Mercurial > repos > bornea > filter_fasta

comparison filter_fasta.py @ 7:e01b49c112b0 draft

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Uploaded
author bornea
date Sat, 06 Aug 2016 17:10:23 -0400
parents 5990c4dbfbaa
children afcea0f23a55
comparison
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6:5990c4dbfbaa 7:e01b49c112b0
77 if temp != []: 77 if temp != []:
78 merged = "\n".join(temp) 78 merged = "\n".join(temp)
79 if merged!="": 79 if merged!="":
80 seq.append(merged) 80 seq.append(merged)
81 cnt=0 81 cnt=0
82 with open("output.fasta","w") as x: 82 x = open("output.fasta","w"):
83 for i in header: 83 for i in header:
84 x.write(i+'\n'+seq[cnt]+'\n') 84 x.write(i+'\n'+seq[cnt]+'\n')
85 cnt+=1 85 cnt+=1
86 x.close()
86 fasta = sys.argv[1] # fasta file to filter 87 fasta = sys.argv[1] # fasta file to filter
87 data = sys.argv[2] # scaffold report #2 -- filename 88 data = sys.argv[2] # scaffold report #2 -- filename
88 89
89 FilterFastaSeq(fasta,getAccessions(data)) 90 FilterFastaSeq(fasta,getAccessions(data))
90 os.rename("output.fasta", sys.argv[3]) 91 os.rename("output.fasta", sys.argv[3])