Jaime Prilusky

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).