Mercurial > repos > bornea > filter_fasta

comparison filter_fasta.py @ 11:573c36ff075f draft

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Uploaded
author bornea
date Tue, 16 Aug 2016 20:40:19 -0400
parents c9e6e2e7697c
children 05d48b118f81
comparison
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10:c9e6e2e7697c 11:573c36ff075f
82 x = open("output.txt","w") 82 x = open("output.txt","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 x.close()
87 #fasta = sys.argv[1] # fasta file to filter 87 fasta = sys.argv[1] # fasta file to filter
88 #data = sys.argv[2] # scaffold report #2 -- filename 88 data = sys.argv[2] # scaffold report #2 -- filename
89 fasta = r"C:\Users\Owner\Desktop\APOSTL\SAINT_preprocessing\SwissProt_HUMAN_2014_08.fasta"
90 data = r"C:\Users\Owner\Desktop\APOSTL\Scaffold\scaffold_EGFR.txt"
91 89
92 FilterFastaSeq(fasta,getAccessions(data)) 90 FilterFastaSeq(fasta,getAccessions(data))
93 os.rename("output.txt", "output1.txt") 91 os.rename("output.txt", "output1.txt")