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Revision 1.4 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
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, caBIG-05Apr06-00, 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, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.3: +17 -0 lines
Add license words.

#
# 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 FIG;
my $fig = new FIG;

# usage: get_nr_entries_without_sims [NR SimsDir]

my $usage = "get_nr_entries_without_sims [NR SimsDir]";

my($nr, $sims_dir);
if (@ARGV == 0)
{
    $nr = $FIG_Config::global/nr;
    $sims_dir = $FIG_Config::data/Sims;
}
elsif (@ARGV == 2)
{
    $nr = shift @ARGV;
    $sims_dir = shift @ARGV;
}
else
{
    die $usage;
}

open(NR, "<$nr") or die "cannot open NR $nr: $!\n";
opendir(SIMS, $sims_dir) or die "could not open sims directory $sims_dir: $!\n";

@files = grep { $_ !~ /^\./ } readdir(SIMS);
closedir(SIMS);

foreach $file (sort @files)
{
    print STDERR "processing $file\n";
    open(SIM,"cut -f1 $sims_dir/$file |")
	|| die "could not open $file";
    while (defined($_ = <SIM>) && ($_ =~ /^(\S+)/))
    {
	$has_sims{$1} = 1;
    }
    close(SIM);
}
print STDERR "finished processing SIM files\n";

if (open(NR,"<$nr"))
{
    $/ = "\n>";
    while (defined($_ = <NR>))
    {
	chomp;
	if ($_ =~ /^>?(\S+)[^\n]*\n(.*)/s)
	{
	    $id  =  $1;
	    $seq =  $2;
	    $seq =~ s/\s//gs;
	    if (! $has_sims{$id})
	    {
		print ">$id\n$seq\n";
	    }
	}
    }
    close(NR);
}

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