Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-03-30

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All times shown according to UTC.

Time Nick Message
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06:15 Drin dbolser: yea I read that email, but you'll still be around yea? xD
07:29 mmlevitt Drin: what does "xD" mean?
08:32 Drin mmlevitt: it's just a face
08:42 mmlevitt Drin: nice! I've been figuring out my cgi-bin interaction with perl interpreters, tonight.
09:11 Drin mmlevitt: nice!
09:11 Drin mmlevitt: I've been trying to understand WormBase, as that's what I think I want to work with (idea#11)
09:15 mmlevitt Drin: I found how to populate postgresql databases, so I wanted to resurrect BioSQL, but for some reason I can't connect to run scripts.
09:15 mmlevitt Drin: brb
09:17 CIA-119 bioperl-live: kortschak master * r8905527 / (Bio/Tools/GuessSeqFormat.pm t/data/example.vcf): Add VCF guesser. Example vcf format for testing - provided from http://www.1000genomes.org/wiki/analysis/vcf4.0 with modification according to definition (spaces -> \t). - http://bit.ly/hBnqKZ
09:18 CIA-119 bioperl-live: kortschak master * rb8cd8ed / t/Tools/GuessSeqFormat.t : GuessSeqFormat tests - build it and they will come. - http://bit.ly/fNUfDe
09:18 CIA-119 bioperl-live: DaveMessina master * r62e2371 / (Bio/Tools/GuessSeqFormat.pm t/data/example.vcf): Merge commit '8905527' - http://bit.ly/gMgH2p
09:18 CIA-119 bioperl-live: DaveMessina master * r69a904b / t/Tools/GuessSeqFormat.t : Merge commit 'b8cd8ed' - http://bit.ly/gkxfl6
09:23 Drin mmlevitt: that sounds cool. and i'm gonna go to my friends to work on homework, so I don't know when I'll be back
09:24 mmlevitt Drin: cool.  Just was checking AceDB, and it is really nice!  Great choice!
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13:04 pyrimidine is AceDB even developed anymore?  I thought it was the precursor to Bio::DB::GFF and Bio::DBB::SeqFeature
13:04 dbolser Drin: yup, I'll be here
13:05 pyrimidine dbolser: o/
13:05 dbolser pyrimidine: afaik AceDB is dead, but zombified in the form of a few databases
13:05 pyrimidine ick
13:06 pyrimidine dbolser: I ran into that weird 'Validation failed' issue you saw.  It's Module::Build-related
13:06 pyrimidine Our hack of a MB subclass is tripping it up, causing the problem
13:07 dbolser MB?
13:07 dbolser oh sorry
13:07 dbolser didn't read back one line
13:08 dbolser right, I thought it may be related to newer MB
13:08 pyrimidine I think it's from the latest version, but it's a long-standing hack/bug in our subclass that is causing the problem
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13:51 buznac hello
13:52 buznac i am trying to make a Bio::SearchIO object with -format => 'blastxml'
13:52 buznac it gives me an error that says it couldn't find blastxml as a format
13:53 pyrimidine buznac: do you have XML::SAX and the other prereqs installed for blastxml?
13:57 buznac aren't they installed automatically by cpan?
14:04 pyrimidine buznac: not unless you specify to do so in the installation step
14:05 buznac @pyrimidine: oh crap...so now I have to install them manually? also where can I find a list with all its dependencies?
14:05 pyrimidine buznac: I also highly suggest installing a good XML::SAX-compatible parser, like XML::SAX::ExpatXS or XML::LibXML if possible, for performance reasons
14:06 pyrimidine buznac: https://github.com/bioperl/biope​rl-live/blob/master/DEPENDENCIES
14:07 pyrimidine buznac: if you run 'perl Build.PL' it will also list those not installed
14:07 pyrimidine buznac: and ask you if you want them to be installed
14:09 buznac @pyrimidine: OK thanks i'll install them now
14:09 pyrimidine ok
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14:52 burvcna @pyrimidine: ok so I installed all dependencies, but now he doesn't find the method next_hit via package "Bio::SearchIO::blastxml
14:54 pyrimidine burvcna: make sure you are calling next_hit on the proper object
14:55 burvcna @pyrimidine: this is the code i'm using: http://pastebin.com/raw.php?i=qxnBndT9
14:55 burvcna oh and by the way is there a paste in this channel?
14:56 pyrimidine burvcna: no, we don't have a pastebot associated with #bioperl (though we have tried)
14:56 pyrimidine change this line:
14:57 pyrimidine while ( my $hit = $in->next_hit )
14:57 pyrimidine to
14:57 pyrimidine while ( my $hit = $result->next_hit )
14:57 pyrimidine and this line:
14:57 pyrimidine while ( my $hsp = $in->next_hsp )
14:57 pyrimidine to
14:57 pyrimidine while ( my $hsp = $hit->next_hsp )
15:02 pyrimidine burvcna: any luck?
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15:04 pyrimidine ah well
15:15 buznac @pyrimidine: thank you so much it works...I have been working at this parser for a week now and ran into all sorts of trubles
15:15 pyrimidine buznac: np
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15:56 buznac i know there is a way to blastn a database made from a multifasta, and to choose which sequence from the multifasta to blast. but I cannot find the option in blastn that does this
16:00 buznac oh yeah the version I have is blast+2.2.24
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16:20 buznac and how can I choose a sequence from a multifasta file that is used as query?
16:26 rbuels buznac: what does 'used as a query' mean
16:26 rbuels oh i think i see
16:27 buznac I mean as input to blastn put the hole multifasta file
16:27 * rbuels reads the blast man page for buznac
16:28 rbuels oh, blast+
16:28 rbuels nm, i don't have it
16:28 buznac yes blast+ 2.2.24
16:28 * rbuels doesn't know, throws up his hands
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21:54 dgk Hello! Is there somewhere a working example of blastpgp? No matter which documentation site I follow, I can't get blastpgp to show me output.
21:55 rbuels dgk: how is that related to bioperl?
21:56 * rbuels also doesn't know the answer
21:56 dgk I'm trying to write a code in Perl which executes a blastpgp, using bioperl modules.
21:57 rbuels dgk: with Bio::Tools::Run::StandAloneBlast?
21:57 dgk Yes.
21:59 rbuels dgk: hmmm, well there's a test of the blastpgp functions starting at https://github.com/bioperl/bioperl-live/blo​b/master/t/Tools/Run/StandAloneBlast.t#L163
22:00 rbuels dgk: not sure if that will help
22:00 rbuels it's not a very comprehensive test
22:00 dgk I'll take a look at that, thank you very much!
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22:15 rdesfo is it?
22:26 rbuels is what
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