File Coverage

blib/lib/Bio/FastParsers/Blast/Xml.pm

Criterion	Covered	Total	%
statement	23	23	100.0
branch	3	4	75.0
condition			n/a
subroutine	6	6	100.0
pod			n/a
total	32	33	96.9

package Bio::FastParsers::Blast::Xml;
# ABSTRACT: Front-end class for XML BLAST parser
# CONTRIBUTOR: Aymeric NAOME <[e-mail]>
$Bio::FastParsers::Blast::Xml::VERSION = '0.213510';
use Moose;
use namespace::autoclean;

use Carp;
use XML::Bare;

extends 'Bio::FastParsers::Base';

use aliased 'Bio::FastParsers::Blast::Xml::BlastOutput';

# TODO: check behavior with single iterations, hits or hsps

# public attributes (some inherited)



has 'blast_output' => (
    is       => 'ro',
    isa      => 'Maybe[Bio::FastParsers::Blast::Xml::BlastOutput]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_blast_output',
);

## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_blast_output {
    my $self = shift;

    my $file = $self->file;
    my $xb = XML::Bare->new( file => $file )
        or croak "Can't open '$file' for reading: $!";

    my $bo = $xb->parse->{'BlastOutput'};
    unless ($bo) {
        carp "Warning: '$file' unexpectedly empty; returning no BlastOutput!";
        return;
    }

    return BlastOutput->new( _root => $bo, _parent => undef);
}

## use critic


__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=head1 NAME

Bio::FastParsers::Blast::Xml - Front-end class for XML BLAST parser

=head1 VERSION

version 0.213510

=head1 SYNOPSIS

    use aliased 'Bio::FastParsers::Blast::Xml';

    # open and parse BLAST report in XML format
    my $infile = 'test/blastp.xml';
    my $report = Xml->new( file => $infile );

    # get main container
    my $bo = $report->blast_output;

    # examine report content
    say $bo->program;               # blastp
    say $bo->version;               # BLASTP 2.2.25+
    say $bo->db;                    # mcl-db-22species

    # get evalue threshold...
    say $bo->parameters->expect;    # 10

    # ...or equivalently
    my $param = $bo->parameters;
    say $param->expect;             # 10
    say $param->matrix;             # BLOSUM62

    # get the number of iterations (= queries)
    say $bo->count_iterations;      # 3

    # loop through iterations (or queries), hits and hsps
    # this is extremely fast because no data is moved around
    for my $iter ($bo->all_iterations) {
        say $iter->count_hits;      # always available!
        for my $hit ($iter->all_hits) {
            for my $hsp ($hit->all_hsps) {
                # ...
            }
        }
    }

    # ...or nearly equivalently (still ultra-fast)
    # here the container is altered by each iterator call
    while (my $iter = $bo->next_iteration) {
        say $iter->count_hits;      # here too!
        while (my $hit = $iter->next_hit) {
            while (my $hsp = $hit->next_hsp) {
                # ...
            }
        }
        say $iter->count_hits;      # 0 (exhausted)
    }

=head1 DESCRIPTION

This module implements a parser for the XML output format of the BLAST program
(e.g., C<-outfmt 5>). It provides methods for iterating over and querying all
elements of the XML tree. The hierarchy is as follows:

=over

=item L<Bio::FastParsers::Blast::Xml>

=item L<Bio::FastParsers::Blast::Xml::BlastOutput>

=item L<Bio::FastParsers::Blast::Xml::Statistics>

=item L<Bio::FastParsers::Blast::Xml::Parameters>

=item L<Bio::FastParsers::Blast::Xml::Iteration>'s

=item L<Bio::FastParsers::Blast::Xml::Hit>'s

=item L<Bio::FastParsers::Blast::Xml::Hsp>'s

=back

Documentation is autogenerated.

=head1 ATTRIBUTES

=head2 file

Path to BLAST report file in XML format to be parsed

=head2 blast_output

L<Bio::FastParsers::Blast::Xml::BlastOutput> composed object

=head1 AUTHOR

Denis BAURAIN <[e-mail]>

=head1 CONTRIBUTOR

=for stopwords Aymeric NAOME

Aymeric NAOME <[e-mail]>

=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