Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-05-16

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Time Nick Message
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05:43 philsf hi, is there anyone awake who can help me parse some nexus tree files? Does the Bio::TreeIO::nexus parser allow one to edit taxa headers? the nodes id() method doesn't seem to get the whole header in my files
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20:22 Guest35173 hey, anyone out there with the patience to help a noobie - i have some questions on using the signalP tool..
20:22 Guest35173 im sort of a programming newbie, especially with perl
20:22 Guest35173 but i am getting an error to the likes of: MSG: file handle Bio::Root::IO=HASH(0xa1c4e48) doesn't appear to be a handle
20:23 Guest35173 my $handle = Bio::Root::IO->new(-file => "tta1_oct2008_finalrelease.aa.fsa");
20:23 Guest35173 i am trying to initialize the handle with this bit
20:24 Guest35173 and the error occurs on the initilization of the signalP parser:
20:24 Guest35173 my $parser = Bio::Tools::Signalp->new(-fh => $handle );
20:26 leont Why would you want to open a file like that?
20:27 Guest35173 oh, i suppose i shouldnt want to..
20:28 Guest35173 i am just trying to use the example script on the api docs
20:28 Guest35173 http://search.cpan.org/~cjfields/Bi‚ÄčoPerl-1.6.901/Bio/Tools/Signalp.pm
20:28 Guest35173 but the initialization needs that $filehandle object
20:29 leont It needs a real filehandle
20:29 Guest35173 is that just a base perl filehandle object?
20:29 Guest35173 not some bioperl specific one?
20:29 leont (or a filename, I presume, but that isn't documented)
20:29 leont Nope, just the normal one
20:30 leont open my $fh, '<', $filename or die "Couldn't open $filename: $!";
20:30 Guest35173 okay, ill give that a try
20:30 Guest35173 thanks a lot!
20:36 Guest35173 hmm, that fixed the errors, but i am not getting any signalP results.. i wonder if this aa file should have any
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