NAME
Bio::DOOP::Sequence - Sequence (promoter region) object
VERSION
Version 0.13
SYNOPSIS
DESCRIPTION
This object represents a specific promoter sequence 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
Creates a new sequence object from the sequence primary id.
Return type: Bio::DOOP::Sequence object
$seq = Bio::DOOP::Sequence->new($db,"1234");new_from_dbid
Creates a new sequence object from the full sequence id which contains the following:
17622344 - 81001020 _ 3712 _ 118 - 617 _ 3 _ + | | | | | | | GI/fakeGI | | | | | | | | | | | | clusterID____| | | | | | taxID___________________| | | | | start_________________________| | | | end_________________________________| | | type_____________________________________| | strand_______________________________________|
Return type: Bio::DOOP::Sequence object
$seq = Bio::DOOP::Sequence->new_from_dbid($db,"17622344-81001020_3712_118-617_3_+");get_id
Returns the sequence primary id. This is the internal ID from the MySQL database.
Return type: string
my $id = $seq->get_id;get_fake_id
Returns the sequence GI or a fake GI if no real GI is available.
Return type: string
my $id = $seq->get_fake_id;get_db_id
Returns the full sequence ID, described at the new_from_dbid method.
Return type: string
my $id = $seq->get_db_id;get_length
Returns the length of the sequence.
Return type: string
my $length = $seq->get_length;get_date
Returns the last modification date of the MySQL record.
Return type: string
my $date = $seq->get_date;get_ver
Returns the version of the sequence.
Return type: string
my $version = $seq->get_ver;get_annot_id
Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type: string
my $annotation_id = $seq->get_annot_id;get_orig_id
This method is not yet implemented.
get_data_id
Returns the sequence data primary id. This is the internal ID from the MySQL database.
Return type: string
my $data_id = $seq->get_data_id;get_taxon_id
Returns the taxon annotation primary id. This is the internal ID from the MySQL database.
Return type: string
my $taxon_id = $seq->get_taxon_id;get_data_main_db_id
Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type: string
my $annotation_id = $seq->get_data_main_db_id;get_utr_length
Returns the length of the 5' UTR included in the sequence.
Return type: string
$utr_length = $seq->get_utr_length;get_desc
Returns the description of the sequence.
Return type: string
print $seq->get_desc,"\n";get_gene_name
Returns the gene name of the promoter. If the gene is unknow or not annotated, it is empty.
Return type: string
$gene_name = $seq->get_gene_name;get_fasta
Returns the promoter sequence in FASTA format.
Return type: string
print $seq->get_fasta;get_raw_seq
Returns the raw sequence without any other identifier.
Return type: string
my $rawseq = $seq->get_raw_seq;get_blast
This method is not yet implemented.
get_taxid
Returns the NCBI taxon ID of the sequence.
Return type: string
$taxid = $seq->get_taxid;get_taxon_name
Returns the scientific name of the sequence's taxon ID.
Return type: string
print $seq->get_taxon_name;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 $seq->get_taxon_class;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
TODO : sometimes it gives back duplicated data
$seq->print_all_xref;get_all_xref_keys
Returns the arrayref of xref names.
Return type: arrayref, the array containing strings (xref names)
@keys = @{$seq->get_all_xref_keys};get_xref_value
Returns the arrayref of a given xref's values'.
Return type: arrayref, the array containg strings (xref values)
@values = @{$seq->get_xref_value("go_id")};get_all_seq_features
Returns the arrayref of all sequence features or -1 in the case of an error.
Return type: arrayref, the array containing Bio::DOOP::SequenceFeature objects
@seqfeat = @{$seq->get_all_seq_features};get_all_subsets
Returns all subsets which contain the sequence.
Return type: arrayref, the array containing Bio::DOOP::ClusterSubset objects
@subsets = @{$seq->get_all_subsets};