/ 
Bio-DOOP-DOOP-0.29
/ Bio::DOOP::Sequence

NAME

Bio::DOOP::Sequence - promoter sequence object

VERSION

Version 0.12

SYNOPSIS

DESCRIPTION

This object represents a specific promoter in the database.
You can access the annotation and the sequence through this object.

AUTHORS

Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

METHODS

new

$seq = Bio::DOOP::Sequence->new($db,"1234");
The arguments are the following : Bio::DOOP::DBSQL object, sequence_primary_id

new_from_dbid

Create new objects form sequence primary id.

get_id

$sequence_id = $sequence->get_id;

Returns the sequence primary id. This is the internal ID from the MySQL database.
Return type : string

get_fake_id

$fake_id = $sequence->get_fake_id;

Returns the sequence fake GI.
Return type : string

get_db_id

$db_id = $sequence->get_db_id;

Returns the full sequence ID.
Return type : string

get_length

$length = $sequence->get_length;

Returns the length of the sequence.
Return type : string

get_date

$date = $sequence->get_date;

Returns the modification date of the MySQL record.
Return type : string

get_ver

$version = $sequence->get_ver;

Returns the version of the sequence.
Return type : string

get_annot_id

$annotation_id = $sequence->get_annot_id;

Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type : string

get_orig_id

This method is not yet implemented.

get_data_id

$data_id = $sequence->get_data_id;

Returns the sequence data primary id. This is the internal ID from the MySQL database.
Return type : string

get_taxon_id

$taxon_id = $sequence->get_taxon_id;

Returns the taxon annotation primary id. This is the internal ID from the MySQL database.
Return type : string

get_data_main_db_id

$data_main_db_id = $sequence->get_data_main_db_id;

Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type : string

get_utr_length

$utr_length = $seq->get_utr_length;

Returns the length of the 5' UTR included in the sequence.
Return type : string

get_desc

print $seq->get_desc,"\n";

Returns the description of the sequence.
Return type : string

get_gene_name

$gene_name = $seq->get_gene_name;

Returns the gene name of the promoter. If the gene is
unknow or not annotated, it is empty.
Return type : string

get_fasta

print $seq->get_fasta;

Returns the promoter sequence in FASTA format.
Return type : string

get_raw_seq

print $seq->get_raw_seq;

Returns the raw sequence without any other identifier
Return type: string

get_blast

This method is not yet implemented.

get_taxid

$taxid = $seq->get_taxid;

Returns the NCBI taxon ID of the sequence.
Return type : string

get_taxon_name

print $seq->get_taxon_name;

Returns the scientific name of the sequence's taxon ID.
Return type : string

get_taxon_class

print $seq->get_taxon_class;

Returns the taxonomic class of the sequence's taxon ID.
Used internally, to create monophyletic sets of sequences
in an orthologous cluster.
Return type : string
$seq->print_all_xref;

Prints all the xrefs to other databases.
Type of xref IDs : 
go_id            : Gene Ontology ID
ncbi_gene_id     : NCBI gene ID
ncbi_cds_gi      : NCBI CDS GI
ncbi_rna_gi      : NCBI RNA GI
ncbi_cds_prot_id : NCBI CDS protein ID
ncbi_rna_tr_id   : NCBI RNA transcript ID
at_no            : At Number

get_all_xref_keys

@keys = @{$seq->get_all_xref_keys};

Returns the arrayref of xref names.

get_xref_value

@values = @{$seq->get_xref_value("go_id")};

Returns the arrayref of a given xref's values'.

get_all_seq_features

@seqfeats = @{$seq->get_all_seq_features};

Returns the arrayref of all sequence features or -1 in case of error.

get_all_subsets

@subsets = @{$seq->get_all_subsets};

Returns the subsets containing the sequence.
Return type : arrayref, the array containig Bio::DOOP::ClusterSubset objects