Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-28

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:42 xp_prg my speaker backed out on me :(
00:42 xp_prg anyone here interested?
01:17 jorvis_ just hopped in: interested in what?
02:04 xp_prg in presenting to my diybio group remotely via justin.tv
02:07 xp_prg jorvis_ you interested?
02:09 jorvis_ I guess it would depend on the topic.  BioPerl, presumably?
04:23 kyanardag joined #bioperl
04:58 jonathan__ joined #bioperl
12:41 kyanardag joined #bioperl
14:29 Vein joined #bioperl
18:06 kyanardag anybody familiar with Bio::DB::GFF use?
18:08 deafferret I think that's what genbank2gff.pl and friends use under the hood
18:08 kyanardag i uploaded GFF files to database, along with fasta
18:09 kyanardag and i'm calculating intersections and extracting DNA sequences
18:09 kyanardag i'm stuck at one point
18:09 kyanardag i have 4 different "peak location" sets
18:10 deafferret can you nopaste your code, input data sample, etc?  http://gist.github.com/
18:10 kyanardag hmm, let me see
18:10 deafferret or at least your error message(s)
18:10 kyanardag it's messy now, i
18:10 kyanardag i'll clean and then paste
18:12 rbuels kyanardag: any reason you're using that instead of Bio::DB::SeqFeature::Store?
18:13 rbuels i've heard that's preferable nowadays
18:13 deafferret rbuels: go up on your roof and cut a pillow with a knife
18:14 rbuels um?
18:14 deafferret THAT IS GOSSIP!
18:14 deafferret --Doubt
18:16 kyanardag rbuels: I set this up earlier.. that's the only reason
18:17 kyanardag I also have a GBrowse setup, for that I use  Bio::DB::SeqFeature::Store
18:17 rbuels eh, no point rewriting it now, probably
18:17 kyanardag exactly
18:17 kyanardag http://pastebin.com/d30e4e65b
18:17 kyanardag here's the code and explanation
18:18 kyanardag I can find the parent (sourceseq, refseq) of a segment, but I cannot find segments within a selected clone/chromosome
18:19 rbuels hmmmm
18:20 deafferret Have you tried spouting random movie references from whatever Netflix movie you watched last night? That's what I usually do.
18:20 rbuels might this be similar to the old gbrowse problem of not defining a default reference feature type?
18:21 * rbuels says this in his official capacity as deafferret's officious seeing eye bitch
18:21 kyanardag how can i define the default reference?
18:21 rbuels kyanardag: yeah that's a good question
18:21 * rbuels looks more
18:21 rbuels deafferret: i have everything is illuminated on the table in the other room right now.
18:21 deafferret rbuels++
18:22 deafferret kyanardag: any chance you could mysqldump some of that data?
18:22 rbuels kyanardag: have you tried prefixing some of the names with types
18:22 deafferret I usually fail to help with this sort of thing until I can perl -d it myself
18:22 rbuels like 'Segment:blahblah'
18:23 kyanardag rbuels: i didn't use prefixes
18:23 deafferret After that I usually fail to help with this sort of thing with no good excuse whatsoever.
18:24 rbuels lol why the hell does your gff have Score= in the attrs and not use the score col in the gff
18:24 * rbuels shakes head
18:24 kyanardag 3-4 months ago, I use the same setup, in which BACs, peaks, gene models were referenced according to chromosomes, and it worked flawlessy. I need to use BAC this time and elements are not connected well
18:24 rbuels but that doesn't matter here
18:24 rbuels hmm
18:25 kyanardag deafferret: I am not how can i do partial dump. entire dump is 2.7GB (maize genome)
18:25 kyanardag deafferret: I am not sure ...
18:26 kyanardag should I try putting, Parent=ACnnnn.n for each peak ?
18:26 kyanardag will that help ?
18:26 deafferret mysqldump --no-data   ... then just a little data?
18:26 kyanardag in 9th column as Attrib..
18:27 rbuels kyanardag: not sure
18:29 kyanardag deafferret: I'm trying.. just a moment
18:29 deafferret am I imagining things or do most Google hits of dbi::mysqlopt say 'deprecated' ?
18:29 rbuels kyanardag: can you look up segments by "Sequence:AC132432..."
18:29 rbuels ?
18:30 rbuels Sequence i think is the default class for source sequences
18:30 kyanardag like my $segment=$db->segment('Sequence:AC132432')  ?
