Roger Pettett > Bio-Das-ProServer > Bio::Das::ProServer::SourceAdaptor::Transport::bed12

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Module Version: 688   Source  

NAME ^

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

VERSION ^

$Revision: 688 $

SYNOPSIS ^

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

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.

SUBROUTINES/METHODS ^

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();

DIAGNOSTICS ^

Run ProServer with the -debug flag.

CONFIGURATION AND ENVIRONMENT ^

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

DEPENDENCIES ^

Bio::Das::ProServer::SourceAdaptor::Transport::csv
DBI
Carp

INCOMPATIBILITIES ^

None reported.

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.

SEE ALSO ^

Bio::Das::ProServer::SourceAdaptor::bed12
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED BED format

AUTHOR ^

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

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.

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