[Bioperl-l] HitTableWriter error

[Steve Chervitz]

Hi Owen

Sorry, I don't have time to look into this right now, but two thoughts:

1) The ResultTableWriter is intended to convert standard blast reports into
a tabular format. So if you already have tabular results, you are sort of
using it "off label", but in principle, it should work.

2) The iteration method is only available to BlastHit objects, since it is
only relevant to PSI-blast results. The fact that you got this error when
working with blast results indicates that the parser did not generate the
correct object type for your hits, using the GenericHit when it should have
used BlastHit. This is just a hunch and would be worth following up on. Can
you submit this as a bug report?

Thanks,
Steve


On Thu, Mar 20, 2008 at 4:56 AM, Owen Lancaster <ol8 at leicester.ac.uk> wrote:

> Hello
>
> I hope you don't mind me emailing you but I have come across a problem
> when trying to use HitTableWriter. The error can be seen below - the
> input for the script is the BLAST tabular output (specified with the -
> m 8 option) from a blastn search.
>
> If you have any idea what the problem might be I would much appreciate
> it! Hope you can help...
>
> Thanks
>
> Owen
>
>
> Using default column map.
>
> ------------- EXCEPTION  -------------
> MSG: Trouble in ResultTableWriter::_set_row_data_func() eval: Can't
> locate object method "iteration" via package
> "Bio::Search::Hit::GenericHit" at (eval 97) line 1, <GEN1> line 2.
>
>
>
> STACK Bio::SearchIO::Writer::ResultTableWriter::__ANON__ /Library/Perl/
> 5.8.8/Bio/SearchIO/Writer/ResultTableWriter.pm:328
> STACK Bio::SearchIO::Writer::HitTableWriter::to_string /Library/Perl/
> 5.8.8/Bio/SearchIO/Writer/HitTableWriter.pm:268
> STACK Bio::SearchIO::write_result /Library/Perl/5.8.8/Bio/SearchIO.pm:
> 331
> STACK Bio::SearchIO::blast::write_result /Library/Perl/5.8.8/Bio/
> SearchIO/blast.pm:2208
> STACK toplevel ./generate_discordant_tails.pl:62
>
> --------------------------------------
>
>