18:30 rbuels yeah try that
18:30 * rbuels crosses fingers
18:31 rbuels but of course use an actuall accession
18:31 rbuels Sequence:AC177841.2
18:32 kyanardag it works, but my $segment=$db->segment('AC177841.2') also works
18:33 rbuels ah, probably appends the default class if you don't have one
18:33 rbuels so does that solve your problem?
18:33 * rbuels kind of forgot what kyanardag's problem was
18:34 deafferret It all started when he opened the briefcase and the golden light lit his face.
18:34 kyanardag my problem is the next line, my @peaks=$segment->feature('peakA'); does not pull peakA from selected segment (in this case :AC177841.2)
18:38 * rbuels strokes his chin
18:39 * deafferret strokes rbuels' chin
18:39 kyanardag i hit my head on the wall..
18:39 rbuels '/me hits his head on the wall'
18:40 deafferret uh oh. he's started in on the 3rd person narrative
18:40 * rbuels welcomes kyanardag to the gratuitous-third-person club
18:40 kyanardag i'm new on xchat.. thanks for the tip
18:40 * kyanardag accepts the welcome
18:41 rbuels kyanardag: is the segment you're getting a RelSegment?
18:41 rbuels (print ref($segment),"\n";
18:41 rbuels )
18:43 rbuels hmmm, how about $segment->features('peakA_aug09:')
18:44 rbuels or the equivalent, i think,  $segment->features(-type => 'peakA_aug09:alper')
18:44 * rbuels reads the pod for Bio::DB::GFF::RelSegment features() method
18:45 kyanardag it's not RelSegment as far as I know, let me try your suggestions
18:49 kyanardag rbuels: no results
18:49 rbuels -types => ['peakA_aug09:alper'] ?
18:50 rbuels kyanardag: just paste the whole horrible code
18:50 * rbuels is used to wading through such things and so is deafferret
18:50 deafferret kyanardag: NOpaste that is
18:50 rbuels oh. yes
18:50 deafferret or github.com it!  :)
18:51 rbuels oh.
18:51 rbuels wait.
18:51 rbuels defining a new segment?
18:51 kyanardag i saw refclass in the POD, how can i say, use 'clone' as refclass ?
18:51 * rbuels looks more
18:51 rbuels clone:foo
18:51 rbuels Bio::DB::GFF uses all kinds of stupid colon-separated things
18:52 kyanardag not a particular clone, I mean use the clones, not chromosomes as reference..
18:52 kyanardag -refclass => 'clone' ?
18:52 rbuels yeah i think
18:52 rbuels if there are clone lines in your gff
18:53 kyanardag yes, they are labeled as clone
18:53 rbuels but that should just affect how the coords are reported, i think
18:57 kyanardag thank good, I put -refclass => 'clone' under new, and now it works..
18:57 kyanardag thank god
18:57 rbuels lol
18:58 rbuels why the hell would that make it work
18:58 * rbuels is mystified
18:58 * deafferret rubs rbuels chin harder
18:58 kyanardag it says it defaults to Sequence
18:58 kyanardag and sequence is corresponding to chromosomes I have
18:58 kyanardag i guess
18:58 rbuels ooooooooh
18:59 rbuels so these peaks have clone sources
18:59 rbuels so these peaks have clone refs
18:59 rbuels i mean
18:59 kyanardag yes
18:59 rbuels and it looks for features on Sequence refs
18:59 rbuels by default
18:59 kyanardag locations in BAC clones
18:59 rbuels yeah i think i see now why it wasn't working
19:04 veinous joined #bioperl
19:08 kyanardag thanks for your help, rbuels and deafferret
19:09 * deafferret raises rbuels fist in victory
19:09 rbuels lol
19:10 rbuels kyanardag: no problem
22:11 * deafferret casts Gogol Bordello on rbuels' DVD player
22:14 rbuels deafferret: shut up i'm watching the wire
22:14 deafferret Season, Ep #?
22:15 deafferret rbuels: Bruce Willis is a ghost the whole time
22:50 deafferret rbuels: pass the popcorn, jerk
22:50 rbuels lol, finished the dsik
22:50 rbuels 'twas the last disk of season 1 i think
22:51 deafferret ah. you hooked?  :)
22:51 rbuels oh wait there's one more season 1
22:51 rbuels yes i'm hooked
22:51 deafferret Prop Joe is me in blackface
22:53 rbuels some guy tweeted "at the point in a data migration script where i have to run it and only find out after 30 minutes if it fails"
22:53 rbuels lol
22:53 deafferret eww
23:05 xp_prg joined #bioperl
23:06 kyanardag joined #bioperl
23:08 deafferret rbuels: The Cost? The Hunt? Cleaning Up? http://en.wikipedia.org/wi​ki/The_Wire_%28season_1%29
23:17 * deafferret 's vicarious slacking is not going very well
23:20 deafferret don't make me go loco with your cake
23:32 deafferret I'll do it. I swear.
