[Bio] / FigKernelScripts / export_similarity_request.pl Repository:
ViewVC logotype

View of /FigKernelScripts/export_similarity_request.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.3 - (download) (as text) (annotate)
Wed Feb 15 22:12:27 2006 UTC (14 years ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.2: +41 -4 lines
minor fixes to assignment for close strains

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#


use strict;
use FIG;

=pod 

=head1 NAME

export_similarity_request - export queued sims as a bundle

=head1 SYNOPSIS

export_similarity_request export_bundle_dir

=head1 DESCRIPTION

B<export_similarity_request> creates a directory bundle that contains a NR, fasta file of new sequences, and
peg.synonyms file. The fasta file is created from the set of queued similarities that were in
place at the time the command was run. The similarity queue is emptied when the bundle is created.

This command locks the similarity queue so that queuing of sims while the export is running (it can take
several minutes to complete) works properly.

When the sims computation has completed, it will have created a sims bundle that can
be installed with import_similarity_bundle.

=cut

    


my $fig = new FIG;

my $usage = "export_similarity_request req-dir";

@ARGV == 1 or die $usage;

my $req_dir = shift(@ARGV);

if (-d $req_dir)
{
    die "Request directory $req_dir already exists, not overwriting\n";
}

if (!mkdir($req_dir))
{
    die "Error creating $req_dir: $!\n";
}

$fig->export_similarity_request($req_dir);

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3