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  • Filtering BLAST results using BioPerl

    Hi all,
    I try to fix the following issue:
    I have a BLAST output from the command line, using PacBio data as queries and a custom database. I have some filtering criteria for my hits, e.g. >db_1 should at least cover 80bp, while >db_2 should cover at least 1000bp.

    In the end I'd like to have a graphical representation of my queries and the corresponding (filtered) hits.
    A refinement would be, if the alignment of db_2 is in total longer than the alignment of db_3, db_3 should be discarded...

    I tried to use Bio::Search::Result::ResultI first. I ended up with a very ugly script, which works and processes my custom blast tab, but I even failed to visualize my results.
    Code:
    while( my $result = $in->next_result ) {
      ## $result is a Bio::Search::Result::ResultI compliant object
      while( my $hit = $result->next_hit ) {
        ## $hit is a Bio::Search::Hit::HitI compliant object
        while( my $hsp = $hit->next_hsp ) {
          ## $hsp is a Bio::Search::HSP::HSPI compliant object
          if( $hit->name =~ m/someexpression/ ) {
           if($hit->name =~ m/db_2/ && $hsp->length('hit')>=90){
                    my $aln = $hsp->get_aln;
                    my $alnIO = Bio::AlignIO->new(-format =>"msf", -file => ">hsp.msf");
                    $alnIO->write_aln($aln);
                    print   $result->query_name, "\t",
                      $hit->name, "\t",
                      $hsp->length('total'), "\t",
                      $hsp->percent_identity, "\t",
                      $hsp->start('query'), "\t",
                      $hsp->end('query'), "\t",
                      $hsp->start('hit'), "\t",
                      $hsp->end('hit'), "\t",
                      $alnIO, "\n";
            }
           elsif($hit->name =~ m/db_2/ && $hsp->length('hit')>=80){
                    my $aln = $hsp->get_aln;
                    my $alnIO = Bio::AlignIO->new(-format =>"msf", -file => ">hsp.msf");
                    $alnIO->write_aln($aln);
                    print   $result->query_name, "\t",
                      $hit->name, "\t",
                      $hsp->length('total'), "\t",
                      $hsp->percent_identity, "\t",
    ...
    Next thing I gave a try was Bio::SearchIO::Writer::HTMLResultWriter;
    Code:
    my $in = new Bio::SearchIO(     -format => 'blast', 
                                    -file   => $ARGV[0]);
    
    
    sub hsp_filter {
            my $hsp = shift;
            return 1 if ($hit->name =~ m/db_1/ && $hsp->length('hit')>=70);
            return 1 if ($hit->name =~ m/db_2/ && $hsp->length('hit')>=65);
     ...
    
    }
    
    my $writer = Bio::SearchIO::Writer::HTMLResultWriter ->new (-filters => {'HSP' => \&hsp_filter});
    my $out = Bio::SearchIO ->new (-writer =>$writer);
    $out ->write_result($in->next_result);
    The problem is, the syntax doesn't work. Of cause, because I mixed up hits and hsp. Is it possible to combine hit and hsp filters?

    I know, that this question is very specific. But maybe anybody struggles on similar issues parsing blast outputs, trying to filter them somehow and visualize the results. I hope I could make my problem clear and maybe anybody could give me a suggestion how to solve it.

    Thanks in advance!

    ps: it doesn't matter whether I parse xml, pure blast or tables, just want to get it to run

  • #2
    Okay, I fixed most of the issues... is anybody aware of how to write multiple panels in an output file using
    while( my $result = $searchio->next_result )
    with
    Bio::Graphics::Panel->new
    ??

    I will post my complete script, when I found a solution and am done

    Comment

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