[Bioperl-l] SearchIO and fasta output

[michael watson (IAH-C)]

Hi

Sorry about the crap report.

Basically I was using bioperl-1.4, and that didn't parse the latest
version of fasta. 
 
So I upgraded to bioperl-1.5 and that works BUT because the script I am
using creates features, my features now contain (the documented 1.5 bug)
"FT /note="Bio::Annotation::SimpleValue=HASH(0x8595360)".

So I'm not sure what to do - if I get the latest version from CVS is the
above bug fixed?

Thanks
Mick

-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at duke.edu] 
Sent: 06 May 2005 13:05
To: michael watson (IAH-C)
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] SearchIO and fasta output


It works great for me.  Concrete examples of a report are essential if 
you want help.
What version of bioperl, FASTA?  etc.  There was an incompatibility 
with the latest version of FASTA output and older bioperl - fixed in 
CVS.

The -m 9 -d 0 will also parse.  For quick and dirty FASTA to tabular I 
use scripts/searchio/fastam9_to_table which turns FASTA m9 output into 
a blastall -m 9 like table (without SearchIO in fact so it is quite 
fast).

There are several test files that get run in the test suite and the 
test t/SearchIO.t which demonstrate FASTA parsing.

On May 6, 2005, at 6:07 AM, michael watson ((IAH-C)) wrote:

> Hi
>
> Is there a particular output format I need to use when parsing FASTA
> output with SearchIO?  I just used the defaults and got really rather
> disastrous results...
>
> Thanks
> Mick
>
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/