[Bioperl-l] exception parsing plain old blast html

[Jason Stajich]

The parser cannot handle html blast.


On Wed, 9 Apr 2003, nkuipers wrote:

> Hello,
>
> OS: Red Hat 8
> Kernel: 2.4-18
> Perl: 5.8.0
> BioPerl: 1.2
>
> message:
> ------------- EXCEPTION  -------------
> MSG: no data for midline <PRE>
> STACK Bio::SearchIO::blast::next_result
> /home/nkuipers/lib/Bio/SearchIO/blast.pm:628
> STACK main::parse test_2.pl:164
> STACK main::blast test_2.pl:115
> STACK main::main test_2.pl:60
> STACK toplevel test_2.pl:40
>
> --------------------------------------
>
> line 163-164:
> my $sio = Bio::SearchIO->new(-file => $tmpblast, -format => 'blast');
> while (my $result = $sio->next_result())
>
> I read the documentation for the nex_result method and it does state that:
>
> "Certain driver modules may encounter entries in the stream that
>            are either misformatted or that use syntax not yet understood
>            by the driver. If such an incident is recoverable, e.g., by
>            dismissing a feature of a feature table or some other non-mandatory
>            part of an entry, the driver will issue a warning. In the case
>            of a non-recoverable situation an exception will be thrown."
>
> Does anyone have any insights or comments about this?
>
> Thanks.
>
> Nathanael
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu