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=head1 NAME

Bio::Das::ProServer::SourceAdaptor::Transport::bed12 - DBI-like access to a BED file

=head1 VERSION

$Revision: 688 $

=head1 SYNOPSIS

  my $rows = $oTransport->query('select * from example.bed where chrom = chr1');

=head1 DESCRIPTION

Transport helper class for BED file access, implemented as an extension to
Bio::Das::ProServer::SourceAdaptor::Transport::csv.

This transport is used by the Bio::Das::ProServer::SourceAdaptor::bed12 adaptor.

=head1 SUBROUTINES/METHODS

=head2 init - Initialises the CSV file with BED-specific functions

  1. Sets the appropriate BED column names.
  2. Sets the number of header lines to be skipped.

  $bedtransport->init();

=head1 DIAGNOSTICS

Run ProServer with the -debug flag.

=head1 CONFIGURATION AND ENVIRONMENT

  [mysource]
  state      = on
  transport  = bed12
  path       = /data/
  filename   = example.bed

=head1 DEPENDENCIES

=over

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::csv|Bio::Das::ProServer::SourceAdaptor::Transport::csv>

=item L<DBI|DBI>

=item L<Carp|Carp>

=back

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

BED is mapped to DAS in the following manner:

1. The BED format allows for "blocks" within each line. Where these are present
   it is assumed that the line represents a group of features, with each block
   representing a single feature within the group. Lines without blocks are
   treated as if they contain a single full-length block.

2. DAS fields are mapped from BED fields as follows:
   
   segment    = <chrom> (minus the "chr" prefix)
   start      = <chromStart> + 1
   end        = <chromEnd>
   ori        = <strand>
   score      = <score>
   group_id   = <name>
   feature_id = <name>:blocknum
   type       = <name>
   method     = string "BED conversion"

3. Browser and track configurations are not parsed because DAS has different
   ways of defining many of these attributes - namely coordinate systems and
   stylesheets. If you wish to define a stylesheet, set the 'stylesheetfile'
   INI property to the path of a suitable DAS stylesheet XML document.

=head1 SEE ALSO

=over

=item L<Bio::Das::ProServer::SourceAdaptor::bed12|Bio::Das::ProServer::SourceAdaptor::bed12>

=item L<http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED|http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED> BED format

=back

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2008 EMBL-EBI

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

=cut