genbank 0.103

Code to work with Genbank files

genbank

Python code to work with Genbank files

This repo contains several classes to help work with Genbank files

The flow goes:

File -> Locus -> Feature

To use:

from genbank.file import File

file = File('infile.gbk')
for locus in file:
	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 manually by specifing the type,strand,location
locus.add_feature('CDS',+1,[['10','20']])
locus.write()

which gives:

LOCUS       test                      20 bp
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"]

$ genbank.py tests/phiX174.gbk -f coverage
phiX174	0.965

Print out the features of the given key:tag

$ genbank.py tests/phiX174.gbk -k CDS:gene > labels.tsv

Change the H of the second gene to something more informative: (ideally you will have columns from other sources, like excel)

perl -pi -e 's/H/Minor spike/' labels.tsv

Now edit all the features of the given key:tag with the updated labels:

$ genbank.py tests/phiX174.gbk -e CDS:gene < labels.tsv | head
LOCUS       phiX174                 5386 bp    DNA      PHG
FEATURES             Location/Qualifiers
     source          1..5386
     rep_origin      13..56
     CDS             100..627
                     /gene="G"
     CDS             636..1622
                     /gene="Minor spike"
     CDS             1659..3227