15a16
> 
71a73,138
> def move_to_failed(fast5):
>     checkfolder = os.path.join(os.path.dirname(fast5),"uploads/failed")
>     if not os.path.exists(checkfolder):
>         os.makedirs(checkfolder)
> 
>     target = os.path.join(os.path.dirname(fast5),"uploads/failed",os.path.basename(fast5))
>     print "Move %s to %s" % (fast5, target)
>     shutil.move(fast5, target)
> 
> def barcode_match(fast5, seq):
> #    return "unclassified"
>     querya = tempfile.NamedTemporaryFile(delete=False)
>     outfile = tempfile.NamedTemporaryFile(delete=False)
>     #print outfile.name
>     outfile.close()
> 
>     querya.write('>querya\n')
>     querya.write(seq)
>     querya.seek(0)
>     #print querya.read()
>     resultdict=dict()
>     for i in ["01","02","03","04","05","06","07","08","09","10","11","12"]:
>         pathtobarcodes=pkg_resources.resource_filename('nanonet', 'barcodes/nb'+i+'.fasta')
>         ospathtobarcodes=os.path.abspath(pathtobarcodes)
>         subprocess.call("matcher -bsequence "+ospathtobarcodes+" -asequence "+querya.name+" -outfile "+outfile.name,shell=True)
>         outfile=open(outfile.name, "r")
>         lines = outfile.readlines()
>         #Barcode
>         resultdict[lines[15].split(": ")[1].rstrip()]=dict()
>         #Length
>         resultdict[lines[15].split(": ")[1].rstrip()]["length"]=float(lines[20].split(": ")[1].rstrip())
>         #Identity
>         resultdict[lines[15].split(": ")[1].rstrip()]["identity"]=float(lines[21].split("(")[1].split("%)")[0].rstrip())
>         #Similarity
>         resultdict[lines[15].split(": ")[1].rstrip()]["similarity"]=float(lines[22].split("(")[1].split("%)")[0].rstrip())
>         #Score
>         resultdict[lines[15].split(": ")[1].rstrip()]["score"]=float(lines[24].split(": ")[1].rstrip())
>         pathtobarcodes=pkg_resources.resource_filename('nanonet', 'barcodes/nb'+i+'_rev.fasta')
>         ospathtobarcodes=os.path.abspath(pathtobarcodes)
>         subprocess.call("matcher -bsequence "+ospathtobarcodes+" -asequence "+querya.name+" -outfile "+outfile.name,shell=True)
>         outfile.seek(0)
>         lines = outfile.readlines()
>         #Barcode
>         resultdict[lines[15].split(": ")[1].rstrip()]=dict()
>         #Length
>         resultdict[lines[15].split(": ")[1].rstrip()]["length"]=float(lines[20].split(": ")[1].rstrip())
>         #Identity
>         resultdict[lines[15].split(": ")[1].rstrip()]["identity"]=float(lines[21].split("(")[1].split("%)")[0].rstrip())
>         #Similarity
>         resultdict[lines[15].split(": ")[1].rstrip()]["similarity"]=float(lines[22].split("(")[1].split("%)")[0].rstrip())
>         #Score
>         resultdict[lines[15].split(": ")[1].rstrip()]["score"]=float(lines[24].split(": ")[1].rstrip())
> 
>     results = sorted([(resultdict[x]["score"],x,resultdict[x]) for x in resultdict.keys()])[::-1]
>     result = results[0]
>     score,ide,details=result
>     print ide.split("_")[0],score,details
> 
>     if score >= 75:
>         next
>     else:
>         ide = "unclassified"
> 
>     querya.close()
>     outfile.close()
>     return ide
80a148,149
>     print "Processing: %s" % ( fast5, )
> 
85d153
< 
94a163
>         move_to_failed(fast5)
95a165
> 
132a203,205
>     #barcode matching
>     ide = barcode_match(fast5, seq)
> 
147a221,222
> 
> 
156c231,237
<         with Fast5(fast5, 'a') as fh:
---
>         tmpfast5 = tempfile.NamedTemporaryFile(delete=False)
> 
>         tmpfast5.close()
> 
>         shutil.copyfile(fast5, tmpfast5.name)
> 
>         with Fast5(tmpfast5.name, 'a') as fh:
160a242
>            fh._add_attrs({"barcode_arrangement":ide.split("_")[0]},"minoTour_meta/barcodes")
167a250,264
>         checkfolder = os.path.join(os.path.dirname(fast5),"downloads")
>         target = os.path.join(os.path.dirname(fast5),"downloads",ide.split("_")[0],os.path.basename(fast5))
>         if not os.path.exists(checkfolder):
>            os.makedirs(checkfolder)
>         d = os.path.dirname(target)
>         if not os.path.exists(d):
>            os.makedirs(d)
> 
>         checkfolder = os.path.join(os.path.dirname(fast5),"uploads")
>         if not os.path.exists(checkfolder):
>            os.makedirs(checkfolder)
> 
>         shutil.move(tmpfast5.name, target)
>         shutil.move(fast5, checkfolder)
> 
176a274
> 
209a308
> 
210a310
>             #    print "result is none"
212a313,315
> 
>             print "Got the name", name
>