Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-03-05

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All times shown according to UTC.

Time Nick Message
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03:12 driveby_bot /home/svn-repositories/bioperl: r16906 (maj) : alias -program_dir to -prog_dir (thanks Ben)
03:12 driveby_bot Diff: http://tinyurl.com/ydklzos
03:31 driveby_bot joined #bioperl
03:31 driveby_bot /home/svn-repositories/bioperl: r16907 (maj) : duh, thanks Ben
03:31 driveby_bot Diff: http://tinyurl.com/y8q822e
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11:19 driveby_bot /home/svn-repositories/bioperl: r16908 (dave_messina) : Fix for bug #3022. Thanks to Emmanuel Quevillon!
11:19 driveby_bot Diff: http://tinyurl.com/yd9ksrr
12:51 _ilbot2 joined #bioperl
12:51 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient.  Paste to http://codepad.org/
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14:23 korb hi
14:23 korb anyone else having problems with the remote blast function?
14:23 korb worked well some days ago
14:23 korb but not anymore
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15:44 driveby_bot /home/svn-repositories/bioperl: r16909 (cjfields) : next, not redo
15:44 driveby_bot Diff: http://tinyurl.com/yenrrhg
15:48 rbuels joined #bioperl
17:21 deafferret ahh! it's the turkeyberry! run!
17:29 rbuels U HAVE BEN INVADED BY TEH DEVILS FIG
17:45 * deafferret knew this day would come
18:02 deafferret Windows: you suck.
19:42 asd joined #bioperl
19:42 Guest99746 yo anyone else problems with retrieving blast reports with remote blast?
19:43 deafferret Haven't tried lately. nopaste your error?
19:43 deafferret http://codepad.org/
19:43 deafferret also your source code so I can try to replicate
19:45 rbuels Guest99746: yes, see the mailing list
19:45 rbuels Guest99746: there's a thread about it
19:45 Guest99746 ok i will, thank u
19:45 deafferret huh? I thought ignorance was bliss?
20:01 deafferret lol   http://lists.open-bio.org/pipermai​l/bioperl-l/2010-March/032433.html
20:09 faceface push @{$gff{$seqid}}, [$start, $end, $attrs];
20:09 faceface my ($start, $end, $attrs) = @$_;
20:09 faceface my @repeats = $gff{$seqid};
20:10 faceface 1,3,2
20:10 faceface look right?
20:10 faceface hi deafferret
20:11 faceface sorry, I'll supply more code
20:12 faceface http://fpaste.org/epOv/
20:12 faceface something is going wrong,and I see: ARRAY(0x1042adf0)ARRAY(0x1​0ac25f0)ARRAY(0x10ac2910)
20:12 faceface [] makes an array ref right?
20:12 faceface ahh
20:13 faceface my @repeats = @{$gff{$seqid}};
20:14 faceface crud, now I find my GFF is wrong!
20:15 faceface tallymer is really nice
20:15 faceface when you finally grok the man
20:17 faceface quick way to dump a sequence wrapped at 80 chars?
20:22 rbuels faceface: Bio::SeqIO->new( -format => 'fasta', -fh => \*STDOUT)->write_seq( $seq)
20:22 rbuels that'll wrap it
20:22 faceface hmm
20:23 faceface is it wrong to think that createing a whole new object each time is wrong?
20:23 faceface or do I have a bad concept
20:24 faceface or should I do it 'properly'
20:28 faceface this is what i call a repeat: ACACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC​CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC​CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC​CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC​CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC​CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
20:28 faceface stupid dna
20:31 deafferret biology--
20:31 faceface ;-)
20:32 faceface where on bioperl should I put my gff2fasta script?
20:35 brunov joined #bioperl
20:39 faceface comments, improvemnts, fish : http://www.bioperl.org/wiki/Get​ting_Fasta_sequencs_from_a_GFF
20:40 * deafferret strangles his ISP
20:41 rbuels faceface: this script will blow up for large GFF3
20:41 rbuels it's OK though
