Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-09-28

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All times shown according to UTC.

Time Nick Message
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15:08 CIA-112 bioperl-live: Carnë Draug master * r95228cd / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: added assembly to exported data - http://git.io/-E0HpA
15:08 CIA-112 bioperl-live: Carnë Draug master * r1a1dc62 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: small typo on documentation - http://git.io/XU3XeQ
15:08 CIA-112 bioperl-live: Carnë Draug master * rd314c39 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: changed default assembly regex - http://git.io/rdLE4Q
15:08 CIA-112 bioperl-live: Carnë Draug master * rb929a54 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl : genbank_ref_extractor: move 'require's to GetOptions section (trying to predict all errors at the start) - http://git.io/arw70w
15:08 CIA-112 bioperl-live: bosborne master * r2ddc772 / scripts/Bio-DB-EUtilities/b​p_genbank_ref_extractor.pl :
15:08 CIA-112 bioperl-live: Merge pull request #25 from carandraug/bp_genbank_ref_extractor
15:08 CIA-112 bioperl-live: Bp genbank ref extractor - http://git.io/cFaCWA
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15:56 paulinpgh hello all
15:56 paulinpgh anybody around to ask BLAST output searchIO question?
16:00 ende_ I can give it a shot
16:01 paulinpgh i have a mulitresult blastn output file using blast+
16:02 paulinpgh when I iterate over the results, $result->algorithm_version only works as expected for the first result
16:02 paulinpgh but is the empty string for each result thereafter
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16:02 paulinpgh something must have recently changed in Bioperl because I have plenty of output where the algorithm_version was working correctly on multi-result blastn output files
16:02 ende_ can you paste to gist.github.com ?
16:03 paulinpgh ok wait a min
16:04 paulinpgh here is the script I'm using : https://gist.github.com/1248338
16:04 paulinpgh here is blastn output from blast+: https://gist.github.com/1248342
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16:05 paulinpgh here is the output I get: https://gist.github.com/1248347
16:06 ende_ ok 1 sec
16:06 paulinpgh notice that algorithm_version is not outputted for the 2nd and 3rd lines
16:07 ende_ Yup
16:07 ende_ What version are you using?
16:07 paulinpgh latest git clone
16:08 ende_ bioperl-live?
16:08 paulinpgh oh yes, sorry
16:09 ende_ gimmie a couple mins to take a look
16:09 paulinpgh ok
16:09 ende_ (ha, my only local copy of bioperl is still svn)
16:10 ende_ so Im gitting it right now, on a sorta slow connection.  Check back in about 10 mins?
16:10 paulinpgh will do
16:13 ende_ Just curious, does algorithm_reference print ?
16:19 ende_ also, have you tried the same code with a different blast report?
16:23 paulinpgh hold on
16:24 paulinpgh I tried algorithm_reference
16:24 paulinpgh it prints ok on first query but gives "uninitialized value" error 2nd and 3rd seqs
16:24 paulinpgh and yes, I've tried the same code on different blast reports.
16:25 paulinpgh the algorithm_version was working fine about a month ago so something has changed
16:32 ende_ yeah
16:32 ende_ Im at a little bit of a loss
16:33 ende_ (I dont really have time to pour over it this second)
16:46 paulinpgh ok thanks for your help
16:47 paulinpgh i'll try the bioperl email list
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