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

$Revision: $

  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

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.

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

Run ProServer with the -debug flag.

See documentation in superclass.

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

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

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

http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED BED format

Bio::Das::ProServer::SourceAdaptor

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

Carp

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

None reported.

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

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.