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Revision 1.4 - (download) (as text) (annotate)
Sun Mar 25 14:21:41 2007 UTC (12 years, 7 months 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 1.3: +1 -1 lines
tighten length constraints for figfam matching

# -*- perl -*-
#
use FIG;
my $fig = new FIG;

$usage = "usage: direct_functional_coupling < PEGS > PEG-PEG-SC";

@pegs = map { chop; $_ =~ /(\S+)$/; 
	      $id = $1;  
	      if ($id =~ /^fig\|/)
	      {
		  $_;
	      }
	      else
	      {
		  if ($peg = $fig->by_alias($id,$genome))
		  {
		      "$_\t$peg";
		  }
		  else
		  {
		      ();
		  }
	      }
            } <STDIN>;

foreach $_ (@pegs)
{
    if ($_ =~ /(fig\|\d+\.\d+\.peg\.\d+)$/)
    {
	$peg = $1;
	my @fc = &directly_coupled($fig,$peg);
#	print STDERR &Dumper(["fc",\@fc]);

	foreach my $tuple (sort { $b->[1] <=> $a->[1] } @fc)
	{
	    print join("\t",($peg,@$tuple)),"\n";
	}
    }
}

sub directly_coupled {
    my($fig,$peg1) = @_;

    return $fig->coupled_to($peg1);
}


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