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bio::primerdesigner::tables(3pm) [debian 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)

Check Out this Related Man Page

Bio::PrimerDesigner::epcr(3pm)				User Contributed Perl Documentation			    Bio::PrimerDesigner::epcr(3pm)

NAME

       Bio::PrimerDesigner::epcr - A class for accessing the epcr binary

SYNOPSIS

	 use Bio::PrimerDesigner::epcr;

DESCRIPTION

       A low-level interface to the e-PCR binary.  Uses supplied PCR primers, DNA sequence and stringency parameters to predict both expected and
       unexpected PCR products.

METHODS

   run
       Sets up the e-PCR request for a single primer combination and returns an Bio::PrimerDesigner::Result object

       If the permute flag is true, all three possible primer combinations will be tested (ie: forward + reverse, forward + forward, reverse +
       reverse)

   request
       Assembles the e-PCR config file and command-line arguments and send the e-PCR request to the local e-PCR binary or remote server.

   verify
       Check to make that the e-PCR binary is installed and functioning properly.  Since e-PCR returns nothing if no PCR product is found in the
       sequence, we have to be able to distinguish between a valid, undefined output from a functioning e-PCR and an undefined output for some
       other reason.  verify uses sham e-PCR data that is known to produce a PCR product.

   binary_name
       Defines the binary's name on the system.

   list_aliases
       There are no aliases to list for epcr.

   list_params
       Returns a list of e-PCR configuration options.  Required e-PCR input is a sequence string or file and the left and right primers.  Default
       values will be used for the remaining options if none are supplied.

AUTHOR

       Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

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.

perl v5.10.0							    2009-08-04					    Bio::PrimerDesigner::epcr(3pm)
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