Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-04-30

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All times shown according to UTC.

Time Nick Message
01:18 rbuels joined #bioperl
02:37 jorvis_ joined #bioperl
03:28 rbuels joined #bioperl
13:13 rbuels joined #bioperl
14:57 faceface joined #bioperl
14:57 faceface buels!!!!
16:34 deafferret faceface!!
16:35 faceface torbjorn !!!!
16:36 deafferret no, no, you have to let a 3rd person do that!  :p   laugh
16:37 rbuels joined #bioperl
16:38 balin balin!
16:42 faceface rbuels: !!!
16:42 rbuels howdy
16:42 faceface hey hey!
16:42 faceface how are you doing?
16:42 rbuels oh my it's too early in the morning in oregon for such enthusiasm
16:42 rbuels i am fine
16:43 faceface Its about time for me to go home...
16:43 faceface sigh
16:43 rbuels where is your home
16:44 faceface Dundee
16:44 faceface near SCRI :D
16:44 faceface so ... you need a list of BAC ID's in the library?
16:45 rbuels yeah let's take the BAC stuff to a query, here
16:45 faceface I'm going through the check list of things that was sent from you via Lukas
18:51 perl_splut wow... so hating the Annotation package in bioperl right now...
18:51 perl_splut when using the as_text method the dumb thing feeds back Value: Tag_Value instead of just giving me Tag_Value...
19:46 deafferret literally 'Value: '  ?
19:47 perl_splut yep
19:47 perl_splut so, instead of getting "1" I get "Value: 1"
19:48 deafferret that strikes me as sub-optimal  :)
19:48 perl_splut yeah, because now I have to filter that, which adds more code, to get what should have been there
19:49 deafferret is it part of a much larger as_text() tree where 'Value: ' is helpful?
19:49 perl_splut http://www.ncbi.nlm.nih.gov/nuccore/73622129
19:49 perl_splut is the gene
19:50 perl_splut ($f->annotation->get_Annotat​ions('number'))[0]->as_text;
19:50 perl_splut is how I'm getting the value...
19:50 perl_splut one sec and I'll show you the relevant code
19:51 deafferret git clone ... ?
19:51 perl_splut no git here
19:51 deafferret github is neato
19:52 perl_splut my code isn't mine to release
19:52 deafferret ah. I'm such an idealist.  :)
19:54 perl_splut http://nopaste.dk/p1041
19:55 perl_splut if I was writing this for myself, then probably would release it. But I'm being paid for my work and that makes the IP belong to my employer
19:56 deafferret sure. maybe $employer can contribute some things / time back to open source.  :)  going to see if I can run your scenario
19:57 perl_splut does that give you enough to see what I'm getting?
19:57 deafferret dunno. I'll find out.  :)
19:57 perl_splut heh, kk
19:59 deafferret do you have a git client?
19:59 perl_splut nope
19:59 deafferret k. nevermind. I was going to slap it into my /sandbox  :)
20:01 deafferret hmm  $f->annotation->get_Annotations('number')   empty array
20:02 perl_splut were you doing that on an exon?
20:02 deafferret yup
20:02 perl_splut cause it isn't empty for me
20:03 perl_splut NM_001031827.1
20:03 perl_splut that is the record I'm pulling in (note the .1 for version of the file)
20:03 deafferret yup. are you on exon 1..774
20:03 deafferret ?
20:03 perl_splut starts with exon 1 and gets me all 3
20:03 perl_splut and shows me Value: 1
20:03 perl_splut Value: 2
20:04 perl_splut Value: 3
20:06 perl_splut (my $exon_no = ($f->annotation->get_Annotati​ons('number'))[0]->as_text)=~ s/(Comment|Value): //;
20:06 perl_splut that's from the mailing list... just wish I didn't have to invoke the RegExp engine for this
20:08 deafferret my $exon_no = ($f->get_tag_values('number'))[0];
20:08 deafferret seems to work here.
20:09 perl_splut ahh, kewl
20:09 deafferret or, more explicitly, you could add a separate line for the arrayishness
20:10 perl_splut not really anticipating them having more than one number
20:12 perl_splut knew I was missing something to get at that key
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