Commit 097cd375 authored by marc's avatar marc

tools/pear.py: add small script for pear pre_process

parent db8d19cb
from os import listdir, path, makedirs
from os.path import isfile, join
import sys
import shutil
import gzip
import subprocess
import argparse
parser = argparse.ArgumentParser(description='Use pear read merger to make a new fastq file and keep unmerged reads')
parser.add_argument("file_R1", help="reverse read file")
parser.add_argument("file_R2", help="forward read file")
parser.add_argument("output_file", help="output file")
parser.add_argument("-r1", "--keep_r1", help="keep unmerged reverse reads", action="store_true")
parser.add_argument("-r2", "--keep_r2", help="keep unmerged forward reads", action="store_true")
args = parser.parse_args()
f_r1 = args.file_R1
f_r2 = args.file_R2
f_out = args.output_file
subprocess.call(["pear",
"-f", f_r1,
"-r", f_r2,
"-o", f_out,
"-n", "100",
"-m", "490",
"-j", "3"])
with gzip.open(f_out, 'w') as outFile:
with open(f_out+'.assembled.fastq', 'rb') as f1:
shutil.copyfileobj(f1, outFile)
if (args.keep_r1):
with open(f_out+'.unassembled.reverse.fastq', 'rb') as f2:
shutil.copyfileobj(f2, outFile)
if (args.keep_r2):
with open(f_out+'.unassembled.forward.fastq', 'rb') as f3:
shutil.copyfileobj(f3, outFile)
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