[Bioperl-l] SearchIO and fasta output

[Jason Stajich]

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/