Hi all,
I've written a simple GFF3 parser, and a GMAP -> ivals parser, as part
of the lamprey genome analysis we're doing; they're here,
http://github.com/ctb/lamprey-est-map/tree/master
files 'gff_parser.py' and 'gmap_pygr.py'.
Some example code:
---
genome = '/scratch/titus/lamprey/supercontigs.fa'
ests = '/scratch/titus/lamprey/Pma200805_collapsed_ESTs.fasta'
genome_db = seqdb.SequenceFileDB(genome)
ests_db = seqdb.SequenceFileDB(ests)
fp = open(sys.argv[1])
ivals = gmap_pygr.build_ivals(fp, genome_db, ests_db)
first100 = list(izip(range(100), ivals))
pprint.pprint(first100)
---
produces:
[(0, ('Pma200805_5.path1', [(-Contig100273[794:831], Pma200805_5[24:61])])),
(1, ('Pma200805_5.path2', [(-Contig100971[763:800], Pma200805_5[24:61])])),
(2, ('Pma200805_5.path3', [(Contig102055[281:318], Pma200805_5[24:61])])),
(3, ('Pma200805_5.path4', [(Contig121568[307:344], Pma200805_5[24:61])])),
(4, ('Pma200805_5.path5', [(-Contig175959[291:328], Pma200805_5[24:61])])),
(5,
('Pma200805_1.path1',
[(Contig100273[253:277], Pma200805_1[7:31]),
(Contig100273[277:307], Pma200805_1[32:62]),
(Contig100273[307:325], Pma200805_1[63:81])])),
(6,
('Pma200805_1.path2',
[(-Contig111318[96:120], Pma200805_1[7:31]),
(-Contig111318[66:96], Pma200805_1[32:62]),
(-Contig111318[48:66], Pma200805_1[63:81])])),
(7,
('Pma200805_1.path3',
[(Contig150286[581:605], Pma200805_1[7:31]),
(Contig150286[605:635], Pma200805_1[32:62]),
(Contig150286[635:653], Pma200805_1[63:81])])),
...
Not being much of an expert on GFF3, I tried to provide the minimal
necessary set of code to be useful, and then put anything that seemed
GMAP specific into gmap_pygr.
Questions & comments welcome! Watch the github space for updates and
bugfixes.
cheers,
--titus
--
C. Titus Brown, [email protected]
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