[Bioperl-l] Please help: upgraded to 1.2.3 and interfaces changed

[Brian Osborne]

David,

"examples/search-blast" is an older directory name, and I've fixed the
documentation. Try "examples/searchio" instead.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of David Trusty
Sent: Wednesday, December 10, 2003 11:15 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Please help: upgraded to 1.2.3 and interfaces changed

Hi,

I am maintaining some code which uses Bioperl.  I had to upgrade our Bioperl
version,
and now the code which uses the Bioperl functions is not working.

Here is a piece of code which is no longer working:
       my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
    my $blast_report = $factory->blastall($seqA);

    print ERROR_LOG "BLAST HITS TABLE\n\n";
    print ERROR_LOG $blast_report->table_labels_tiled();
    print ERROR_LOG $blast_report->table_tiled;

I get this error:
   Can't locate object method "table_labels_tiled" via package
"Bio::SearchIO::blast" at exon.cgi line 511.

And for this code

    foreach $hit ($blast_report->hits) {

I get this error:
    Can't locate object method "hits" via package "Bio::SearchIO::blast" at
exon.cgi line 534.

Is there a replacement for table_labels_tiled?

I think I need to ask the factory to give me a
Bio::Search::Result::BlastResult object, and then a
Bio::Search::Hit::BlastHit.  Do you agree?

I've been looking for an example, but can't seem to find one.  How can I
change the code to get a Bio::Search::Result::BlastResult and then a
Bio::Search::Hit::BlastHit object?

The web site mentions examples in a directory called examples/search-blast,
but I can't find it.
Is there an example I can look at?

Thanks,

David

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