[Bioperl-l] blastxml to table

[Robson de Souza]

Hi Chris, just submitted the problem to Bugzilla (Bug 3089).
Robson

On Tue, Jun 1, 2010 at 5:47 PM, Chris Fields <cjfields at illinois.edu> wrote:
> That's a bug; it appears the iteration method is being called w/o checking whether the specific Hit class has implemented it.  Can you report this?  I can't get to it (going out of town until Friday).
>
> chris
>
> On Jun 1, 2010, at 3:23 PM, Robson de Souza wrote:
>
>> Hello!
>>
>> I'm trying to convert BLAST XML output to a BLAST table which should
>> be identical to a BLAST output generated using "-m 8".
>> In the script below, if $type is "BLAST", the script works if $writer
>> is TextResultWriter but when I try to generate BLAST compatible (i.e.
>> like "-m 8") tables using $writer = "HSPTableWriter" it fails with the
>> message
>>
>> Using default column map.
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Trouble in ResultTableWriter::_set_row_data_func() eval: Can't
>> locate object method "iteration" via package
>> "Bio::Search::Hit::GenericHit" at (eval 58) line 1, <GEN50> line 3020.
>>
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw
>> /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/Root/Root.pm:368
>> STACK: try{} block
>> /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO/Writer/ResultTableWriter.pm:339
>> STACK: Bio::SearchIO::Writer::HSPTableWriter::to_string
>> /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO/Writer/HSPTableWriter.pm:263
>> STACK: Bio::SearchIO::write_result
>> /panfs/pan1/proteinworld/tools/perl/lib/site_perl/5.8.8/Bio/SearchIO.pm:344
>> STACK: /home/desouza/projects/mytools/bin/blastxml2blast:22
>> -----------------------------------------------------------
>>
>> Is there a way to fix this? Or should I use another approach to get
>> "-m 8" compatible tables?
>> Thanks,
>> Robson
>>
>> #!/usr/bin/env perl
>> #====================
>>
>> use strict;
>> use warnings;
>> use Bio::SearchIO;
>> use Getopt::Long;
>>
>> my $writer = "TextResultWriter";
>> my $type = "PSIBLAST";
>> GetOptions("w=s"=>\$writer,
>>                 "t=s" => \$type);
>>
>> # Load writer
>> use Module::Load;
>> my $writer = "Bio::SearchIO::Writer::".$writer;
>> load $writer;
>> $writer = $writer->new();
>>
>> # Open and convert input
>> my $out = Bio::SearchIO->new(-writer => $writer);
>> foreach my $file (@ARGV) {
>>   my $in = Bio::SearchIO->new(-format => "blastxml",
>>                               -file   => "<$file");
>>   $in->blasttype($type);
>>   while( my $r = $in->next_result) {
>>       $out->write_result($r);
>>   }
>> }
>>
>> exit 0;
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>
>