Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-04-20

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All times shown according to UTC.

Time Nick Message
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15:18 elTigre hey, does somebody here know how to extract exon information from ncbi gene?
15:18 deafferret not I, sorry
15:19 deafferret if you have a genbank fine then Bio::SeqIO can extract whatever features you're interested in
15:19 deafferret I don't know if an "ncbi gene" is something else
15:19 elTigre that's an idea.... thank you
15:19 elTigre ncbi gene, the database
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17:04 pyrimidine elTigre: you can try out Bio::DB::EntrezGene to remotely retrieve the sequence annotation, but I believe the data returned is just the annotation (no actual sequence)
17:05 pyrimidine also, this might help:
17:05 pyrimidine http://www.bioperl.org/wiki/HO​WTO:Getting_Genomic_Sequences
17:05 pyrimidine I actually use the Ensembl API myself, YMMV
17:06 elTigre I'd happily use Ensembl
17:07 elTigre but it just contains about 2/3 of the exons known to NCBI
17:07 pyrimidine I would go with that, exon data is much easier to retrieve
17:07 pyrimidine oh
17:08 elTigre at least I had a few genes where a lot of exons are simply missing
17:08 pyrimidine might be worth doing a comparison at the very least...
17:09 elTigre it might also be a problem with the horse assembly
17:09 pyrimidine BTW, latest ensembl does work with the latest bioperl (1.6.0 and svn), at least with what I'm using
17:09 pyrimidine yes, that could very well be it
17:09 pyrimidine (possible differences in gene prediction)
17:09 pyrimidine (assembly differences)
17:10 pyrimidine etc etc
17:10 elTigre no, assembly should be the same
17:10 pyrimidine when was the last one?
17:10 elTigre gene prediction maybe
17:10 elTigre September 2007
17:10 elTigre equcab2
17:11 pyrimidine ah
17:11 pyrimidine which gene models are newer, Ensembl or EntrezGene?
17:12 elTigre I don't know exactly
17:12 elTigre the date above refers to the assembly version
17:13 * pyrimidine wonders who's curating the horse assembly at ensembl...
17:14 pyrimidine I'm a bit spoiled; I worked with mouse, though I may start working with zebrafinch soonish...
17:15 pyrimidine just checked entrezgene, date = sept 26, 2008 for most recent transcripts
17:16 pyrimidine some from dec. 2008 as well...
17:17 elTigre Well, all that doesn't help me... I need to know all exons
17:17 elTigre thanks anyway
17:18 pyrimidine well, if you retrieve the gene using Bio::DB::EntrezGene, it 'should' contain the exon information as sequence features
17:18 pyrimidine (I say 'should' b/c I haven't tried it)
17:20 elTigre hm
17:20 elTigre now I just have to learn perl....
17:21 pyrimidine heh
17:25 pyrimidine I'm actually testing Bio::DB::EntrezGene out and am not seeing exon information; my guess is this is retrieved from the transcript associated with the gene ID
17:29 pyrimidine so exon retrieval appears borken
17:29 * pyrimidine filing a bug report...
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18:18 balin_ Hi all. Can bioperl read distance matrices made by clustalw?
18:38 pyrimidine Maybe.  You can try Bio::Matrix::IO
18:38 pyrimidine It has a 'scoring' format:
18:38 pyrimidine Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies
18:38 pyrimidine that seems to fit
19:09 balin_ ok, I'll try it. Thanks!
19:27 balin_ it looks like the formats are different - I get parsing errors
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19:43 pyrimidine _balin: what does the format look like (nopaste it, http://sial.org/pbot/)
19:45 pyrimidine (and copy the resulting link here so I can see it if I need to backlog; I have a meeting in 15 min)
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