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package Bio::DOOP::Util::Filt; |
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use strict; |
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use warnings; |
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=head1 NAME |
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Bio::DOOP::Util::Filt - Filter a cluster list |
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=head1 VERSION |
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Version 0.3 |
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=cut |
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our $VERSION = '0.3'; |
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=head1 SYNOPSIS |
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use Bio::DOOP::DOOP; |
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@list = ("81001020","81001110","81001200","80100006"); |
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$db = Bio::DOOP::DBSQL->connect("username","passwd","doop-chordate-1_4","localhost"); |
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$filt = Bio::DOOP::Util::Filt->new_by_list($db,\@list,500); |
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@res = @{$filt->filt_by_goid("0046872")}; |
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for(@res){ |
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print $_->get_cluster_id,"\n"; |
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} |
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=head1 DESCRIPTION |
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This object filters a clusterlist. It is useful to find a smaller cluster set from a |
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large mofext or fuzznuc search result. |
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=head1 AUTHORS |
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Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary |
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=head1 METHODS |
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=head2 new |
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Creates a new filter object from a cluster object array. |
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=cut |
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sub new { |
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my $self = {}; |
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my $dummy = shift; |
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my $db = shift; |
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my $clarray = shift; |
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my $prom = shift; |
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$self->{CLARRAY} = $clarray; |
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$self->{DB} = $db; |
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$self->{PROM} = $prom; |
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bless $self; |
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return($self); |
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} |
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=head2 new_by_list |
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Creates a new filter class from a cluster id array. |
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=cut |
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sub new_by_list { |
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my $self = {}; |
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my $dummy = shift; |
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my $db = shift; |
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my $clarray_id = shift; |
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my $prom = shift; |
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my @clarray; |
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for my $id (@{$clarray_id}){ |
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my $cl = Bio::DOOP::Cluster->new($db,$id,$prom); |
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if ($cl == -1){ |
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next; |
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} |
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push @clarray,$cl; |
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} |
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$self->{CLARRAY} = \@clarray; |
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$self->{DB} = $db; |
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$self->{PROM} = $prom; |
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bless $self; |
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return($self); |
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} |
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=head2 new_by_id |
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Creates a new filter class from a cluster primary id array. |
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=cut |
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sub new_by_id { |
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my $self = {}; |
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my $dummy = shift; |
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my $db = shift; |
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my $clarray_id = shift; |
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my @clarray; |
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for my $id (@{$clarray_id}){ |
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my $cl = Bio::DOOP::Cluster->new_by_id($db,$id); |
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if ($cl == -1){ |
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next; |
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} |
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push @clarray,$cl; |
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} |
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$self->{CLARRAY} = \@clarray; |
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$self->{DB} = $db; |
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bless $self; |
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return($self); |
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} |
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=head2 filt_by_goid |
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Filter the cluster list by GO ids. |
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@filtered = @{$filt->filt_by_goid("0006523")}; |
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=cut |
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sub filt_by_goid { |
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my $self = shift; |
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my $goid = shift; |
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my @cl = @{$self->{CLARRAY}}; |
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my @ret; |
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CLUSTER:for my $cl (@cl){ |
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my @seqs = @{$cl->get_all_seqs}; |
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for my $seq (@seqs){ |
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my $goids = $seq->get_xref_value("go_id"); |
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if ($goids == -1){next} |
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for my $id (@{$goids}){ |
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if ($id eq $goid){ |
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push @ret,$cl; |
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next CLUSTER; |
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} |
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} |
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} |
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} |
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return(\@ret); |
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} |
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1; |