Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-15

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All times shown according to UTC.

Time Nick Message
02:28 CIA-119 bioperl6: takadonet master * raba620b / (6 files in 5 dirs):
02:28 CIA-119 bioperl6: Action and Grammar now only parse one fasta record at a time instead of
02:28 CIA-119 bioperl6: multiple. Allows for 'lazy' grammars. Cleaned up FastaIO and SeqIO abit to
02:28 CIA-119 bioperl6: reflect the new changes with using Role::IO.pm role however still needs a
02:28 CIA-119 bioperl6: redesign - http://bit.ly/dVE2zk
03:29 CIA-119 bioperl-db: Chris Fields master * r3205877 / MANIFEST.SKIP : add MANIFEST.SKIP - http://bit.ly/fJNuwA
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03:58 genehack pyrimidine++ ## yay release \o/
03:58 genehack so, i was teaching a bioperl course tonight
03:59 genehack and we were going over bio::tools::run::remoteblast
03:59 genehack and some of the students, when running a blast, got result objects that yielded hit objects, that didn't contain any HSP objects.
03:59 genehack what up with that?
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09:35 dbolser grep Bio::SeqFeature::Store -r t/ # no hits
09:35 dbolser how do I get hold of the 'test' database settings passed at build time?
09:36 dbolser rbuels, pyrimidine: I want you to start sleeping in shifts, k?
09:37 dbolser pyrimidine: please install SMW on the bp wiki
09:37 dbolser I'll then implement test coverage statistics, and we can use game mechanics to get more tests
09:38 * dbolser notices his grep is broken
09:39 dbolser t/LocalDB/SeqFeature_mysql.t
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11:06 dbolser away until Monday
12:56 pyrimidine genehack: if there are hits reported in the BLAST hit table but not reported with alignments, they will have minimal hit object created that contain the hit table stats, but no HSP info (b/c there is none in the report)
12:56 pyrimidine so, maybe that's it?
12:56 pyrimidine dbolser: huh?
13:05 * pyrimidine is really thinking about changing all the script names to bp_* in core
13:07 pyrimidine they're installed that way anyway, doesn't make sense to convert them over at the build step (and the docs on search.cpan.org list the *original* name, not the bp_* version)
13:26 genehack pyrimidine: maybe -- didn't have time to dig into it last night. student claimed that BLASTing same accession number via NCBI web site didn't have those hits at all.
13:27 genehack i've got the accession number he was using. hopefully i'll find a tuit or two to rub on it.
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13:41 pyrimidine genehack: could be a bug in the parser; if the hit table is parsed and the HSPs aren't (for instance), the final step in the process is to generate the minimal hits.
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14:26 genehack k. if i get it to that point, i'll file a real bug report.
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18:53 CIA-119 bioperl-db: Chris Fields master * re279cd3 / MANIFEST.SKIP : update skipped files - http://bit.ly/gEQcxO
19:29 CIA-119 bioperl-db: Chris Fields master * rfefd74e / Changes : updates since last release - http://bit.ly/eEUFbc
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