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package Bio::MUST::Apps::OmpaPa::Blast;
# ABSTRACT: internal class for XML BLAST parser
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
$Bio::MUST::Apps::OmpaPa::Blast::VERSION = '0.201810';
use Moose;
use namespace::autoclean;
use autodie;
use feature qw(say);
use Smart::Comments;
extends 'Bio::FastParsers::Blast::Xml';
with 'Bio::MUST::Apps::OmpaPa::Roles::Parsable';
sub collect_hits {
    my $self = shift;
    my @hits;
    # parse BLAST report
    my $iter = $self->blast_output->next_iteration;
    my $qlen = $iter->query_len;
    while (my $hit = $iter->next_hit) {
        # split hit desc on Ctrl-A and keep only first line (nr database)
        # this is needed for table formatting as Ctrl-A has zero-width
        my ($desc) = split /\cA.*/xms, $hit->def;
        my $hsp = $hit->next_hsp;
        # collect useful hit/HSP attributes
        push @hits, {
            'acc'       => $hit->id,
            'dsc'       => $desc,
            'exp'       => $hsp->evalue,
            'bit'       => $hsp->bit_score,
            'qlen'      => $qlen,               # TODO: improve this
            'len'       => $hit->len,           # only available in XML format
            'hmm_from'  => $hsp->query_start,   # hmm to have the same annotation than hmmer
            'hmm_to'    => $hsp->query_end,
        };
    }
    return \@hits;
}
__PACKAGE__->meta->make_immutable;
1;
__END__
HideShow 37 lines of Pod
=pod
=head1 NAME
Bio::MUST::Apps::OmpaPa::Blast - internal class for XML BLAST parser
=head1 VERSION
version 0.201810
=head1 SYNOPSIS
    # TODO
=head1 DESCRIPTION
    # TODO
=head1 AUTHOR
Denis BAURAIN <denis.baurain@uliege.be>
=head1 CONTRIBUTOR
=for stopwords Amandine BERTRAND
Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
=head1 COPYRIGHT AND LICENSE
This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
=cut