[Bioperl-l] seq_inds method question for blast parsing...

Sajeev Batra batra@operon.com
Mon, 11 Nov 2002 12:06:42 -0800

Hi Jason and others,
A while back you suggested if I want to useq the seq_inds() method for
Washu and NCBI blastn output, that I should use the 'blast' format in
SearchIO instead of 'psiblast'.  Thank you for your tip but
I tried to that but need another tip from you guys.

Here's my error msg:
Can't locate object method "hits" via package
"Bio::Search::Result::GenericResult" at ./custom_writer_sajeev2.pl line
48, <STDIN> line 315.

Any suggestions?  Does anyone have a sample code in where they are using
the seq_inds function for the 'blast' format successfully?  Your
feedback is appreciated and thank you.

Here's my code:

use strict;
use lib '../../../';
use Bio::Root::Root;
use Bio::SearchIO::SearchWriterI;

use vars qw( @ISA );
@ISA = qw( Bio::Root::Root Bio::SearchIO::SearchWriterI );

sub to_string {
    my ($self, $result, @args) = @_;
    my $str = '';

    my $hits_reported = 0;

    foreach my $hit($result->hits) {


      my @seq_inds_array = $hit->seq_inds('query','identical',1);
      my @test_inds_array = $hit->seq_inds('subject','identical',1);

      my $query_matches = $#seq_inds_array  + 1;

      print "seq_inds_array id ",@seq_inds_array, "\n";
      print "test_inds_array co ",@test_inds_array,"\n";

      $str .= sprintf "%s\t%s\t%d\t%d\t%d\t%d\t%d\t%.1e\t%d\t%d\t%f\n",
                $result->query_name, $hit->name, $result->query_length,
                $hit->score, $hit->bits, $hit->iteration, $hit->expect,
                $query_matches, $hit->length_aln('query'),



package main;

# Start of script

use strict;

use lib '../../../';
use Bio::SearchIO;

select STDOUT; $|=1;

my $in     = Bio::SearchIO->new( -format => 'blast' );
my $writer = MyBlastWriter->new();
my $out    = Bio::SearchIO->new( -format => 'blast',
     -writer => $writer );

while ( my $result = $in->next_result() ) {
    #printf STDERR "Report %d: $result\n", $in->report_count;