[Bioperl-l] Bio::Tools::Genewise.pm problems
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Thu Nov 18 11:22:15 EST 2004
I would use SearchIO but the exon phase information seems to get lost...
Thanks for the tip, Genewise.pm now works fine.
From: Jason Stajich [mailto:jason.stajich at duke.edu]
Sent: 18 November 2004 16:01
To: michael watson (IAH-C)
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] Bio::Tools::Genewise.pm problems
You need -genesf. If you want the protein and DNA sequence names
parsed out add -para as well.
So -genesf -para
Bio::SearchIO::wise may be more forgiving, I don't remember - we
probably shouldn't be throwing errors with the parser as you saw, but
we basically get all the data from the -genesf option so without it I
don't think the parser can do much. We don't make any attempt to parse
the wise alignment block.
You can always look at the tests in t/ to get a sense of how an object
is used (there will be a reference to a datafile in the test script
On Nov 18, 2004, at 10:50 AM, michael watson (IAH-C) wrote:
> I'm on Bioperl 1.4 on linux.
> Are there any particular output options I need to specify when using
> genewise and the BioPerl parser?
> I have a genewise output, using default options. When I use the
> sample code in Bio::Tools::Genewise, nothing is printed out. When I
> use the sample code with an example output from the wise2 package
> (basic_genomic.out) I get a error trace:
> MSG: Need a start
> STACK Bio::Tools::Genewise::_get_strand Genewise.pm::116
> Is anyone using this parser without any errors? If so, any tips on
> how to get it to work?
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
jason.stajich at duke.edu
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