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
print_all_xref
$seq->print_all_xref;
Prints all the xrefs to other databases.
Type of xref IDs :
go_id : Gene Ontology ID
ncbi_gene_id : NCBI gene ID
ncbi_cds_gi : NCBI CDS GI
ncbi_rna_gi : NCBI RNA GI
ncbi_cds_prot_id : NCBI CDS protein ID
ncbi_rna_tr_id : NCBI RNA transcript ID
at_no : At Number
get_all_xref_keys
@keys = @{$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