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(3pm) User Contributed Perl Documentation Bio::PrimerDesigner(3pm) NAME
Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr SYNOPSIS
use Bio::PrimerDesigner; my $pd = Bio::PrimerDesigner->new; # # Define the DNA sequence, etc. # my $dna = "CGTGC...TTCGC"; my $seqID = "sequence 1"; # # Define design parameters (native primer3 syntax) # my %params = ( PRIMER_NUM_RETURN => 2, PRIMER_SEQUENCE_ID => $seqID, SEQUENCE => $dna, PRIMER_PRODUCT_SIZE => '500-600' ); # # Or use input aliases # %param = ( num => 2, id => $seqID, seq => $dna, sizerange => '500-600' ); # # Design primers # my $results = $pd->design( %params ) or die $pd->error; # # Make sure the design was successful # if ( !$results->left ) { die "No primers found ", $results->raw_data; } # # Get results (single primer set) # my $left_primer = $results->left; my $right_primer = $results->right; my $left_tm = $results->lefttm; # # Get results (multiple primer sets) # my @left_primers = $results->left(1..3); my @right_primers = $results->right(1..3); my @left_tms = $results->lefttm(1..3); DESCRIPTION
Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported. METHODS
binary_path Gets/sets path to the primer3 binary. design Makes the primer design or e-PCR request. Returns an Bio::PrimerDesigner::Result object. epcr_example Run test e-PCR job. Returns an Bio::PrimerDesigner::Results object. list_aliases Lists aliases for primer3 input/output options list_params Lists input options for primer3 or epcr, depending on the context method Gets/sets method of accessing primer3 or epcr binaries. os_is_unix Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0. primer3_example Runs a sample design job for primers. Returns an Bio::PrimerDesigner::Results object. program Gets/sets which program to use. run Alias to "design." url Gets/sets the URL for accessing the remote binaries. verify Tests local installations of primer3 or e-PCR to ensure that they are working properly. AUTHORS
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, Bio::PrimerDesigner::epcr. perl v5.10.0 2009-08-04 Bio::PrimerDesigner(3pm)