Mercurial > repos > bornea > filter_fasta
comparison filter_fasta.py @ 9:6794a638a504 draft
Uploaded
author | bornea |
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date | Sat, 06 Aug 2016 17:15:14 -0400 |
parents | afcea0f23a55 |
children | c9e6e2e7697c |
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8:afcea0f23a55 | 9:6794a638a504 |
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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 x = open("output.fasta","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 | 89 |
90 FilterFastaSeq(fasta,getAccessions(data)) | 90 FilterFastaSeq(fasta,getAccessions(data)) |
91 os.rename("output.fasta", sys.argv[3]) | 91 os.rename("output.txt", sys.argv[3]) |