NAME

Bio::Das::ProServer::SourceAdaptor::bed12

VERSION

$Revision: 688 $

SYNOPSIS

  Features by segment:
  <host>/das/<source>/features?segment=X:1,100
  
  Features by group ID:
  <host>/das/<source>/features?group_id=TRAN1
  
  Features by feature ID:
  <host>/das/<source>/features?feature_id=TRAN1:4

DESCRIPTION

Serves up features DAS responses from BED files. See http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED for details of the file format.

The BED and DAS formats contain an intersection of information. That is, not all DAS fields are supported in BED, and vice versa. In order to be adapted to the DAS protocol, some basic assumptions need to be made and some configurability is lost. See the BUGS AND LIMITATIONS section for more details.

CONFIGURATION AND ENVIRONMENT

  [mybed]
  state       = on
  adaptor     = bed12
  path        = /data/
  filename    = example.bed
  ; coordinates -> test segment
  coordinates = NCBI_36,Chromosome,Homo sapiens -> X:1,100

DIAGNOSTICS

Run ProServer with the -debug flag.

SUBROUTINES/METHODS

build_features - Builds the DAS response

See documentation in superclass.

capabilities - Provides details of the adaptor's capabilities

This adaptor supports the 'features' command, including the 'feature-by-id' and 'group-by-id' variants.

init - Initialises the SourceAdaptor

Adds the 'bed12' transport to the source's configuration (if not already set).

SEE ALSO

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

DEPENDENCIES

Bio::Das::ProServer::SourceAdaptor
Bio::Das::ProServer::SourceAdaptor::Transport::bed12
Carp

BUGS AND LIMITATIONS

See the BUGS AND LIMITATIONS section of Bio::ProServer::SourceAdaptor::Transport::bed12 for details.

INCOMPATIBILITIES

None reported.

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.