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Revision 1.2 - (download) (as text) (annotate)
Thu Dec 17 22:55:26 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, 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, rast_rel_2011_0119, 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, mgrast_dev_04012011, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.1: +4 -0 lines
Fixed POD errors.

#!/usr/bin/perl

use SeedEnv;

#
# This is a SAS Component
#


=head1 svr_similar_to [CutOff] < PEG > PEG1-Sc-PEG

Get similarities for a PEG

Input is PEG id's on STDIN

Output is tab separated list of PEG, Score, PEG on STDOUT

------
Example: svr_similar_to < peg_file
------

=head2 Command-Line Options

=over 4

=item CutOff

An optional cutoff score.

=back

=head2 Output Format

The standard output is a file where each line contains a peg\tscore\tpeg

=cut

my $usage = "usage: svr_similar_to [CutOff] < PEG > PEG1-Sc-PEG";

my($cutoff,$pair,$peg);
$cutoff = shift @ARGV;
$cutoff = defined($cutoff) ? $cutoff : 1.0e-10;

my $id;
@pegs = map { chop; $_ =~ /(\S+)$/; 
	      $id = $1;  
	       ($id =~ /^fig\|/) ? $id : ()
            } <STDIN>;

foreach my $sim (&SeedUtils::sims(\@pegs,300,$cutoff ? $cutoff : 1.0e-5,'fig',10000))
{
    print join("\t",($sim->id1,$sim->psc,$sim->id2)),"\n";
}

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