Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-22

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All times shown according to UTC.

Time Nick Message
00:48 brandi joined #bioperl
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06:57 XaeroOne joined #bioperl
09:19 bio-in joined #bioperl
09:19 bio-in Hi all
09:19 bio-in I have a short question
09:20 bio-in is there a Perl / Bio-perl script /library that calculates distances between two biological features taking strand into account (enhancer to exon distance for instance)
09:20 bio-in ?
09:35 kai not that I'm aware of, but I actually never tried
09:38 bio-in thx for your answer Kai
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13:02 deafferret bio-in: define "distance"   :)
13:11 bio-in Thx Deafferret
13:12 bio-in Distance for me is the distance separating two features on the DNA sequence. for instance, I have a series of regulatory modules defines by their genomic coordinates. I would like to assign genes to each of these CRMs. One way to do that is to identify the closest gene and thus assign this gene to the CRM.
13:13 bio-in For this, I need to search over the genome, taking strand into account, for genes that are close to my CRMs (Cis Regulatory Modules)
13:23 deafferret hi, sorry, I'm in a meeting so it'll take me a minute
13:34 pcantalupo joined #bioperl
13:34 pcantalupo hello
13:34 pcantalupo anybody on?
13:39 pcantalupo how does one submit a code change to fix a minor bug?
13:40 XaeroOne usually submit a patch
13:41 pcantalupo i don't know how to do that
13:41 XaeroOne me niether
13:41 pcantalupo lol
13:41 pcantalupo should I use bugzilla maybe?
13:41 XaeroOne but i think from what i can remember reading you use a program called diff
13:41 pcantalupo yeah, i have the diff output
13:41 XaeroOne diff -u and then some filenames
13:42 pcantalupo so should I send it to bioperl-l@lists.open-bio.org?
13:42 XaeroOne btw, did you know that larry wall is the authour of the patch stuff
13:42 pcantalupo no
13:42 XaeroOne i dunno about that
13:43 XaeroOne maybe if you hang around someone might tell you something
13:43 pcantalupo ok i'll leave the chat up on my browser
13:43 pcantalupo do you do alot of bioperl development?
13:44 XaeroOne i know nothing about bioperl
13:44 pcantalupo lol
13:44 pcantalupo then what are you doing on this channel?
13:44 XaeroOne i am learning perl
13:44 XaeroOne i saw a perl in the channel name and joined
13:44 pcantalupo oh
13:45 XaeroOne but this is what i usually do, if someone asks a question that I might know something about
13:47 XaeroOne incase no one show up: i've seen people post the output of diff to a mailing list so you could try that or attach it to bugzilla
13:48 XaeroOne btw what do you use bio perl for?
13:49 pcantalupo i work in a biology research lab
13:49 pcantalupo collect alot of sequence data
13:49 pcantalupo use bioperl to organize, and analyze the sequence data
13:49 pcantalupo alot of parsing of BLAST reports
13:50 XaeroOne is bio perl like regular perl?
13:52 pcantalupo yes and no
13:53 pcantalupo bioperl is written in perl
13:53 pcantalupo it is a collection of object-oriented perl modules
13:56 XaeroOne i read some stuff on docs.bioperl.org but i can't understands nuttin' :o
13:57 pcantalupo it is best to start learning Perl here: http://learn.perl.org/
13:57 pcantalupo before diving into Bioperl
14:02 XaeroOne yeah been reading it
14:04 deafferret sorry, I'm at YAPC (Perl Conference), so I'm VERY distracted   :)
14:06 pcantalupo hi deafferret
14:06 pcantalupo i found a minor bug in one of the utility scripts
14:06 deafferret oh? cool! thanks!
14:06 pcantalupo should I send a git diff patch to the bioperl list?
14:06 deafferret are you familiar with github?
14:06 pcantalupo i've never done this before
14:06 deafferret or git?
14:06 pcantalupo a little
14:07 deafferret k. if you want to fork github.com/bioperl/bioperl-live and patch it I'll pull your patch
14:07 pcantalupo sorry i'm not that familiar
14:07 deafferret do you have a github.com account?
14:08 pcantalupo no
14:08 deafferret want to sign up?  :)
14:08 pcantalupo i have the public git clone of bioperl-live
14:08 deafferret ah
14:08 deafferret how big is the patch?
14:08 pcantalupo i removed one character from one line ...lol
14:08 deafferret throw it in gist.github.com?
14:08 deafferret oh laugh
14:08 pcantalupo a very simple bug
14:09 deafferret gist.github.com the diff
14:10 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git
14:10 pcantalupo ok
14:10 pcantalupo thank you
14:13 pcantalupo i posted the git diff
14:13 pcantalupo gist: 448511
14:17 deafferret pcantalupo: What author credit do you want in the commit method? Name/email? your choice
14:17 deafferret commit messages I meant
14:18 pcantalupo use both thank you
14:18 deafferret what are they?   :)
14:18 pcantalupo sorry I thought you could see them on gist
14:18 deafferret oh, right sorry
14:18 pcantalupo Paul Cantalupo    pcantalupo@gmail.com
14:19 deafferret pushed. thanks!
14:19 pcantalupo deafferret, i'm thinking about looking into implementing the length() sub in Contig.pm
14:19 CIA-95 bioperl-live: Jay Hannah master * rbc3b504 / scripts/utilities/download_query_genbank.PLS :
14:19 CIA-95 bioperl-live: Typo correction
14:19 CIA-95 bioperl-live: Thanks to Paul Cantalupo <pcantalupo@gmail.com> in IRC! - http://bit.ly/aMT3Hd
14:19 pcantalupo how should I go about doing this?
14:20 pcantalupo advice?
14:20 deafferret ah, cool. I know very little about contigs, and am at this conference. you might want to email bioperl-l
14:20 pcantalupo ok thank you
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16:01 CIA-95 bioperl-live: Chris Fields master * r41c9494 / (16 files in 14 dirs): fix conflict (+7 more commits...) - http://bit.ly/9E6OoU

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