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21:18 driveby_bot /home/svn-repositories/bioperl: r16910 (hartzell) :
21:18 driveby_bot Diff: http://tinyurl.com/yas6wfy
21:21 deafferret faceface: ok, I'm done kicking my ISP. did you get whatever that was figured out?
21:27 * deafferret growls fiercly at computers
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22:34 driveby_bot /home/svn-repositories/bioperl: r16911 (cjfields) : email for einfo
22:34 driveby_bot Diff: http://tinyurl.com/y9qryr2
22:39 faceface deafferret: I think so
22:39 faceface rbuels: comment is correct, but in my case it dosn't matter
22:39 * deafferret hugs gzip: gbbct25.seq.gz: unexpected end of file
22:39 faceface he suggested using Bio::index:::something
22:40 faceface heh
22:40 faceface good attitude ;-)
22:40 faceface hug the unhelpfull
22:40 faceface kiss the useless
22:40 deafferret :)
22:40 faceface Bio::Index::Fasta
22:41 deafferret (Bio::Index::Fasta)++
22:41 faceface I'll make a note of that on the discussion page for the gff2fasta
22:41 deafferret (Bio::Index::GenBank)++
22:41 faceface he said that too... but I fear what I don't know
22:42 deafferret very cool stuff. simple, but oh so much better than my ugly hackery
22:42 deafferret $undergrad_who_showed_me_that++
22:44 * faceface should read it
22:45 deafferret If Bio::Index::GenBank also indexed organism info I could die a happy man
22:45 deafferret (taxonomy junk (ORGANISM))
22:46 deafferret $idx->fetch("Staph*")    :)
22:46 faceface I made a taxonomy db at one point if you'd like to just clone it
22:46 faceface you could then just query the org of choice..
22:46 deafferret we have several of those going too...
22:46 faceface i see
22:47 deafferret but we download a new genbank every month and try to rebuild everything and...
22:47 deafferret it's a hassle
22:47 deafferret rsync of http://www.bio-mirror.net/ is our next stab at it
22:48 deafferret but that won't let me fetch("Staph*") either  :)
22:48 * deafferret shrugs
22:48 faceface I had a whole pipeline for building the DB... Just hit one shell script and it rsynced the files, processed and loaded the data
22:48 faceface iirc...
22:48 faceface perha[s there was a manual step or two ;-)
22:49 deafferret ya. ours works by itself sometimes
22:49 deafferret when, for example, gzip -d doesn't assplode  :D
22:50 faceface I have so many indexes on this fa... Basically I knew this would be another
22:52 faceface blast idx, ssaha idx, tallymer idx, smalt idx, bowtie idx...
22:52 faceface and now... BPIDX!
22:53 * faceface summons a universal fasta index format
22:55 deafferret I need a pipeline framework. this is beyond silly
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23:09 deafferret sigh.... http://galaxy.psu.edu/ is up, but http://getgalaxy.org/ is down
23:13 deafferret hg clone http://bitbucket.org/galaxy/galaxy-central/
23:13 deafferret what's hg?
23:14 deafferret Mercurial?  sigh
23:15 brandi left #bioperl
23:16 brunov omg deja vu
23:16 * brunov shakes it off
23:18 * deafferret wants some kind of master job scheduler dashboard clicky thing
23:18 deafferret to re/run all this random crap
23:18 deafferret I guess Nagios + lots of Perl is the realistic answer
23:18 * deafferret wants a magic wand
23:26 deafferret the frustrating thing is that we build these chains of things, and something novel breaks in the middle of the chain, and it's not easy to resume in the middle
23:26 deafferret surely this wheel has been invented 2000 times. a system to piece together resumable task chains
23:28 deafferret hmmm   http://search.cpan.org/~enoor/Ta​skForest-1.36/lib/TaskForest.pm
23:58 deafferret rbuels: ooo! #uno is playing insider baseball! #cxgn can suck it!
23:58 * deafferret wonders when his humour switched to hostilily humour
23:58 * deafferret ponders, rubbing rbuels' chin

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