Author image Endre Sebestyen
and 1 contributors

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;

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};