Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-01-22

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All times shown according to UTC.

Time Nick Message
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00:08 driveby_bot /home/svn-repositories/bioperl: r16734 (kortsch) : POD fixes
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00:08 driveby_bot /home/svn-repositories/bioperl: r16735 (kortsch) : Make bowtie result return extensible - NB API change: want_raw removed -> want 'type'.
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00:26 driveby_bot /home/svn-repositories/bioperl: r16736 (kortsch) : POD changes to reflect API change
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18:17 deafferret ...o.. o o@
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19:14 driveby_bot /home/svn-repositories/bioperl: r16737 (jason) : add an alphabet init arg and get/setter
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19:16 driveby_bot /home/svn-repositories/bioperl: r16738 (jason) : migrate alphabet method up to Bio::AlignIO parent. Can pass in alphabet as init argument to Bio::AlignIO to prevent alphabet guessing code in Bio::PrimarySeq from being invoked. Should be speed up and removes warnings when there are seqs with very gappy (or all gaps) in alignments
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19:17 driveby_bot /home/svn-repositories/bioperl: r16739 (jason) : Can pass in -alphabet as init argument to Bio::AlignIO to prevent alphabet guessing code in Bio::PrimarySeq from being invoked. Should be speed up and removes warnings when there are seqs with very gappy (or all gaps) in alignments
19:27 rbuels deafferret: you do a lot of blast parsing right?
19:27 rbuels deafferret: did you ever use the old bplite?
19:27 rbuels i'm porting a thing over from that to SearchIO...
19:27 rbuels and i'm trying to find equivalents
19:30 * deafferret doesn't know what bplite is
19:31 rbuels that was an old blast parser that used to be in bioperl
19:31 deafferret ya, I'm starting at blast results right now, matter of fact
19:31 deafferret k. so, what are you trying to add to SearchIO?
19:31 rbuels no i'm not adding anything
19:31 rbuels i'm just porting this script over from bplite to searchio
19:31 rbuels and you're no help!
19:31 rbuels none!
19:32 deafferret oh, I see. I know searchIO pretty well (BLAST flavor).
19:32 * deafferret tries harder
19:32 rbuels lol
19:32 deafferret show me your code or something, jerky
19:32 deafferret and go install Vector NTI for that guy, would ya?
19:32 * deafferret doesn't want to drive all the way over there
19:33 rbuels i don't remember the vector nti thing
19:33 deafferret you're no help!
19:33 deafferret none!
19:34 rbuels touche!  a touch, i do confess!
19:36 deafferret so ... what are you trying to do that you're not yet doing?, specifically
19:36 deafferret or show me the old stuff
19:36 deafferret and go install 5 VNTIs at Lied 11706 at 3pm
19:40 rbuels yay done
19:41 rbuels i'll show you the diff
19:41 rbuels for your edification
19:41 * deafferret takes all the credit
19:41 deafferret (Bio::BroodComb)++
19:41 * deafferret publishes
19:42 rbuels http://codepad.org:80/dUGcvldv
19:42 deafferret "It even converts old programs to modern BioPerl for you." --Jay Hannah, Esq., BroodComb project founder
19:43 deafferret $self->{blast_outfile}  ?
19:44 rbuels this is terrible stuff that i am porting.  the diff is there to show you what bplite was
19:44 rbuels actually it might be something that could go in bioperl...
19:44 rbuels well, bio::graphics
19:44 deafferret interesting ... the API is identical, the method names changed?
19:45 deafferret oh? pretty pictures I can see?
19:45 rbuels it's pretty similar api yes
19:45 rbuels well here's an example of this thing running ...
19:45 * rbuels gets a link
19:45 * deafferret drums his fingers patiently
19:45 * deafferret looks at his watch
19:45 * deafferret drums his fingers patiently
19:45 * deafferret looks at his watch
19:45 * deafferret falls asleep
19:46 rbuels http://solgenomics.net/tools/blast/view_result.​pl?output_graphs=bioperl_histogram&filterq=​&file=&maxhits=100&matrix=BLOSUM62&​amp;program=blastn&database=51&interfac​e_type=simple&outformat=0&expect=1e-10&​amp;seq_count=1&report_file=IkzKkRwKsN
19:46 * deafferret startles, wakes
19:46 rbuels this is the conservedness histogram
19:47 deafferret pretty cool!
19:47 deafferret (is Conservedness a word?)
19:47 rbuels http://solgenomics.net/tools/blast/view_result.​pl?output_graphs=bioperl_histogram&filterq=​&file=&maxhits=100&matrix=BLOSUM62&​amp;program=blastn&database=90&interfac​e_type=simple&outformat=0&expect=1e-10&​amp;seq_count=1&report_file=BS16hJS8FT
19:47 rbuels well, evan thought it was
19:47 rbuels it probably is.....
