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centrifuge.py
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centrifuge.py
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#!/usr/bin/env python
import sys
import re
import glob
import subprocess as sp
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]
#folder = os.path.expanduser(folder)
filelist=glob.glob(folder)
filelist.sort(key=tokenize)
outfolder=sys.argv[2]
outsuffix=sys.argv[3]
db=sys.argv[4]
threads=sys.argv[5]
stype=sys.argv[6] #f for fasta q for fastq.. unaligned saved reads are fastq
print filelist
for i in filelist:
print i
outputfile=outfolder+"/"+i.split("/")[-1].split(".")[0]+outsuffix+".cent"
reportfile=outfolder+"/"+i.split("/")[-1].split(".")[0]+outsuffix+".report"
outnomatch=outfolder+"/"+i.split("/")[-1].split(".")[0]+outsuffix+".nohit.fasta"
p1= sp.Popen("/stornext/HPCScratch/home/allnutt.t/bin/centrifuge/centrifuge -x %s -U %s -S %s --report-file %s --un %s --min-hitlen 50 -k 1 -p %s -%s --verbose" %(db,i,outputfile,reportfile,outnomatch,threads,stype), shell=True).wait()