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Bio-DB-CCDS-0.03
River stage zero No dependents
++
/ Bio::DB::CCDS

NAME

CCDS - The great new CCDS!

VERSION

Version 0.01

SYNOPSIS

CCDS or Consensus Coding Sequences are protein coding regions that are identically annotated on the various human and mouse genome assemblies, which are represented by accession numbers. They contain exon coordinates, the gene name, Entrezgene ID, chromosome number, and Accession Number. Archive found at: ftp://ftp.ncbi.nih.gov/pub/CCDS/

#!/usr/bin/perl -w use strict; use Bio::DB::CCDS

#Replace /CCDS.curr... with the full file path my $test = Bio::DB::CCDS->new("/CCDS.current.2_22_15.txt");

#get a list of CCDS ids the correspond to a gene-id my @ccds = $test->Get_CCDS_IDs('gene_id' => '118424'); print "@ccds\n";

#Get all the information that corresponds to a particular ID- chromosome#, accession, etc. my @gene = $test->Get_gene("$ccds[0]"); print "@gene\n"; @gene = $test->gene_coordinates("$ccds[0]"); print "@gene\n"; my %exolocs = $test->Get_exons("$ccds[0]"); foreach(keys %exolocs){ print "$_ - "; print "$exolocs{$_}\n"; } @gene = $test->Genes_list('Withdrawn', @ccds); print "@gene\n"; @thing = $test->Write_ccds($ccds[0]); print "@gene\n"; @thing = $test->Get_strand('+'); print "@gene[0..20]\n"; @thing = $test->Get_strand('-'); print "@gene[0..20]\n"; @thing = $test->Get_strand('+', @ccds); print "@gene here\n"; @thing = $test->Get_strand('-', @ccds); print "@gene there\n"; @thing = $test->Gene_id('1', 'Withdrawn'); print "@gene\n"; print @gene."\n"; @thing = $test->Gene_count('1', '+', 'Withdrawn'); print "@gene\n"; print @gene."\n";

SUBROUTINES/METHODS new Get_CCDS_IDs Get_gene gene_coordinates Get_exons Genes_list Write_ccds Get_strand Gene_id Gene_count =head2 new Title : new Usage : my $object = Bio::DB::CCDS->new($filepath); Function: Initialize a new CCDS object by passing in the CCDS filepath Returns : A new Bio::DB::CCDS object. Args : path to file

Get_CCDS_IDs Title : Get_CCDS_IDs Usage : my @ccds = $object->Get_CCDS_IDs('#chromosome' => '1'); Function: Takes two arguments, first is the type of the argument you want to send and the second argument is the actual argument you give to find the associated CCDS ids. Returns : A list of CCDS ids associated with the argument Args : '#chromosome' => chromosome number 'accession' => accession number 'gene' => gene name 'gene_id' or 'id' => gene id

Get_gene Title : Get_gene Usage : my @gene = $object->Get_gene($ccds[3]); Function: Gives you all the information associated with a CCDS id in order Returns : All information associated with the CCDS id Args : CCDS id

gene_coordinates Title : gene_coordinates Usage : my @location = $object->gene_coordinates($ccds[3]); Function: Gives you the chromosome number, and position of the CCDS on the chromosome Returns : a list of the chromosome number, the start position, and the end location, in that order Args : CCDS id Warning : Be aware of the accession number

Get_exons Title : Get_exons Usage : my %exons = $object->Get_exons($ccds[3]); foreach(keys %exons){ print "$_ - "; print "$exons{$_}\n"; } Function: Gives you the exon coordinates. Every position will be subtracted by the starting position so the first exon starts at 0, add the numbers to the starting position from gene_coordinates for the actual location Returns : a hash of the exons the the keys as the beginnings of the exons and the values as the end Args : CCDS id

Genes_list Title : Genes_list Usage : my @customwithdrawn = $object->Genes_list('Withdrawn' => @ccds); my @public = $object->Genes_list('Public'); Function: You can choose whether to retrieve a list of public or withdrawn sequences from your own CCDS id list or from the whole file Returns all public CCDS ids by default Does not return ids that are under review Returns : CCDS id list Args : None by default First: 'Withdrawn' or 'Public' Second: CCDS id list or nothing

Write_ccds Title : Write_ccds Usage : print "$object->Genes_list($ccds[1])"; Function: Gives you a tab separated string representation of everything associated with the CCDS id Returns : Tab formatted string representation of everything associated with the CCDS id Args : CCDS id

Get_strand Title : Get_strand Usage : my @plus = $object->Get_strand('+' => @ccds); Function: Takes a list of CCDS ids and isolates the ids associated with either the sense or antisense strands. Looks at all ids by default. Returns : list or CCDS ids that are sense or antisense Args : First: '+' or '-' Second optional: list of CCDS ids to perform operation on

Gene_id Title : Gene_id Usage : my @custom = $object->Gene_id('1', 'Withdrawn' => @ccds); Function: Get genes of a certain chromosome and status from your own CCDS id list or from the whole file Returns : CCDS id list Args : First: #chromosome Second: 'Withdrawn' or 'Public' Third: @ccds or nothing

Gene_count Title : Gene_count Usage : my @custom = $object->Gene_count('1','+', 'Withdrawn' => @ccds); Function: Get genes of a certain chromosome, strand, and status from your own CCDS id list or from the whole file Returns : CCDS id list Args : First: #chromosome Second: '+' or '-' Third: 'Withdrawn' or 'Public' Fourth: @ccds or nothing

AUTHOR

Adur Pandya, <anp375 at nyu.edu> under supervision of Mgavi Elombe Brathwaite,

BUGS

Please report any bugs or feature requests to bug-ccds at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=CCDS. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc CCDS

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright (C) 2016 by Adur Pandya

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.