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Bio-Das-ProServer-2.9
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/ Bio::Das::ProServer::SourceAdaptor::Transport::bed12

NAME

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

VERSION

$Revision: 548 $

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.