19:48 rbuels in biology.
19:48 deafferret (Terminal.app has tabs? whoah)
19:49 rbuels wha ha?
19:49 deafferret so in that first long link -- why does the bottom yellow bar have a long stretch of yellow, with no yellow in the mountain above?
19:50 rbuels erm, i think the yellow is 100% conservedness or something
19:50 rbuels oh
19:51 deafferret conservedness in (100,299)
19:51 rbuels erm...
19:51 deafferret whats the green vs blue in the mound?
19:51 deafferret oh  nm
19:51 deafferret reading is fundamental.   got it
19:51 deafferret VERY COOL
19:51 * deafferret likes it
19:52 rbuels yeah doesn't say what yellow is ...
19:52 rbuels i should fix that
19:52 deafferret ya it does. it's all good
19:52 rbuels (what?
19:52 rbuels where?
19:52 deafferret mouse over the yellow and it tells you the range
19:52 deafferret the colors in the mound are unrelated to the colors in the stripe
19:53 deafferret which is what confused me initially
19:53 deafferret so if I knew what conservedness '200' meant, I think I would grok this whole thing
19:54 * deafferret groks loco with the cake
19:54 rbuels yeah...
19:54 deafferret how much work to stuff into Bio::Graphics?
19:54 deafferret that would be fun
19:55 rbuels not much probably, it's a small module
19:55 * rbuels git svn clones Bio::Graphics
19:55 deafferret has lincoln seen it?
19:55 deafferret the output?
19:55 rbuels i dunno
19:56 rbuels i'll commit it with some example outputs
19:56 deafferret in a branch, right?
19:56 * rbuels grins evilly
19:56 deafferret hmm... wherez the hive mind of Bio::Graphics?
19:56 rbuels there isn't one, it's scott and lincoln
19:56 * deafferret thought lots of openbio was still in CVS
19:57 rbuels oh, the repo?
19:57 deafferret yessir
19:57 * rbuels gets the link
19:57 * rbuels slooowwly
19:57 rbuels sourceforge blows goats
19:58 rbuels https://gmod.svn.sourceforge.net​/svnroot/gmod/Bio-Graphics/trunk
19:58 deafferret you git cloned that?
19:58 rbuels git-svn
19:58 deafferret right, but then branches are borked, aren't they?
19:58 rbuels well yes ..
19:59 rbuels oh all right
19:59 * rbuels svn co's it
19:59 deafferret WAIT YUR TURN
19:59 deafferret ok, proceed
19:59 deafferret :)
20:00 deafferret wow. 35K lines of .pm
20:00 deafferret that's a spicy meatball
20:00 rbuels that's graphics for you
20:00 rbuels it's not dense logic, mostly
20:01 rbuels graphics is just usually tons of lines
20:01 rbuels "draw this", "draw that"
20:01 deafferret Bio/Graphics/Glyph/wiggle_it_just_a_little_bit.pm  ??
20:01 rbuels O RLY?
20:01 deafferret fucking kids
20:02 rbuels heeeeey wait
20:02 rbuels that's not really in there
20:02 rbuels you kidder
20:02 deafferret :o)
20:02 rbuels gee whiz
20:02 deafferret Bio/Graphics/Glyph/conservedness.pm  ?
20:03 * deafferret thinks this might be easy-ish?
20:03 rbuels it's not a glyph, it's .... a blast graphic thing really
20:03 rbuels maybe it should go in with that other thing...
20:03 deafferret o right, sorry
20:03 rbuels http://gmod.svn.sourceforge.net/​viewvc/gmod/blastGraphic/trunk/
20:03 rbuels probably should go there
20:04 rbuels or that should go into Bio::Graphics
20:04 rbuels or something
20:04 * deafferret downloads more stuff
20:04 rbuels blastGraphic is the other graphic you see on our blast page
20:11 deafferret wow. lotza stuff here. gotta go play windows admin for a couple hours, back later
20:11 deafferret i would like to help if you make a move
20:11 rbuels hrm ok
20:11 deafferret rbuels++ # general good guyness
20:11 rbuels i can give you a commit bit on the gmod repo
20:11 deafferret oh jeez
20:12 rbuels then you can hack gbrowse too
20:12 rbuels lol
20:12 deafferret wow...  :)
20:12 deafferret &
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23:26 driveby_bot /home/svn-repositories/bioperl: r16740 (kortsch) : More reliable format determination for stored results.
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