File Coverage

blib/lib/Bio/FastParsers/CdHit.pm

Criterion	Covered	Total	%
statement	34	34	100.0
branch	8	10	80.0
condition			n/a
subroutine	5	5	100.0
pod	0	1	0.0
total	47	50	94.0

package Bio::FastParsers::CdHit;
# ABSTRACT: Front-end class for CD-HIT parser
# CONTRIBUTOR: Amandine BERTRAND <[e-mail]>
$Bio::FastParsers::CdHit::VERSION = '0.201110';
use Moose;
use namespace::autoclean;

use autodie;

use Tie::IxHash;

extends 'Bio::FastParsers::Base';


# public attributes (inherited)


with 'Bio::FastParsers::Roles::Clusterable';


sub BUILD {
    my $self = shift;

    my $cluster_like = qr{\>Cluster \s (\d+)}xms;
    my $repr_id_like = qr{\d+ \t \d+\w{2}\, \s \>([\w\|\.]+) .{4} \*      }xms;
    my $memb_id_like = qr{\d+ \t \d+\w{2}\, \s \>([\w\|\.]+) .{4} at .* \%}xms;

    my $infile = $self->filename;
    open my $in, '<', $infile;

    tie my %members_for, 'Tie::IxHash';

    my $repr_id;
    my @members;

    while (my $line = <$in>) {
        chomp $line;

        if ($line =~ $cluster_like){
            #### cluster: $line
            push @{ $members_for{$repr_id} }, @members
                if $repr_id;
            $repr_id = q{};
            @members = ();
            #### $repr_id
            #### @members
            #### %members_for
        }

        elsif ($line =~ $repr_id_like) {
            #### reference sequence: $line
            $repr_id = $1;
            #### $repr_id
        }

        # find other seq (array)
        elsif ($line =~ $memb_id_like){
            #### member sequence: $line
            my $memb_id = $1;
            push @members, $memb_id;
            #### @members
        }
    }

    push @{ $members_for{$repr_id} }, @members
        if $repr_id;
    #### %members_for

    # store representative and member sequence ids
    $self->_set_members_for( \%members_for );

    return;
}

__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=head1 NAME

Bio::FastParsers::CdHit - Front-end class for CD-HIT parser

=head1 VERSION

version 0.201110

=head1 SYNOPSIS

    use aliased 'Bio::FastParsers::CdHit';

    # open and parse CD-HIT report (cluster file)
    my $infile = 'test/cdHit.out.clstr';
    my $report = CdHit->new( file => $infile );

    # loop through representatives to get members
    for my $repr ( $report->all_representatives ) {
        my $members = $report->members_for($repr);
        # ...
    }

    # get representatives ordered by descending cluster size
    my @reprs = $report->all_representatives_by_cluster_size;

    # create IdMapper
    # Note: this requires Bio::MUST::Core
    my $mapper = $report->clust_mapper(':');
    my @long_ids = $mapper->all_long_ids;

    # ...

=head1 DESCRIPTION

This module implements a parser for the output file of the CD-HIT program. It
provides methods for getting the ids of the representative sequences (either
sorted by descending cluster size or not) and for obtaining the members of any
cluster from the id of its representative.

It also has a method for facilitating the re-mapping of all the ids of every
cluster on a phylogenetic tree through a L<Bio::MUST::Core::IdMapper> object.

=head1 ATTRIBUTES

=head2 file

Path to CD-HIT report file to be parsed

=head1 METHODS

=head2 all_representatives

Returns all the ids of the representative sequences of the clusters (not an
array reference).

    # $report is a Bio::FastParsers::CdHit
    for my $repr ( $report->all_representatives ) {
        # process $repr
        # ...
    }

This method does not accept any arguments.

=head2 all_representatives_by_cluster_size

Returns all the ids of the representative sequences of the clusters (not an
array reference) sorted by descending cluster size (and then lexically by id).

    # $report is a Bio::FastParsers::CdHit
    for my $repr ( $report->all_representatives_by_cluster_size ) {
        # process $repr
        # ...
    }

This method does not accept any arguments.

=head2 members_for

Returns all the ids of the member sequences of the cluster corresponding to
the id of the specified representative (as an array refrence).

    # $report is a Bio::FastParsers::CdHit
    for my $repr ( $report->all_representatives ) {
        my $members = $report->members_for($repr);
        # process $members ArrayRef
        # ...
    }

This method requires one argument: the id of the representative.

=head2 clust_mapper

Returns a L<Bio::MUST::Core::IdMapper> object associating representative
sequence ids to stringified full lists of their member sequence ids (including
the representatives themselves).

This method needs L<Bio::MUST::Core> to be installed on the computer.

    # $report is a Bio::FastParsers::CdHit
    my $mapper = $report->clust_mapper(':');

The native methods from L<Bio::MUST::Core::IdMapper> can be applied on
C<$mapper>, e.g., C<all_long_ids> or C<long_id_for>.

This method accepts an optional argument: the id separator (default: C</>).

=head1 AUTHOR

Denis BAURAIN <[e-mail]>

=head1 CONTRIBUTOR

=for stopwords Amandine BERTRAND

Amandine BERTRAND <[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