Bio::DOOP::SequenceFeature - Object for the sequence features
Index
Code Index:
NAME
Bio::DOOP::SequenceFeature - Object for the sequence features
VERSION
SYNOPSIS
my $seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
my $type = $seqfeat->get_type;
DESCRIPTION
This object gives access to the sequence features (conserved motif, repeat, CpG island,
TFBS and TSS annotation).
AUTHORS
Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary
METHODS
new
Creates a new sequence feature object from the sequence feature primary id.
Return type: Bio::DOOP::SequenceFeature object
$seqfeat = Bio::DOOP::SequenceFeature->new($db,"112");
get_id
Returns the primary ID of the feature. This is the internal ID from the MySQL database.
get_score
This method is not yet implemented.
get_start
Returns the start position of the feature.
get_end
Returns the end position of the feature.
length
Returns the length of the feature.
get_seq
Returns the sequence of the feature.
get_type
Returns the type of the feature. (con, ssr, tfbs, rep, cpg, tss).
con : evolutionary conserved non-coding region
ssr : simple sequence repeat
tfbs : transcription factor binding site
rep : repeat
cpg : cpg island
tss : transcription start site
get_motifid
Returns the motif primary ID, if the feature type is "con".
get_tfbsid
Returns the tfbs primary ID, if the feature type is "tfbs".
get_cpgid
Returns the cpg primary ID, if the feature type is "cpg".
get_repeatid
Returns the repeat primary ID, if the feature type is "rep".
get_ssrid
Returns the ssr primary ID, if the feature type is "ssr".
get_tssid
Returns the tss primary ID, if the feature type is "tss".
get_seqid
Returns the primary ID of the sequence containing this feature.
get_subsetid
Returns the subset primary ID of the feature, if the feature type is "con".
get_motif
Returns the motif object associated with the feature.
If the feature type is not "con" this value is NULL.
get_tss_type
Returns the tss type, if the feature type is "tss".
get_tss_id
Returns the tss id, if the feature type is "tss".
get_tss_desc
Returns the description of the tss, if the feature type is "tss".
get_tss_xref
Returns the xref of the tss, if the feature type is "tss".
package Bio::DOOP::SequenceFeature;
use strict;
use warnings;
our $VERSION = '0.10';
sub new {
my $self = {};
my $dummy = shift;
my $db = shift;
my $id = shift;
my $ret = $db->query("SELECT * FROM sequence_feature WHERE sequence_feature_primary_id = \"$id\";");
if ($#$ret == -1) {
return(-1);
}
my @fields = @{$$ret[0]};
$self->{PRIMARY} = $fields[0];
$self->{SCORE} = $fields[1];
$self->{START} = $fields[2];
$self->{END} = $fields[3];
$self->{SEQ} = $fields[4];
$self->{TYPE} = $fields[5];
$self->{MOTIFID} = $fields[6];
$self->{TFBSID} = $fields[7];
$self->{CPGID} = $fields[8];
$self->{REPEATID} = $fields[9];
$self->{SSRID} = $fields[10];
$self->{TSSID} = $fields[11];
$self->{SUBSET_ID} = $fields[12];
$self->{SEQ_ID} = $fields[13];
if ($self->{TYPE} eq "ssr"){
$ret = $db->query("SELECT * FROM ssr_annotation WHERE ssr_primary_id = \"".$self->{SSRID}."\";");
@fields = @{$$ret[0]};
$self->{SSRUNIT} = $fields[1];
}
elsif ($self->{TYPE} eq "rep"){
$ret = $db->query("SELECT * FROM repeat_annotation WHERE repeat_primary_id = \"".$self->{REPEATID}."\";");
@fields = @{$$ret[0]};
$self->{R_NAME} = $fields[1];
$self->{R_CLASS} = $fields[2];
$self->{R_DESC} = $fields[3];
$self->{R_XREF} = $fields[4];
}
elsif ($self->{TYPE} eq "tfbs"){
$ret = $db->query("SELECT * FROM tfbs_annotation WHERE tfbs_primary_id = \"".$self->{TFBSID}."\";");
@fields = @{$$ret[0]};
$self->{TF_NAME} = $fields[1];
$self->{TF_ORIG} = $fields[2];
$self->{TF_DESC} = $fields[3];
$self->{TF_TYPE} = $fields[4];
$self->{TF_CONS} = $fields[5];
$self->{TF_MTRX} = $fields[6];
$self->{TF_XREF} = $fields[7];
}
elsif ($self->{TYPE} eq "cpg"){
$ret = $db->query("SELECT * FROM cpg_annotation WHERE cpg_primary_id = \"".$self->{CPGID}."\";");
@fields = @{$$ret[0]};
$self->{CPG_P} = $fields[1];
}
elsif ($self->{TYPE} eq "tss"){
$ret = $db->query("SELECT * FROM tss_annotation WHERE tss_primary_id = \"".$self->{TSSID}."\";");
@fields = @{$$ret[0]};
$self->{T_TYPE} = $fields[1];
$self->{T_ID} = $fields[2];
$self->{T_DESC} = $fields[3];
$self->{T_XREF} = $fields[4];
}
elsif ($self->{TYPE} eq "con"){
my $motif = Bio::DOOP::Motif->new($db,$self->{MOTIFID});
$self->{MOTIF} = $motif;
}
bless $self;
return($self);
}
sub get_id {
my $self = shift;
return($self->{PRIMARY});
}
sub get_score {
my $self = shift;
return($self->{SCORE});
}
sub get_start {
my $self = shift;
return($self->{START});
}
sub get_end {
my $self = shift;
return($self->{END});
}
sub length {
my $self = shift;
return($self->{END} - $self->{START} + 1);
}
sub get_seq {
my $self = shift;
return($self->{SEQ});
}
sub get_type {
my $self = shift;
return($self->{TYPE});
}
sub get_motifid {
my $self = shift;
return($self->{MOTIFID});
}
sub get_tfbsid {
my $self = shift;
return($self->{TFBSID});
}
sub get_cpgid {
my $self = shift;
return($self->{CPGID});
}
sub get_repeatid {
my $self = shift;
return($self->{REPEATID});
}
sub get_ssrid {
my $self = shift;
return($self->{SSRID});
}
sub get_tssid {
my $self = shift;
return($self->{TSSID});
}
sub get_seqid {
my $self = shift;
return($self->{SEQ_ID});
}
sub get_subsetid {
my $self = shift;
return($self->{SUBSET_ID});
}
sub get_motif {
my $self = shift;
return($self->{MOTIF});
}
sub get_tss_type {
my $self = shift;
return($self->{T_TYPE});
}
sub get_tss_id {
my $self = shift;
return($self->{T_ID});
}
sub get_tss_desc {
my $self = shift;
return($self->{T_DESC});
}
sub get_tss_xref {
my $self = shift;
return($self->{T_XREF});
}
1;