Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-10-05

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All times shown according to UTC.

Time Nick Message
04:05 Biome joined #bioperl
04:05 Biome biome: Chris Fields master SHA1-860bb82
04:05 Biome remove Build cruft
04:05 Biome http://bit.ly/I2WaB
04:05 Biome left #bioperl
04:06 Biome joined #bioperl
04:06 Biome biome: Chris Fields master SHA1-97175f8
04:06 Biome remove mor Build cruft
04:06 Biome http://bit.ly/2MH8lL
04:06 Biome left #bioperl
08:33 timp_ joined #bioperl
12:02 faceface rbuels: working with the potato assembly at all?
12:49 kyanardag_ joined #bioperl
13:02 flu joined #bioperl
15:23 perl_splut joined #bioperl
16:27 rbuels faceface: no i'm not doing anything on that.  is it available for download?
16:32 * deafferret checks the Chinese torrent sites
16:54 MrAristo joined #bioperl
16:56 MrAristo Curious.
16:57 MrAristo left #bioperl
16:57 * deafferret agrees
17:01 rbuels yes, that was curious.
18:59 ptl_ joined #bioperl
21:37 * deafferret agrees
22:12 deafferret surely emboss has a 'netfetch'...
22:13 deafferret seqret, seqretall ...
22:42 deafferret hmm... Can't find 'build_params' in _build at /usr/local/share/perl/5.8.8/Module/Build/Base.pm line 1011.
22:43 deafferret BEGIN failed--compilation aborted at t/RemoteDB/EUtilities.t line 51.
22:44 deafferret how do I get that error from running this?  perl -c t/RemoteDB/EUtilities.t
22:44 * deafferret scratches rbuels' chin
22:44 rbuels erm...
22:45 rbuels that's strange, but you probably just need to run 'perl Build.PL' in that distro
22:45 deafferret but I don't wanna
22:45 deafferret I just want to run this h'year .t file
22:45 rbuels the power of pyrimidine compells you!
22:45 deafferret damn
22:46 rbuels they probably need to put a check for it in their t files
22:47 * deafferret completely fails to understand
22:48 rbuels just run the build.pl.  it doesn't install it, just configures it
22:49 deafferret http://gist.github.com/202575
22:49 deafferret k. /me will comply
22:49 deafferret blindly
22:50 rbuels oh, this is bioperl!  i thought this was emboss or something
22:50 rbuels hmmm
22:50 * rbuels looks
22:50 deafferret w t f
22:50 deafferret now it runs
22:50 deafferret i'm so confused
22:52 deafferret oh..... Bio::Root::Test is going loco with my cake
23:17 deafferret eww... eutils.ncbi.nlm.nih.gov kicks out \n\n at the end...
23:18 rbuels so?
23:18 deafferret so eutils run >> file  twice leaves a gap in the .fasta
23:19 * deafferret boos
23:19 rbuels oh.
23:20 deafferret I wonder if a hip SYNOPSIS for Bio::DB::EUtilities would simply print the HTTP::Response as a scalar, or if it would always Bio::Seq it...
23:20 deafferret I do so want to contribute another patch to BioPerl
23:20 rbuels oh, i say.
23:31 deafferret my brain cannot grok the intent and usage of most of Bio::DB::EUtilities.
23:32 deafferret there seems to be a dirth of usage docs
23:32 rbuels use Bio::DB::Genbank
23:33 deafferret oh. that SYNOPSIS takes all the challenge out of things
23:33 deafferret I almost feel like I don't have to write it myself
23:34 rbuels if gist wasn't hammered, i would have had a module that uses it pasted by now
23:34 rbuels stupid rails.
23:34 rbuels http://gist.github.com/202596
23:34 rbuels they're gonna lose my biznaz if they don't get their act together
23:35 deafferret how will they replace the rbuels subscription revenue stream?  :)
23:35 deafferret :(
23:35 rbuels that's a good question
23:37 deafferret ooo, groovy (not the Java thing): bp_fetch.pl net::genbank:NM_001014797
23:54 deafferret huh. Bio::DB::Genbank uses eutils under the hood
23:55 rbuels yes.
23:55 rbuels don't look at the code, your hair will turn white.
23:55 rbuels mine did.
23:55 rbuels and then it fell out.
23:55 deafferret too late. so far my mirror specs are holding on
23:58 deafferret i want genbank format, dammit.
23:58 rbuels Bio::SeqIO::genbank
23:58 rbuels or you just want to fetch genbank records and save them to disk?
23:58 deafferret huh? I want to fetch Genbank from the intertubes
23:58 deafferret ya, I guess
23:58 rbuels don't use bioperl for that.
23:58 rbuels hah.  crazy guy.
23:58 rbuels just use some stupid loop with bare eutils
23:58 deafferret this ticket says I'm supposed to.  :)
23:59 deafferret ya, if I could find the bare eutils that did Genbank format
23:59 rbuels for accession in blah blah {  system wget blah blah blah > foo.gb; done
23:59 * rbuels has it
23:59 rbuels hold on
23:59 rbuels use constant FETCHFORM => 'http://eutils.ncbi.nlm.nih.gov/entrez/eu​tils/efetch.fcgi?retmode=text&rettyp​e=gbwithparts&db=nucleotide&id=%s&usehistory=n&email=sgn-feedback@sgn.cornell.edu&tool=sgn_bac_pipeline';

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