Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-07

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

All times shown according to UTC.

Time Nick Message
01:28 kyanardag_ joined #bioperl
01:30 evolab334 left #bioperl
04:00 driveby_bot joined #bioperl
04:00 driveby_bot /home/svn-repositories/bioperl: r16946 (cjfields) : [bug 2399] n() should be at least 1, but not an empty string.  This required some fixes to old tiling code to ignore n().  Tests added
04:00 driveby_bot Diff: http://tinyurl.com/y9vasqe
05:02 driveby_bot joined #bioperl
05:02 driveby_bot /home/svn-repositories/bioperl: r16947 (cjfields) : [bug 2975]
05:02 driveby_bot Diff: http://tinyurl.com/yh46w3o
05:33 bag_ joined #bioperl
05:51 garruk12 joined #bioperl
07:14 kyanardag joined #bioperl
14:31 kyanardag_ joined #bioperl
16:42 deafferret ...o   @
17:16 spekkio joined #bioperl
19:35 rosalind joined #bioperl
19:41 rosalind please help
19:41 rosalind http://pastebin.com/P2CvJZai
19:42 rosalind i want this code to find all tRNA genes and gab their promotors
19:43 rosalind later i will have to store them in a table coloum 1 = gene name, colume 2 = 100bp sequence
19:44 deafferret you need to create your $out object before you start looping.   my $out = new Bio::SeqIO(...
19:47 rosalind out is blank untill the loop? sorry please explain
19:49 deafferret read this SYNOPSIS, DESCRIPTION  http://search.cpan.org/~cjfiel​ds/BioPerl-1.6.1/Bio/SeqIO.pm
19:50 deafferret also  http://www.bioperl.org/wiki/HOWTO:SeqIO
19:52 rbuels joined #bioperl
19:59 rosalind ok
20:00 rosalind the promotor is a new seq object
20:07 rosalind i have this feeling that this still wont store all the tRNA promotor regions
20:09 deafferret hmm...?  you probably want $feat->spliced_seq()   looks like you're working awfully hard. BioPerl will do the start/end math for you
20:09 deafferret especially if your feature has a complex location
20:10 deafferret e.g.   400..423,475..532,555..580
20:10 deafferret complement
20:10 deafferret etc
20:10 deafferret and yes, it will grab everything in your genbank file. I personally guarantee that.  :)
20:10 deafferret if it's in GenBank, it'll be in BioPerl.  :)
20:14 rosalind my engmish is'nt great sorry; i know it will get every bit of info out of genbank. i'm trying to get the promotor regions not the genes themselves.
20:15 rosalind so dosen't feat->splice_seq() get the gene's sequence not the upstream promotor region?
20:17 deafferret correct. it gets whatever the actual feature location is
20:17 deafferret i don't remember seeing an upstream() method... hmmm
20:17 deafferret so maybe yours is fine  :)
20:17 deafferret just be careful of complex locations
20:18 deafferret if your application cares about that sort of thing
20:18 rosalind thats why i'm doing -100 or revcom +100
20:19 deafferret yup.  :)
20:19 rosalind thanx for the warning on complex locations
20:19 deafferret ya, that's a fun way to get burned  :)
20:21 rosalind i had a table with gene name start end and starnd tab delimited but that was hard to get perl to patern match strand and use start if.. else use end revcom
20:23 rosalind so i ditch that way sence there are many ways to do things in perl and tried this
20:25 deafferret i have a conference call in 5 minutes. you're all set for now?
20:25 rosalind yes thanx
20:25 deafferret :)
21:03 bag__ joined #bioperl
22:04 driveby_bot joined #bioperl
22:04 driveby_bot /home/svn-repositories/bioperl: r16948 (cjfields) : Add a -string parameter, allows one to pass a string in to be converted to a filehandle.  Tests added to RootIO.t.
22:04 driveby_bot Diff: http://tinyurl.com/ydlrj6x

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