[Bioperl-l] Problems with my first Bioperl Script

[Aaron J Mackey]

Unfortunately, you may have a FASTA output file that's just different
enough to break our parser; can you send it to me?

Although, after rereading your problem, I'm worried that you're confusing
FASTA search result output with FASTA sequence format.  Does your t.fasta
look something like this:

>seq name
ADEFHIKLDMNEADEEDKLME...

If so, you need to use the SeqIO system, not the SearchIO system.

Otherwise, thanks for sending me your FASTA result output.

-Aaron

On Wed, 26 Feb 2003, Brian Carlson wrote:

> Here's my script
>
>
> #!/usr/bin/perl
>
> use Bio::SearchIO;
>
> my $searchio = new Bio::SearchIO ( -format => 'fasta',
>                                    -file   => 't.fasta');
> $i=1;
>
> while ($result = $searchio->next_result)
> {
>   print "$i\n";
>   $i++;
> }
>
>
> When I run this, I get:  unreognized FASTA Family report file
>
> What could cause this?
>
> FYI:
> I'm trying to get fimilar with BioPerl.  What I'm moving towards
> is the ability to enter a base-pair range, and get the sequence
> from the fasta.  Simple stuff hopefully.
>
> Thanks,
> Brian
>
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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu