCTACA -p {} -r {} -s {} -e {} -d {}".format(genome,basename,basename,primer,primer_chr,primer_start,primer_end,primer_strand)
print(cmd)
os.system(cmd)
print("######## 02 Barcode Extract... ########")
cmd = "rmb_dedup_v4.py {} 17 CCACGCGTGCTCTACA".format(basename)
print(cmd)
os.system(cmd)
print("######## 03 Define transloc... ########")
cmd = "define_transloc_v5.1_mpf.py {} {}".format(basename, cutsite)
print(cmd)
os.system(cmd)
print("######## 04 Define indels... ########")
cmd = "define_indel_v5.1_mpf.py {} {} {}".format(basename, cutsite, primer_strand)
print(cmd)
os.system(cmd)
print("######## 05 DEDUP... ########")
cmd = "dedup_v5.1_mpf.py {}".format(basename)
print(cmd)
os.system(cmd)
print("######## 06 substitutions... ########")
cmd = "define_substitution.py {} {} {} {}".format(basename,cutsite,10,primer_strand)
print(cmd)
os.system(cmd)
print("######## 07 filter and Statistics... ########")
cmd = "define_statistics_add_filter.py {} {} {} {} {} {} {} CCACGCGTGCTCTACA".format(basename,genome,cutsite,500000,primer,primer_chr,primer_strand)
print(cmd)
os.system(cmd)
# print("######## revise microhomology... ########")
# cmd = "revise_microhomolog.py {} {} {}".format(basename,cutsite,primer_strand)
# print(cmd)
# os.system(cmd)
# print("######## 08 processing translocation filter... ########")
# cmd = "DSB_filter_update.py {} {} {} {} {} {}".format(basename,primer_chr,cutsite,primer_strand,"3fe","_Translocations")
# print(cmd)
# os.system(cmd)
# print("######## 09 multiple mapping filter... ########")
# cmd = "multiple_mapping_filter.py {} ".format(basename)
# print(cmd)
# os.system(cmd)
print("All done, please check log files!")
print("PEM-Q Done in {}s".format(round(time()-start_time, 3)))
def main():
args = docopt(__doc__,version='PEM-Q v5.1s')
kwargs = {'sample':args['<sample>'], 'cutsite':args['<cutsite>'],'genome':args['<genome>'],\
'primer':args['<primer>'],'primer_chr':args['<primer_chr>'],'primer_start':args['<primer_start>'],\
'primer_end':args['<primer_end>'],'primer_strand':args['<primer_strand>']}
print('[PEM-Q] genome: ' + str(kwargs['genome']))
print('[PEM-Q] sample: ' + str(kwargs['sample']))
print('[PEM-Q] cutsite: ' + str(kwargs['cutsite']))
print('[PEM-Q] primer: ' + str(kwargs['primer']))
print('[PEM-Q] primer_chr: ' + str(kwargs['primer_chr']))
print('[PEM-Q] primer_start: ' + str(kwargs['primer_start']))
print('[PEM-Q] primer_end: ' + str(kwargs['primer_end']))
print('[PEM-Q] primer_strand: ' + str(kwargs['primer_strand']))
try:
run_script(**kwargs)
except KeyboardInterrupt:
sys.stderr.write("See you~ :)\n")
sys.exit(0)
if __name__ == "__main__":
main()