Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-05

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All times shown according to UTC.

Time Nick Message
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01:30 driveby_bot /home/svn-repositories/bioperl: r16332 (maj) : tests+data for bug#2942
01:32 deafferret yay! a clean driveby_bot msg
01:32 * deafferret hugs /ignore JOIN QUIT
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03:35 rbuels driveby_bot is a good name.
04:10 * deafferret jams his ghetto blaster
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09:26 driveby_bot /home/svn-repositories/bioperl: r16333 (fangly) : Made the assemblers wrapper (Phrap, Cap3, TigrAssembler) share the same interfaces and code created in Bio::Tools::Run::AssemblerBase
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09:33 driveby_bot /home/svn-repositories/bioperl: r16334 (fangly) : Minor Bio::Assembly::IO related updates
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15:44 Brandi_ I was wondering if anyone has used a Bio::Search object to write a Bio::Seq object?
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15:53 rbuels brandi: that's a rather strange thing to do.  what are you trying to accomplish with this?
15:54 brandi I would like to extract protein sequences from blastx alignments and then build SEQ files in Genbank or XML to share with collaborators
15:56 rbuels oh i guess i see.  so you're not actually implementing a new perl class that inherits from Bio::Seq, you just want to use the output of a searchIO to build a Bio::Seq::RichSeq and write it out in genbank or some other format
15:57 brandi right
15:57 brandi I was just looking and perhaps I just need to build the obj with SeqFactory
15:58 rbuels no, probably not.
15:58 rbuels just have a look at the Bio::SearchIO pod
15:58 rbuels and the Bio::SeqIO pod
15:58 rbuels and....
15:58 brandi I have been reading those all morning
15:58 * rbuels checks to see if there are any tutorials on the wiki with bearing on this
15:59 rbuels yeah, it can be really hard to get started with bioperl.  the POD is really sort of a reference manual, not a tutorial for getting started
15:59 brandi read the tutorials too
16:00 rbuels hmmm
16:00 brandi I have been using bioperl for 7 years, but have never needed to do this particular task, normally I would just output fasta, but I don't want have to write a new script for each collaborator who wants it in a different format
16:01 rbuels it's just Bio::SeqIO->new(...) with whatever format for the output part
16:01 brandi also I have 2 different sequences
16:01 brandi the dna seq and the protein seq
16:01 rbuels well you'll need to combine them.....
16:01 rbuels oh
16:02 rbuels hm
16:02 brandi b/c in genbank the protein seq is a "feature" of the dna seq
16:02 rbuels ah yes.
16:02 * rbuels writes some pseudocode
16:05 rbuels so really the sticking point here is how to work with annotations on a sequence?
16:05 rbuels cause the seqIO for gb format can output annotations i think
16:06 rbuels when it outputs a record
16:06 rbuels you can just make an annotation object, attach it to the sequence you're building, and then when you write it out it should come out with it
16:14 rbuels something along the lines of http://gist.github.com/227164
16:15 rbuels does that look approximately what you're after?
16:19 brandi yeah, looks like that could work
16:19 brandi thanks
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