[Bioperl-l] SearchIO and fasta output

[Hilmar Lapp]

Yes, I think so. -hilmar

On Friday, May 6, 2005, at 06:03  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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>> Bioperl-l at portal.open-bio.org
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>>
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
>
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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