Bio::Das::ProServer::SourceAdaptor::Transport::bed12 - DBI-like access to a BED file
$Revision: 688 $
my $rows = $oTransport->query('select * from example.bed where chrom = chr1');
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.
1. Sets the appropriate BED column names. 2. Sets the number of header lines to be skipped. $bedtransport->init();
Run ProServer with the -debug flag.
[mysource] state = on transport = bed12 path = /data/ filename = example.bed
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.
Andy Jenkinson <email@example.com>
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.