davisp / nebgb
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Branch:
master
nebgb /
| name | age | message | |
|---|---|---|---|
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.gitignore | Fri Jul 03 22:51:36 -0700 2009 | |
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LICENSE | Fri Jul 03 22:33:37 -0700 2009 | |
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MANIFEST.in | Mon Jul 27 10:46:28 -0700 2009 | |
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README.md | ||
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ez_setup.py | Fri Jul 03 22:33:37 -0700 2009 | |
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nebgb.py | Fri Jul 31 12:45:48 -0700 2009 | |
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setup.py | Fri Jul 31 12:45:48 -0700 2009 | |
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test/ | Mon Jul 27 10:44:14 -0700 2009 |
README.md
nebgb - Genbank File Parser
Usage:
>>> import nebgb
>>> rec = nebgb.parse_file("./test/data/simple-1.gb").next()
>>> rec.locus["name"]
'NP_034640'
>>> rec.locus["length"]
182
>>> rec.keywords["source"]["name"]
'house mouse'
>>> rec.features[1]["properties"]["product"]
'interferon beta, fibroblast'
>>> for seq in rec.seqiter:
... print seq
mnnrwilhaafllcfsttalsinykqlqlqertnirkcqelleqlngkinltyradfkip
memtekmqksytafaiqemlqnvflvfrnnfsstgwnetivvrlldelhqqtvflktvle
ekqeerltwemsstalhlksyywrvqrylklmkynsyawmvvraeifrnfliirrltrnf
qn
Alternatively you can use nebgb.parse() to parse a string or iterator that yields lines of a Genbank file.

