An object to encapsulate a Chromosome within an Assembly.
An object that corresponds to specific chromosomes within an assembly. Because Chrom is tied to a specific assembly, an instance of a Chrom identifies not only the chromosome, but also the assembly and species
As with all objects in EEDB, Chrom interits from MQdb::DBObject and MQdb::MappedQuery. Please refer to these documents for all superclass methods
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 : class level method to turn on/off global caching of Chromsome objects since these are very small and used heavily, it is on my default and it is recommended to not turn it off. Parameter[1] : scalar 0/1 to turn the caching off/on Returntype : none Exceptions : none
Description : get count of Chroms currently in the memory cache Returntype : scalar count Exceptions : none
Description: initialize a new instance of this object. generally not needed for users to call this method Returntype : $self Exceptions : none
Description : simple getter/setter method for the chromosome name Parameter[1] : <optional> if specififed it will set the chromsome name Returntype : string Exceptions : none
Description : simple getter/setter method for the chromosome type Parameter[1] : <optional> if specififed it will set the chromsome type Returntype : string Exceptions : none
Description : simple getter/setter method for the chromosome description Parameter[1] : <optional> if specififed it will set the chromsome description Returntype : string Exceptions : none
Description : simple getter/setter method for the Assembly of this Chrom Parameter[1] : <optional> of type EEDB::Assembly. if specififed it will set the assembly Returntype : EEDB::Assembly instance Exceptions : none
Description : simple getter/setter method for the chromosome length Parameter[1] : <optional scalar> if specififed it will set the chromsome length Returntype : scalar Exceptions : none
Description : overrides the superclass method. returns a debugging description of this instance. calling display_info() will print this display_desc to STDOUT Returntype : string Exceptions : none
Description : overrides the superclass method. returns the start of the XML description of this instance Returntype : string Exceptions : none
Description : overrides the superclass method. returns the end tag of the XML description of this instance Returntype : string Exceptions : none
Description : overrides the superclass method. returns the complete XML description of this instance Returntype : string Exceptions : none
Description : uses ChromChunk objects and the sequence in the database to return the actual sequence in this region. Since the Chrom is assigned to a specific Assembly one only needs to specify the start/end and an optional strand to fetch the sequence. Parameter[1] : chrom_start the chromosome start of the region to fetch Parameter[2] : chrom_end the chromosome end of the region to fetch Parameter[3] : strand <optional> as "-" or "+" the strand of the sequence. if "-" then it will return the sequence on the reverse strand by reverse complementing the sequence Returntype : Bio::Seq instance or undef if a data error happens Errors : if the region is not valid or if data is not present it will return undef Exceptions : none
Description : store this instance into an EEDB database on return the instance will have the primary_id() set. Parameter[1] : a MQdb::Database to store into Returntype : $self or undef if a problem occurred Exceptions : none
Description : updates the data of this instance. require the Chrom to have been fetched from database. It must have database() and primary_id() Returntype : $self Exceptions : none
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.