FAHASH(1) User Commands FAHASH(1)NAME
fahash - sequence hash builder for reverse e-PCR
SYNOPSIS
fahash [-hV] -b hash-file [-w wdsize] [-f period] [-F fragment_min,fragment_max] [-k] [-c cachesize] [-v 1|2] famap-file ...
fahash [-hV] -T hash-file [-o outfile]
DESCRIPTION
The program fahash is part of the e-PCR suite and is used to build hash-files, and output word usage statistics for reverse e-PCR searches.
OPTIONS -b hash-file
Build hash tables (hash-file) from sequence files,
-T hash-file
Print word usage statistics for hash-file
-o outfile
Write output to file `outfile'
build-options:
-w wordsize
Set word size when building hash tables
-f period
Set discontiguity when building hash tables
-k Skip repeats when building hash-file
-F min,max
Set watermarks for fragment size (in Mb) (version 1 only)
-c cachesize
Set cache size (version 2 only)
-v ver Use format version (1|2, 2 is default)
EXAMPLE
famap -tN -b genome.famap org/chr_*.fa
fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
See famap(1) and re-pcr(1)SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), e-pcr(1), famap(1) and re-pcr(1)AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
Reverse e-PCR: sequence hash builder version 2.3.9 April 2008 FAHASH(1)
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)