23:36 rbuels man you be trippin
23:36 rbuels i just finished "Lessons"
23:37 deafferret :)
23:38 rbuels that wik page told me too much dammit
23:38 rbuels don't ever give me that link again
23:38 deafferret aye aye
23:40 rbuels ferretsmack
23:40 rbuels lol
23:40 * deafferret ferretsmacks Oracle
23:40 rbuels is oracle really worth the X thousands of dollars in licenses?
23:41 rbuels is it really that much more powerful or featureful than postgres?
23:41 * deafferret rubs rbuels' chin
23:41 deafferret no
23:41 rbuels does it, for instance, have a nice tool for making schema diagrams?
23:41 deafferret but it does mandate multiple very expensive full time DBAs to do the same things I do in MySQL "in my free time"
23:41 rbuels i'd pay for that
23:42 rbuels god really?
23:42 deafferret I've never seen an ORM of any of our Oracle BS
23:42 rbuels it's that bad?
23:42 deafferret yup. as far as I can tell it is that bad
23:42 rbuels "it does mandate multiple very expensive full time DBAs to do the same things I do in MySQL "in my free time""
23:42 rbuels them's some pretty strong words
23:42 deafferret I REGRET NOTHING!
23:43 deafferret dammit. come here DBD::Proxy. We're gonna panty raid that bitch again
23:45 rbuels what would you need dbd::proxy for/
23:45 deafferret Our crack DBAs can't figure out native Oracle clients. JDBC is buggy
23:46 rbuels and if you're using it......what listens for your connections?
23:46 deafferret ha!!! 0:58  http://www.youtube.com/watch?​v=NSQztZbSC9M&feature=fvw
23:47 rbuels damn yo
23:47 deafferret The Oracle server itself is the only box in $CF that has functional drivers, so we proxy through another Linux box to that one
23:48 rbuels why proxy?
23:48 rbuels oracle box can't take remote connections
23:48 rbuels ?
23:48 rbuels or......firewall not open for it...?
23:49 deafferret um
23:49 * deafferret chekcs
23:49 rbuels cash flow is not nearly as funny as loco with the cake
23:49 * deafferret lools
23:49 deafferret but pause at 0:58. anyone look familiar?
23:49 deafferret maybe this is a season 3 thing
23:50 rbuels i have not gotten to season 3
23:50 rbuels is that guy in the blue hat from the wire?
23:50 deafferret ah. season 3. nevermind
23:51 rbuels do not tell me anything!!!!!!
23:51 deafferret not even this?   http://en.wikipedia.org/wiki​/Felicia_%22Snoop%22_Pearson
23:51 deafferret pretty sure 0:58 is Snoop
23:51 rbuels i will feast on your entrails
23:51 * deafferret is so gangsta
23:52 * rbuels is just plain white-boy murda psycho
23:52 deafferret tee hee
23:52 rbuels good job, there went driley
23:52 rbuels your fault.
23:53 * deafferret summons driley
23:53 rbuels how was your colorado trip?
23:53 rbuels or did it happen yet
23:53 * rbuels forgot when that was gonna go down
23:53 deafferret oh, it was really cool. pretty lakes
23:53 deafferret just got back
23:53 deafferret glad you missed me
23:53 rbuels lol
23:54 rbuels have a nice time with dhoss?
23:54 deafferret we ate pizza, but @parents uninvited him to hike with us  :/
23:55 rbuels uninvited?
23:55 deafferret quality time
23:55 rbuels lol
23:55 rbuels uh oh, wife's home, gotta go
23:55 deafferret "sure you can come. why not?"   ... "oops, @parents want quality time"
23:55 deafferret cya
23:55 * deafferret waves at $wife
23:55 rbuels if she catches me on the computer, i'll get none for a week!
23:55 rbuels lol
23:55 deafferret a week? god. I wish I had that problem
23:56 deafferret is it 2010 yet?
23:56 * deafferret drums his fingers, waiting for $anniversary_date_night
23:57 deafferret $birthday->{2009} = undef;   # cry
23:59 deafferret hell, Snoop is all over this video

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary