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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)

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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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