[Bioperl-l] Bio::Tools::Genewise.pm problems

[michael watson (IAH-C)]

Hi

I would use SearchIO but the exon phase information seems to get lost...

Thanks for the tip, Genewise.pm now works fine.

Mick

-----Original Message-----
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 
usually)

-jason
On Nov 18, 2004, at 10:50 AM, michael watson (IAH-C) wrote:

> Hi
>
> 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:
>
> EXCEPTION
> 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?
>
> Thanks
>
> Mick
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/