NAME
Bio::Das::ProServer::SourceAdaptor::bed12
VERSION
$Revision: $
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=TRAN1:4DESCRIPTION
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:1,100DIAGNOSTICS
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
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.