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Genbank format parsing via pyparser — Read more

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Fixed a bug in the DBLINK parsing. 
davisp (author)
Fri Jul 31 12:45:48 -0700 2009
commit  ed423e1e71d080a35626f716afb4eb054145cae8
tree    2d39a7e5a97e6f3ea1c82b9fe7732adeb034b30d
parent  fe0ad889794966c20912ea86be7050c3fba7071c
nebgb /
name age
history
message
file .gitignore Fri Jul 03 22:51:36 -0700 2009 Updated README to show seqiter is an iterator. [Paul J. Davis]
file LICENSE Fri Jul 03 22:33:37 -0700 2009 Adding release files. Registering on PyPI [Paul J. Davis]
file MANIFEST.in Mon Jul 27 10:46:28 -0700 2009 Bumped version and released. [davisp]
file README.md Loading commit data...
file ez_setup.py Fri Jul 03 22:33:37 -0700 2009 Adding release files. Registering on PyPI [Paul J. Davis]
file nebgb.py Fri Jul 31 12:45:48 -0700 2009 Fixed a bug in the DBLINK parsing. [davisp]
file setup.py Fri Jul 31 12:45:48 -0700 2009 Fixed a bug in the DBLINK parsing. [davisp]
directory test/ Mon Jul 27 10:44:14 -0700 2009 Conditional position on references. [davisp]
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.

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