[Bioperl-l] SearchIO and fasta output

[Jason Stajich]

Yell at the people who put the feature stuff in 1.5.0 that wasn't 
backwards compatible... okay that won't actually be productive.

Upgrade to the CVS version if you can, otherwise you might be able to 
just drop in the Bio/SearchIO/fasta.pm from 1.5 into 1.4.  I don't 
remember if there were any other knockoff effects to other modules that 
needed to be done, I think it was just a regexp fix.

We should really put a 1.5.1 out to deal with the problems introduced 
with feature/annotations in 1.5.0 so that the old API is respected.

-jason
On May 6, 2005, at 9:03 AM, michael watson ((IAH-C)) wrote:

> 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/
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/