Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-01-20

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18:02 wizi hi everyone
18:02 wizi i am trying to get the COMMENT line from *.gb file
18:02 wizi does anyone know how do to this?
18:02 wizi thank you
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18:54 deafferret step 1: more patience in IRC
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22:27 philsf hello, is Bio::SearchIO::hmmer supposed to parse hmmer 3.0 results files? I'm always getting no hits in my tests so far
22:34 splut I have a vague recollection that some changes were made to allow parsing of version 2 versus version 3
22:35 splut http://doc.bioperl.org/releases/bioperl-cu​rrent/bioperl-live/Bio/SearchIO/hmmer.html
22:35 splut Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
22:39 splut looks like the changes went in place back in early November
22:40 philsf but I'm using 1.6.1, it has the same tag line and it doesn't look it does
22:40 philsf also, the $results->algorithm returns something like [M=81], for a given result
22:41 splut that is from live. I think 1.6.1 was released before November
22:41 philsf the whole line reads: Query:       cd06445.FASTA.fasta  [M=81]
22:41 philsf I'm guessing this is some length
22:42 splut yep, 1.6.1 is from Sept 2009
22:42 philsf (length of something)
22:42 splut you need to update your version
22:42 splut or wait for 1.6.2
22:42 philsf splut, thanks, but why did the doc show the info for a parser not yet available?
22:42 splut probably because the author thought it could
22:43 philsf lol
22:43 philsf thanks
22:44 philsf btw, by november do you mean 2010, or 2009?
22:45 splut Nov. 2010
22:45 philsf thank you
22:45 splut https://github.com/bioperl/bioperl-live

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