Jaime Prilusky > Bio-Maxd > Bio::Maxd

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Module Version: 0.04   Source  

NAME ^

Bio::Maxd - Perl extension for storing and retrieving data from maxd

SYNOPSIS ^

  use Bio::Maxd;
  my $maxd_db = new Bio::Maxd (-user=>'user', -pass=>'pass', 
                               -host=>'host', -dbase=>'database');
  $maxd_db->load_file(-file=>'path_to_data_file',
                  -experiment=>'experimentName', -array_type=>'geneChipName');
  $maxd_db->disconnect();

DESCRIPTION ^

Bio::Maxd provides methods for uploading and retrieving data to/from a maxd (MySQL) database.

"maxd" is a data warehouse and visualization environment for microarray expression data developed by the Microarray Group at Manchester Bioinformatics (http://www.bioinf.man.ac.uk/microarray/)

Bio::Maxd METHODS

new(), This is the constructor for Bio::Maxd.

 my $maxd_db = new Bio::Maxd();

This is the constructor for Bio::Maxd. It establishes a database connection, or session, to the requested database. Parameters:

-user and -pass, default to $ENV{'MAXD_USERID'} with user/password.
-host, defaults to $ENV{'MAXD_DBHOST'}, hostname or "localhost".
-dbase, defaults to 'maxd'.
-verbose, defaults to false.

load_file(), Parses and loads a datafile into a maxd database..

-file, datafile to parse.
-format, data file format; Bio::Maxd will guess it, if not provided. Valid values are 'AFF' (Affimetrix matrics file)
-experiment, Experiment ID or Experiment name.
-array_type, ArrayType ID or ArrayType name

export(), Exports data from maxd database..

-verbose, reports activity.
-format, desired format for the data to be exporte to. Valid values are 'GeneSpring'.
-submitter, submitter name or id.
-experiment, experiment name or id.
-array_type, array name, i.e. 'HG-U95A2'
-repository_URL, where to install files.
-image, image name or id.
-hybridisation, hybridisation name or id.

MISCELLANEOUS ^

version() Returns Bio::Maxd version

$ENV{'MAXD_USERID'}, contains userid/password

$ENV{'MAXD_HOSTDB'}, contains database host

$ENV{'MAXD_TEMPLATES'}, directory for export templates

EXAMPLES ^

  use Bio::Maxd;
  my $maxd_db = new Bio::Maxd (-user=>'user', -pass=>'pass',
                               -host=>'host', -dbase=>'database');
  $maxd_db->load_file(-file=>'path_to_data_file',
                  -experiment=>'experimentName', -array_type=>'geneChipName');
  $maxd_db->disconnect();

See the 'examples' directory in the distribution for scripts loadData and exportData

EXPORT ^

None by default.

KNOWN BUGS ^

None, but that does not mean there are not any.

COPYRIGHT ^

Copyright (C) 2002 Jaime Prilusky. All rights reserved.

AUTHOR ^

Jaime Prilusky <Jaime.Prilusky@weizmann.ac.il>

SEE ALSO ^

perl(1).

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