Hi all, I just wanted to share some of my recent coding adventures... the first is 'blastkit',
http://github.com/ctb/blastkit/tree/master
in which I've swiped pygr's parse_blast and adapted my old blastparser
code to run on top of it. blastkit was written so that I and others
could set up a simple CGI-based BLAST server that supported more
interesting post-BLAST parsing than the NCBI version. I'm not saying
it's anything stunningly new but early reports are that it is easy to
use and works reliably for building interesting BLAST sites.
--
The second is some code I've written for the lamprey genome project,
http://github.com/ctb/lamprey-est-map/tree/master
which includes the simple GFF3 parser I posted a few days ago, as well
as a gmap-to-nlmsa script, a trivial bowtie parser, and a
bowtie-to-nlmsa script.
--
The third is an update to pygr-draw,
http://github.com/ctb/pygr-draw/tree/master
which I've now updated to support extremely easy drawing/display of
features from full NLMSAs. Warning, the code is a gigantic mess and at
the moment only the PNG output works ;). Coming soon: PDF and JSON
output.
Here's a doctest for the pygr-draw stuff,
http://lyorn.idyll.org/~t/transfer/pygr-draw/doc/wrapper-example.html
showing how to draw stuff from an NLMSA,
>>> al += seq1
>>> al[seq1[50:500]] += seq2[100:550]
>>> al[seq1[2000:2100]] += seq2[400:500]
>>> al.build()
>>> wrapper = pygr_draw.annotation.SequenceWrapperFactory(color='red')
>>> pygr_draw.draw_annotation_maps(seq1, (al,), wrappers=(wrapper,), ...)
---
Where I'm going with all of this should now be obvious to anyone working
with next-gen sequence data, but just to belabor the point, here is a
script to graph RNAseq data against GMAP ESTs, both mapped onto the
lamprey genome:
http://github.com/ctb/lamprey-est-map/blob/46c84aec690fe8d9cbc8cec9644a80867a9f1164/draw.py
I've attached a sample PNG. Yes, the black line at the bottom is a
bug...
I'm particularly excited about this stage because I can now build NLMSAs
with annotations or alignments, work with the information through pygr's
normal object APIs, and then produce graphics of any particular view!
Nerdvana.
cheers,
--titus
--
C. Titus Brown, [email protected]
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