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miRNA_bbmap.py
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miRNA_bbmap.py
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#!/usr/bin/python
import sys
import re
import glob
import subprocess
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
ref=sys.argv[2]
outfolder=sys.argv[3]
bam=sys.argv[4] #bam file y/n
p3 = subprocess.Popen('mkdir -p %s' %(outfolder), shell=True)
p3 = subprocess.Popen('mkdir -p %s/unmapped' %(outfolder), shell=True)
p3 = subprocess.Popen('mkdir -p %s/mapped' %(outfolder), shell=True)
for i in filelist:
print i
name = i.split("/")[-1].split(".")[0]
if bam=="y":
p1= subprocess.Popen("bbmap.sh ref=%s ambig=all vslow perfectmode maxsites=10000 nzo=t mappedonly=t outu=%s/unmapped/%s.unmapped.fasta scafstats=%s/mapped/%s.map in=%s out=%s/mapped/%s.sam noheader=t " %(ref,outfolder,name,outfolder,name,i,outfolder,name), shell=True).wait() #&& samtools view -bSh1 %s/mapped/%s.sam | samtools sort -m 80G -@ 3 -o %s/mapped/%s_sorted.bam && samtools index %s/mapped/%s_sorted.bam && rm %s/mapped/%s.sam
else:
p1= subprocess.Popen("bbmap.sh ref=%s ambig=all vslow perfectmode maxsites=10000 nzo=t mappedonly=t outu=%s/unmapped/%s.unmapped.fasta scafstats=%s/mapped/%s.map in=%s" %(ref,outfolder,name,outfolder,name,i), shell=True).wait()