Jessica Severin <severin@gsc.riken.jp>
* 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: * * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * * 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. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ''AS IS'' AND ANY * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * DISCLAIMED. IN NO EVENT SHALL COPYRIGHT HOLDERS BE LIABLE FOR ANY * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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; } }
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
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.
To install EEDB, copy and paste the appropriate command in to your terminal.
cpanm
cpanm EEDB
CPAN shell
perl -MCPAN -e shell install EEDB
For more information on module installation, please visit the detailed CPAN module installation guide.