Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::Sequence

Download:
Bio-DOOP-DOOP-1.02.tar.gz

Dependencies

Annotate this POD

View/Report Bugs
Module Version: 0.12   Source   Latest Release: Bio-DOOP-DOOP-1.04

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

  Returns the sequence primary id. This is the internal ID from the MySQL database.

get_fake_id

  Returns the sequence fake GI.

get_db_id

  Returns the full sequence ID.

get_length

  Returns the length of the sequence.

get_date

  Returns the modification date of the MySQL record.

get_ver

  Returns the version of the sequence.

get_annot_id

  Returns the sequence annotation primary id. This is the internal ID from the MySQL database.

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.

get_taxon_id

  Returns the taxon annotation primary id. This is the internal ID from the MySQL database.

get_data_main_db_id

  Returns the sequence annotation primary id. This is the internal ID from the MySQL database.

get_utr_length

  $utr_length = $seq->get_utr_length;

  Returns the length of the 5' UTR included in the sequence.

get_desc

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

  Returns the description of the sequence.

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.

get_fasta

  print $seq->get_fasta;

  Returns the promoter sequence in FASTA format.

get_raw_seq

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

get_blast

  print $seq->get_blast;

  This method is not yet implemented.

get_taxid

  $taxid = $seq->get_taxid;

  Returns the NCBI taxon ID of the sequence.

get_taxon_name

  print $seq->get_taxon_name;

  Returns the scientific name of the sequence's taxon ID.

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.

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

  TODO : sometimes it gives back duplicated data

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

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

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

get_all_subsets

  Returns the subset containing the sequence.
syntax highlighting: