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Bio::Parser::Homologene::Record

[source code]
NAME
SYNOPSIS
DESCRIPTION
PUBLIC METHODS
Constructor Methods
Accessor Methods
Inherited from Bio::Parser::Record
SEE ALSO
AUTHORS
COPYRIGHT

NAME

Bio::Parser::Homologene::Record - Homologene Record

SYNOPSIS

  use Bio::Parser::Homologene::FileParser;

  $hml = 'homologene.data';
  $parser = Bio::Parser::Homolgene::FileParser->new( -file => $hml );
  $parser->object_mode(1);

  $hrec = $parser->next_record();
  $a = $hrec->HID();
  @a = @{ $hrec->members() };

  while (my $hrec = $parser->next_record) {
      print "HID     ", $hrec->HID, "\n";
      print join( "\t", $_->{taxID},
                        $_->{geneID},
                        $_->{symbol},
                        $_->{prot_gi},
                        $_->{accessn} ), "\n"
            foreach @{ $hrec->members };
  }

This module is used by Bio::Parser::Homologene::FileParser as a data container to store all of the data for a single Homologene record. It is not designed for standalone use and consequently it only has "get" accessor methods and no "set" accessor methods.

PUBLIC METHODS

Constructor Methods

new()

This is not very useful in practice as the lack of set accessor methods pretty much rules out creating your own Homologene records. Maybe later.

Accessor Methods

Homologene records consist of an ID (see HID()) and a collection of members, each of which has a number of attributes.

HID()

  my $id = $hrec->HID();

The Homologene ID for this record.

members()

  my $ra_members = $hrec->members();
  my @members = @{ $hrec->members() };

Each item in the members array is a hash containing information about a sequence that is a member of this Homologene record. Each member has the attributes shown in this example:

  { 'geneID'  => '34',
    'taxID'   => '9606',
    'symbol'  => 'ACADM',
    'prot_gi' => '4557231',
    'accessn' => 'NP_000007.1' }

Inherited from Bio::Parser::Record

These 2 methods do not return values that are part of the record itself. They relate to values set during the process of serializing the Homologene database. prev_id and next_id return the Homologene ID numbers of the records that occurred immediately before and immediately after the current record in the original homologene.data text file distributed by NCBI.

prev_id()

next_id()

AUTHORS

John Pearson, bioinfresearch@tgen.org
Carol Barner

COPYRIGHT

BioParser is copyright 2005-7 by The Translational Genomics Research Institute. All rights reserved. This License is limited to, and you may use the Software solely for, your own internal and non-commercial use for academic and research purposes. Without limiting the foregoing, you may not use the Software as part of, or in any way in connection with the production, marketing, sale or support of any commercial product or service or for any governmental purposes. For commercial or governmental use, please contact licensing@tgen.org. By installing this Software you are agreeing to the terms of the LICENSE file distributed with this software.

In any work or product derived from the use of this Software, proper attribution of the authors as the source of the software or data must be made. The following URL should be cited:

http://bioinformatics.tgen.org/software/bioparser/