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Revision 1.7 - (download) (as text) (annotate)
Wed Sep 5 21:12:21 2007 UTC (12 years, 2 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, 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 1.6: +1 -1 lines
rollup of changes for anno clearinghouse, RAST->SEED import.

#
# 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;

my $usage = "usage: flip_sims sims.dir sorted\n";
my($in_dir, $sorted);

(
 ($in_dir  = shift @ARGV) &&
 ($sorted = shift @ARGV) &&
 (@ARGV == 0)
)
    || die $usage;


#
# if in_dir is actually a file, just flip that file.
#

my @files;
if (-f $in_dir)
{
    @files = ($in_dir);
}
else
{
    opendir(SIMS,$in_dir)
	|| die "could not open $in_dir";
    @files = grep { $_ !~ /^\./ } readdir(SIMS);
    closedir(SIMS);
    @files = map { "$in_dir/$_" } @files;
}

open(SORT, "| sort $ENV{SORT_ARGS} > $sorted") or die "cannot open $sorted: $!\n";
foreach my $new_sims (@files)
{
    open(NEWSIMS,"<$new_sims")
	|| die "could not open $new_sims";
    while (defined(my $sim = <NEWSIMS>))
    {
	if ($sim =~ /^\S+\t(\S+)/)
	{
	    my $rev = &rev_sim($sim);
	    print SORT $rev;
        }
    }
    close(NEWSIMS);
}

close(SORT);

sub rev_sim {
    my($sim) = @_;

    chomp $sim;
    my($id1,$id2,$iden,$ali_ln,$mismatches,$gaps,$b1,$e1,$b2,$e2,$psc,$bsc,$ln1,$ln2) = split(/\t/,$sim);
    return join("\t",($id2,$id1,$iden,$ali_ln,$mismatches,$gaps,$b2,$e2,$b1,$e1,$psc,$bsc,$ln2,$ln1)) . "\n";
}

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