Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-09-15

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All times shown according to UTC.

Time Nick Message
02:16 Complete_Newbie joined #bioperl
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02:38 _alex_s Hey, I'm parsing a blast file in tabular format with the SearchIO module, but the first Result object retrieved via the next_result method has a query_length of 0....which doesn't make sense.
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02:45 _alex_s https://gist.github.com/1218396
02:58 deafferret hmm... maybe I need your blast file to reproduce
03:00 _alex_s Yeah I wrote another script to reproduce the problem. I'll do a file drop of the script and the file. One second.
03:02 deafferret sounds good
03:03 _alex_s http://www.filedropper.com/stevbi3runcontig2ktop42
03:03 _alex_s That's the data.
03:04 _alex_s https://gist.github.com/1218423
03:04 _alex_s That's a minimal script.
03:16 deafferret huh. filedropper download is not working. github is a great place to put files  :)
03:16 _alex_s https://github.com/bioperl/bioperl-live​/blob/master/Bio/SearchIO/blasttable.pm ....There is never any value assigned to the query_length
03:19 _alex_s K here is the blast file on gist. https://gist.github.com/1218441
03:25 deafferret cloning bioperl-live. it takes a while  :)
03:26 _alex_s Did you test the script and the file?
03:26 deafferret doing that now
03:27 _alex_s Cool, thanks for helping out.
03:36 _alex_s So is it working for you? Unless I'm missing something, it's a bug in bioperl and the fix is extremely obvious.
03:36 deafferret ya, i don't see a test for it
03:37 deafferret bioperl-live/t/SearchIO/blasttable.t
03:39 _alex_s I mean, from looking at it, there's a ton of attributes missing that Result should normally have. The data's already there so adding it in is not hard. I guess I'll look into how to submit a patch...
03:39 _alex_s Just to verify though, when you ran the script on that blast file you got 0?
03:41 deafferret i don't see an issue in redmine. dont see a relevant one in the old bugzilla either  http://bugzilla.open-bio.org/bug​list.cgi?quicksearch=blasttable
03:41 deafferret all 0s, ya
03:42 _alex_s k
03:42 _alex_s Will file bug and submit patch. Thanks for verifying.
03:42 deafferret you're welcome :)   http://www.bioperl.org/wiki/Bugs
03:43 deafferret if you see where to patch that's awesome. you can fork in github and send a pull request.    or just email the patch to bioperl-l, if you prefer
03:43 deafferret an ideal patch also adds a test  :)
03:48 _alex_s Will do, thanks.
03:50 deafferret https://github.com/jhannah/​sandbox/tree/master/alex_s
06:20 Complete_Newbie Hi, so I logged on yesterday for the first time
06:20 Complete_Newbie I'm a lot new to all this bioperl (or perl for that matter) business
06:21 Complete_Newbie I have a quite small data set to analyse and was wondering if bioperl would suit my purpose (actually, I know it would, if only I knew how to code in it)
06:22 Complete_Newbie essentially, I had a list of genes that I wanted to find sequences for, and then do a non redundant blast on these sequences to pull out the...say top five hits for each
06:23 Complete_Newbie since reading a bit, I think that it may be possible to show an alignment with these as well ideally, against the original sequence, but that is not entirely necessary
06:26 Complete_Newbie so far I have managed to discern how genbank generates urls to give an output, and  concatenate the relevant strings together in excel to return the appropriate genbank files for each gene of interest (amalgamated into one large genbank file)
06:27 Complete_Newbie that was all in shell though
06:28 Complete_Newbie I've also managed to cobble together some script in bioperl to glean the gene id and nt sequence, and return the results in one large fasta file
06:29 Complete_Newbie the problem is that I am now stuck trying to parse this file through blast and return the hits as stated above
06:30 Complete_Newbie I realise it will probably utilise the SearchIO module, but I'm not sure where to go from here
06:30 Complete_Newbie any ideas?
06:43 kblin uhm
06:44 kblin so, just to recap, so far you have the sequences of the genes you're interested in
06:44 kblin and now you need to blast them and get the five best hits againts nr for each?
06:46 kblin I'm not sure if dumping all this together into one huge genbank or fasta file doesn't make your job harder than necessary
06:47 kblin are you planning to run blast locally?
06:50 kblin whoops, need to get myself to work, be back in a bit
07:17 Complete_Newbie sure, I'm in and out of work as well.  I could possibly download and run it locally I suppose.  No real preference my end really.
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08:13 kai Complete_Newbie: in the bioperl-run repository there's perl modules taking care of running blast(-plus) for you and parsing the output, you might want to have a look at that
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16:25 dbolser http://www.mendeley.com/group​s/1171581/personal-genomics/
16:25 dbolser join if you like M
16:25 dbolser and GWaS
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18:28 * rbuels doesn't particularly like any of those letters
18:29 rbuels i kind of like Q though ... what group should i join for that?
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