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Module detail: Database.pm |
ArrayExpress::Curator::Database - a module used by expt_check.pl
use ArrayExpress::Curator::Database qw(retrieve_AE_adf parse_adf);
my $db_id = 123456789; my ( $fh, $accession ) = retrieve_AE_adf( $db_id, undef, \*STDERR, 0 ); my $array_design = parse_adf( $fh, $accession );
This module provides a set of subroutines used by the experiment checker script to interact with the ArrayExpress databases. Queries may be redirected to local ArrayExpress instances by editing values in the the ArrayExpress::Curator::Config manpage package.
get_ae_dbh()Returns a singleton database handle for the currently-configured ArrayExpress repository database instance.
get_aedw_dbh()Returns a singleton database handle for the currently-configured ArrayExpress warehouse database instance.
retrieve_AE_adf( $db_id, $accession,
$error_fh, $skip_adf_download )Given either AE database table row identifier or AE accession, an open filehandle for error reporting and a flag indicating whether the ADF should be downloaded, check for the existence of said ADF (by database id or accession), download it and return an opened filehandle and the accession number (the latter is useful when querying by database id).
retrieve_AE_featurelist(
$accession )Given an array accession number, return a hashref where the keys are q{.}-delimited lists of MetaColumn.MetaRow.Column.Row feature coordinates, and the values are Reporter identifiers.
parse_adf( $adf_fh, $accno,
$reporter_prefix, $compseq_prefix )Passed an ADF filehandle and an accession number (see retrieve_AE_adf()), and optional Reporter or Composite Sequence identifier prefixes, parse the ADF and return an ArrayDesign object (see the ArrayExpress::Datafile::ArrayDesign manpage).
arrayaccession_in_aedw(
$accession )Given an array design accession number, return true if the design is loaded into the currently-configured AE data warehouse, false otherwise.
map_affy_accno_to_name(
$accession )Given an array design accession number, attempt to match it to an Affymetrix design name. This relies on the names of loaded Affy array designs including the design name (e.g. HG-U133A) in square brackets (e.g. ``Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]'').
Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2008.
Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.