IRC log for #bioperl, 2010-03-05

All times shown according to UTC.

Time	Nick	Message
01:11		brunov joined #bioperl
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03:12		driveby_bot joined #bioperl
03:12	driveby_bot	/home/svn-repositories/bioperl: r16906 (maj) : alias -program_dir to -prog_dir (thanks Ben)
03:12		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		Diff: http://tinyurl.com/y8q822e
06:34		bag joined #bioperl
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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		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		anyone else having problems with the remote blast function?
14:23		worked well some days ago
14:23		but not anymore
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15:44	driveby_bot	/home/svn-repositories/bioperl: r16909 (cjfields) : next, not redo
15:44		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		http://codepad.org/
19:43		also your source code so I can try to replicate
19:45	rbuels	Guest99746: yes, see the mailing list
19:45		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		lol http://lists.open-bio.org/pipe[…]March/032433.html
20:09	faceface	push @{$gff{$seqid}}, [$start, $end, $attrs];
20:09		my ($start, $end, $attrs) = @$_;
20:09		my @repeats = $gff{$seqid};
20:10		1,3,2
20:10		look right?
20:10		hi deafferret
20:11		sorry, I'll supply more code
20:12		http://fpaste.org/epOv/
20:12		something is going wrong,and I see: ARRAY(0x1042adf0)ARRAY(0x10ac25f0)ARRAY(0x10ac2910)
20:12		[] makes an array ref right?
20:12		ahh
20:13		my @repeats = @{$gff{$seqid}};
20:14		crud, now I find my GFF is wrong!
20:15		tallymer is really nice
20:15		when you finally grok the man
20:17		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		that'll wrap it
20:22	faceface	hmm
20:23		is it wrong to think that createing a whole new object each time is wrong?
20:23		or do I have a bad concept
20:24		or should I do it 'properly'
20:28		this is what i call a repeat: ACACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
20:28		stupid dna
20:31	deafferret	biology--
20:31	faceface	;-)
20:32		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/Ge[…]quencs_from_a_GFF
20:40	* deafferret	strangles his ISP
20:41	rbuels	faceface: this script will blow up for large GFF3
20:41		it's OK though
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21:18	driveby_bot	/home/svn-repositories/bioperl: r16910 (hartzell) :
21:18		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		Diff: http://tinyurl.com/y9qryr2
22:39	faceface	deafferret: I think so
22:39		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		heh
22:40		good attitude ;-)
22:40		hug the unhelpfull
22:40		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		$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		(taxonomy junk (ORGANISM))
22:46		$idx->fetch("Staph*") :)
22:46	faceface	I made a taxonomy db at one point if you'd like to just clone it
22:46		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		it's a hassle
22:47		rsync of http://www.bio-mirror.net/ is our next stab at it
22:48		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		iirc...
22:48		perha[s there was a manual step or two ;-)
22:49	deafferret	ya. ours works by itself sometimes
22:49		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		blast idx, ssaha idx, tallymer idx, smalt idx, bowtie idx...
22:52		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		hg clone http://bitbucket.org/galaxy/galaxy-central/
23:13		what's hg?
23:14		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		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		surely this wheel has been invented 2000 times. a system to piece together resumable task chains
23:28		hmmm http://search.cpan.org/~enoor/[…]lib/TaskForest.pm
23:58		rbuels: ooo! #uno is playing insider baseball! #cxgn can suck it!
23:58	* deafferret	wonders when his humour switched to hostilily humour
23:58		ponders, rubbing rbuels' chin