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ublast.py
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ublast.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]
maxhits=sys.argv[5]
pid=sys.argv[6]
threads=sys.argv[7]
print filelist
for i in filelist:
print i
outputfile=outfolder+"/"+i.split("/")[-1].split(".")[0]+outsuffix+".ublast"
outnomatch=outfolder+"/"+i.split("/")[-1].split(".")[0]+outsuffix+".nohit.fasta"
p1= sp.Popen("/stornext/HPCScratch/home/allnutt.t/bin/usearch10 -ublast %s -db %s -strand both -maxhits %s -userout %s -userfields query+target+id+ql+qlo+qhi+tl+tlo+thi+alnlen+evalue+bits -id %s -notmatched %s -threads %s -termidd 0.1 -accel 0.1 -evalue 1e-9" %(i,db,maxhits,outputfile,pid,outnomatch,threads), shell=True).wait()