Python code to work with Genbank files
This repo contains several classes to help work with Genbank files
The flow goes:
File > Read > Locus > Feature
To use:
from genbank.file import File
f = File('infile.gbk')
for name,locus in f.items():
print(name)
for feature in locus:
print(feature)You can also build a Locus object from the ground up:
from genbank.locus import Locus
locus = Locus('test', 'actgactgatcgtagctagc')
# then add a feature by parsing text of a genbank feature
locus.read_feature(' CDS 1..10')
# or add one by manually specifing the type,strand,and locations
locus.add_feature('CDS',+1,[['10','20']])
locus.write()which gives:
LOCUS test 20 bp DNA UNK
DEFINITION test
FEATURES Location/Qualifiers
CDS 1..10
CDS 10..20
ORIGIN
1 actgactgat cgtagctagc
//
This package also allows you to perform various conversions on a given genome file:
$ genbank.py tests/phiX174.gbk -f tabular
'phiX174' 'CDS' (('100', '627'),) {'gene': "G"}
'phiX174' 'CDS' (('636', '1622'),) {'gene': "H"}
'phiX174' 'CDS' (('1659', '3227'),) {'gene': "A"}
'phiX174' 'CDS' (('2780', '3142'),) {'gene': "B"}
'phiX174' 'CDS' (('3142', '3312'),) {'gene': "K"}
$ genbank.py tests/phiX174.gbk -f fasta
>phiX174
gtgtgaggttataacgccgaagcggtaaaaattttaatttttgccgctgagggg
ttgaccaagcgaagcgcggtaggttttctgcttaggagtttaatcatgtttcag
$ genbank.py tests/phiX174.gbk -f fna
>phiX174_CDS_[100..627] [gene="G"]
atgtttcagacttttatttctcgccataattcaaactttttttctgataag
>phiX174_CDS_[636..1622] [gene="H"]
atgtttggtgctattgctggcggtattgcttctgctcttgctggtggcgcc
>phiX174_CDS_[1659..3227]
$ genbank.py tests/phiX174.gbk -f faa
>phiX174_CDS_[100..627] [gene="G"]
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNA
>phiX174_CDS_[636..1622] [gene="H"]
MFGAIAGGIASALAGGAMSKLFGGGQKAASGGIQGDVLATDNNTVGMGDAG
>phiX174_CDS_[1659..3227] [gene="A"]