PRIMER_DESIGNER(1p) User Contributed Perl Documentation PRIMER_DESIGNER(1p)NAME
primer_designer.pl -- command-line interface Bio::PrimerDesigner
SYNOPSIS
./primer_designer.pl [options] [dna_sequence or file]
Options:
-p|--program Program (default "primer3")
-n|--number Number of primer sets to return (default "5")
-b|--binary Path to binary executable (default "/usr/local/bin")
-m|--method "local" or "remote" (default "local")
-u|--url URL of remote primer3/e-PCR system (default
"aceserver.biotech.ubc.ca/cgi-bin/primer_designer.cgi")
--list-aliases Print alias list to primer3 input options and exit
--list-params Print a list of primer3/e-PCR input options and exit
-h|--help Print help and exit
DESCRIPTION
This script tests/demonstrates the Bio::PrimerDesigner interface to primer3 and e-PCR. It can be used with a local installation of the
unix binaries or remotely via an HTTP/CGI request.
AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.
SEE ALSO
Bio::PrimerDesigner.
LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
the Free Software Foundation; version 3 or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
perl v5.10.0 2009-08-04 PRIMER_DESIGNER(1p)
Check Out this Related Man Page
Bio::PrimerDesigner::Tables(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::Tables(3pm)NAME
Bio::PrimerDesigner::Table -- Draw HTML tables for PCR primer display
DESCRIPTION
Draws simple HTML tables to display Bio::PrimerDesigner PCR primer design and e-PCR results for web applications.
METHODS
info_table
Prints a two-column table for generic, key-value style annotations. Expects to be passed the name of the gene/feature/etc. and a hash of
attributes. If there is an 'image' key, the value is assumed to be an image URL, which is printed in a double-wide cell at the bottom of
the table.
my $gene = 'Abc-1';
my %gene_info = (
Chromosome => I,
Start => 100450,
Stop => 102893,
Strand => '+'
);
my $page = Bio::PrimerDesigner::Tables->new;
$page->info_table( $gene, %gene_info );
PCR_header
Returns a generic header for the PCR primer table. Does not expect any argumments.
PCR_set
Returns the top row for the PCR primer table. Expects the primer set number as its only argument.
PCR_row
Returns table rows with PCR primer info. Should be called once for each primer pair. Expects to be passed a hash containing the
Bio::PrimerDesigner::Result object and the primer set number and an (optional) label.
my $pcr_row = PCR_row(
primers => $result_obj,
setnum => $set_number,
label => $label
);
ePCR_row
Returns table rows summarizing e-PCR results. Expects to be passed an Bio::PrimerDesigner::Result e-PCR results object and an optional
e-PCR label.
render
Renders the image URL. Expects to be passed a hash of the map start and stop, and other features to be mapped (i.e.
gene,forward_primer,reverse_primer, label,start and stop of each feature, and gene strand).
my $image = $page->render(
start => $startleft,
stop => $startright,
feat => $features
);
PCR_map
Returns a 6 column wide table cell with the <IMG ...> info. Will display the image of mapped primers in the browser when passed the image
URL.
AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>.
LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
the Free Software Foundation; version 3 or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
SEE ALSO
Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr.
perl v5.10.0 2009-08-04 Bio::PrimerDesigner::Tables(3pm)