Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-06-12

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All times shown according to UTC.

Time Nick Message
05:27 XimDev joined #bioperl
06:11 torbjorn_ joined #bioperl
11:04 torbjorn joined #bioperl
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12:46 XimDev joined #bioperl
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16:54 XimDev joined #bioperl
16:55 XimDev hello all
16:56 XimDev is the name attribute accessible for gff feature object?
17:22 XimDev when I try to parse $feature->display_name I get the error Use of uninitialized value in print at gffparser1.pl line 15, <STDIN> line 20.
17:22 XimDev the paste bot is down
17:31 rbuels XimDev: depends on where you're getting the feature from, i think
17:32 XimDev GFF v2 file
17:32 rbuels via Bio::FeatureIO::gff?
17:32 XimDev i am trying to get the name of the protein
17:32 XimDev yep
17:32 XimDev nope
17:32 XimDev Bio::Tools::GFF
17:32 rbuels ah.
17:32 * rbuels looks
17:33 rbuels yeah, Bio::Tools::GFF does not seem to set the display_name for features
17:34 rbuels cause really there's no way to tell what to set it to
17:34 rbuels cause there are so many different things you could put in gff
17:34 rbuels you should decide which parts of the gff you want and use those
17:35 rbuels let me rephrase..
17:36 rbuels well, for example, you could do print "got a ".$feat->primary." feature with score ".$feat->score."\n"
17:36 rbuels which would produce something like "got a repeat feature with score 0.3232\n"
17:36 XimDev yes
17:37 XimDev i do similar thing
17:41 XimDev the problem is the protein name is stored in the name tag
17:43 XimDev I do $feat->get_tag_values('name') and it works for now so i suspect this may be a bug
17:45 XimDev because $feat->display_name should display the name attribute
22:25 alper_ joined #bioperl

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