Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-03

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All times shown according to UTC.

Time Nick Message
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15:46 kai uhm, is there a way to guess the SearchIO format of a file I'm trying to parse?
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15:52 rbuels kai: i think SeqIO does some format guessing, but i'm not sure that's implemented for SearchIO
15:57 kai I just tested, if you don't give a -format, SearchIO seems to assume blast
15:57 kai joy :)
15:57 kai I guess I'll have to go and merge the hmmer2 and hmmer3 parsers after all
15:57 kai and sneak in the changes before pyrimidine goes and releases 1.6.2
15:58 pyrimidine :)
15:59 kai maybe a time to go and clean up that code a little, anyway :)
15:59 pyrimidine kai: there is a bit of guessing for Bio::SearchIO (look for _guess_format)
15:59 kai oh?
16:00 pyrimidine kai: but it looks as if hmmer isn't mentioned
16:00 pyrimidine just blast, fasta, exonerate, blastxml
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16:01 kai khan!
16:01 kai but that seems to be looking at the file ending
16:01 pyrimidine right
16:01 kai which for both hmmer2 and hmmer3 seems to be .hsr
16:01 pyrimidine there isn't a Bio::SearchIO equivalent of Bio::Tools::GuessSeqFormat
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16:02 pyrimidine Not sure that would be easy to implement
16:03 pyrimidine (for all the various formats)
16:05 kai I think fixing the hmmer parser to parse both 2 and 3 is the better way to go
16:05 kai especially as it seems like hmmer 2 and 3 will coexist for a while
16:06 kai hmmer3 can't do global alignments, which really hurts if you're trying to use it for domain identification
16:07 CIA-57 bioperl-live: Chris Fields master * ra9d6712 / Bio/SeqFeature/Lite.pm : display_name should be settable, like name() - http://bit.ly/b1l1G3
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16:09 pyrimidine kai: you can always run a lazy check for the first few lines to determine which format is correct, then delegate to the proper hmmer2/hmmer3 parser
16:09 kai yeah, that's more or less the plan
16:09 kai anyway, time to get home
16:10 pyrimidine o7
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