Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-10-13

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All times shown according to UTC.

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09:40 push[RAX] in bioperl, if I have a Seq object with a protein sequence, is there a way to extract the nucleotide sequence that codes that protein?
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10:57 kai push[RAX]: which of them?
11:21 push[RAX] kai: well the subsequence from the official nucleotide reference for that specific genome in genbank would be good
11:21 push[RAX] but I can't see to map NP_xxxxx to NC_xxxxxx entries automatically
11:21 push[RAX] s/see/seem/
11:21 kai ah
11:22 kai I'm not sure there is a mapping like that
11:23 push[RAX] well when using the web interface for the protein db to get the NP_xxxxxx entry, there is a reference field with the NC reference
11:24 push[RAX] http://www.ncbi.nlm.nih.gov/protein/115494666
11:24 push[RAX] see REFSEQ field
11:30 push[RAX] ah, nvm it's in the Bio::DB namespace
11:30 push[RAX] Bio::DB::RefSeq
12:22 kai ah
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13:44 dbolser oh hai
13:44 kai dbolser: ^^^
13:44 kai multi-channel conversations ftw
13:45 dbolser ;-)
13:45 dbolser push[RAX]: what protein db?
13:45 dbolser swissprot?
13:50 push[RAX] dbolser: genbank
13:52 dbolser the mapping should be in refseq
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15:42 CIA-95 bioperl-live: Jonathan "Duke" Leto master * red246bc / (4 files in 4 dirs): Merge branch 'topic/leto_interpro_relationship' - http://bit.ly/92zlER
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15:49 dukeleto hola
16:12 dbolser buenas dias
17:30 deafferret gracias
17:43 arcsine como esta?
17:50 deafferret una mas serveca por favor
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18:01 pyrimidine Baxter!  You know I don't speak Spanish!
18:14 deafferret these are known unknowns, which are trivial compared to the unknown unknowns
18:19 deafferret err... I guess the ratio is unknown
18:19 deafferret a known unknown
19:10 pyrimidine dukeleto: thanks for merging that one in; was planning on checking up on branch status to gear up for the final 1.6 release, when I have tuits
19:11 pyrimidine by 'that one', meaning the topic branch. of course :)
19:14 CIA-95 bioperl-live: Chris Fields master * rbe285e2 / Bio/Tools/EUtilities/EUtilParameters.pm : catch using simple string instead of array ref for id param, so one doesn't have to do []; this broke recently when adding code allowing the use of POST for large requests - http://bit.ly/bSJNPB
19:24 pyrimidine um, wow.  I just tried grabbing 9000 accs via eutils using Bio::DB::EUtilities now with one run, and it worked
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