Jessica Michelle Severin

NAME - EEDB::Feature

SYNOPSIS

DESCRIPTION

CONTACT

Jessica Severin <severin@gsc.riken.jp>

LICENSE

 * Software License Agreement (BSD License)
 * EdgeExpressDB [eeDB] system
 * copyright (c) 2007-2009 Jessica Severin RIKEN OSC
 * All rights reserved.
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
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 *     * Redistributions in binary form must reproduce the above copyright
 *       notice, this list of conditions and the following disclaimer in the
 *       documentation and/or other materials provided with the distribution.
 *     * Neither the name of Jessica Severin RIKEN OSC nor the
 *       names of its contributors may be used to endorse or promote products
 *       derived from this software without specific prior written permission.
 *
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APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

fetch_all_by_chrom

  Description     : uses an EEDB::Chrom object to stream all features in sorted order by chrom start,end
  Parameter[1]    : EEDB::Chrom object with database connection 
  Parameter[2...] : optional EEDB::FeatureSource(s) to limit the feature stream
  Returntype      : array reference of EEDB::Feature objects 
  Exceptions      : die if anything other than EEDB::FeatureSource(s) are passed in the optional parameter list

stream_all

  Description: stream all features out of database with a given set of source filters
  Arg (1)    : $database (MQdb::Database)
  Arg (2...) : hash named filter parameters. 
                 sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
  Returntype : a DBStream instance
  Exceptions : none 

stream_by_chrom

  Description     : uses an EEDB::Chrom object to stream all features in sorted order by chrom start,end
                    Useful for feeding features into EEDB::Tools::OverlapCompare2
  Arg [1]         : EEDB::Chrom object with database connection 
  Arg (2...)      : hash named filter parameters. 
                      sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
  Returntype      : MQdb::DBStream object 
  Exceptions      : die if anything other than EEDB::FeatureSource(s) are passed in the optional parameter list
  Example         :   
                    my $chroms = EEDB::Chrom->fetch_all_by_assembly($assembly);
                    foreach my $chrom (@$chroms) {
                      my $stream  = EEDB::Feature->stream_by_chrom($chrom, sources=>[$fsrc1, $fsrc2]);
                      my $feature1 = $stream1->next_in_stream;
                      while($feature1) {
                        #do something
                        $feature1 = $stream1->next_in_stream;
                      }
                    }

stream_by_named_region

  Description: stream all features from a specific region on a genome
               with a given set of source filters
  Arg (1)    : $database (MQdb::Database)
  Arg (2)    : $assembly_name (string)
  Arg (3)    : $chrom_name (string)
  Arg (4)    : $chrom_start (integer)
  Arg (5)    : $chrom_end (integer)
  Arg (6...) : hash named filter parameters. 
                 sources=>[$fsrc1, $fsrc2,$fsrc3],  instances of EEDB::FeatureSource
  Returntype : a DBStream instance
  Exceptions : none 

stream_all_by_source

  Description: stream all features from a single FeatureSource
  Arg (1)    : $sourcedatabase (EEDB::FeatureSource with database)
  Returntype : a DBStream instance
  Exceptions : none 
  Comments   : this is an older API method and despite being simple and fast
               the stream_all() method now replaces this call.  It may be 
               deprecated in the near future.