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trimmo.py
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trimmo.py
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#!/usr/bin/python
#trimmomatic python wrapper for folders
import sys
import re
import glob
import subprocess
import os
digits = re.compile(r'(\d+)')
def tokenize(filename):
return tuple(int(token) if match else token
for token, match in
((fragment, digits.search(fragment))
for fragment in digits.split(filename)))
folder = sys.argv[1]
filelist=glob.glob(folder)
filelist.sort(key=tokenize)
print filelist
threads=sys.argv[2]
adaptors=sys.argv[3]
num=sys.argv[4] #s=single unpaired file, p = paired two files
multi=sys.argv[5]
devnull = open(os.devnull, 'wb')
if num=="s":
print "Trimmomatic single end mode"
p0=subprocess.Popen("mkdir -p clip", shell=True).wait
for i in filelist:
print i
name = i.split("/")[-1]
if multi=="y":
p1= subprocess.Popen("java -jar ~/bin/Trimmomatic-0.36/trimmomatic-0.36.jar SE -threads %s %s clip/%s ILLUMINACLIP:%s:2:30:10 SLIDINGWINDOW:5:25 MINLEN:100" %(threads,i,name,adaptors), shell=True,stderr=devnull)
if multi=="n":
p1= subprocess.check_output("java -jar ~/bin/Trimmomatic-0.36/trimmomatic-0.36.jar SE -threads %s %s clip/%s ILLUMINACLIP:%s:2:30:10 SLIDINGWINDOW:5:25 MINLEN:100" %(threads,i,name,adaptors), shell=True,stderr=devnull)
if num=="p":
print "Trimmomatic paired end mode"
p0=subprocess.Popen("mkdir -p clip && mkdir -p unpaired", shell=True).wait
for i in xrange(0,len(filelist)-1,2):
print filelist[i],filelist[i+1]
name1 = filelist[i]
name2 = filelist[i+1]
outname1 = filelist[i].split("/")[-1]
outname2 = filelist[i+1].split("/")[-1]
if multi=="y":
p1= subprocess.Popen("java -jar ~/bin/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads %s %s %s clip/%s unpaired/%s clip/%s unpaired/%s ILLUMINACLIP:%s:2:30:10 SLIDINGWINDOW:5:25 MINLEN:100" %(threads,name1,name2,outname1,outname1,outname2,outname2,adaptors), shell=True,stderr=devnull)
if multi=="n":
p1= subprocess.check_output("java -jar ~/bin/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads %s %s %s clip/%s unpaired/%s clip/%s unpaired/%s ILLUMINACLIP:%s:2:30:10 SLIDINGWINDOW:5:25 MINLEN:100" %(threads,name1,name2,outname1,outname1,outname2,outname2,adaptors), shell=True,stderr=devnull)
print "done"