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Revision 1.1 - (download) (as text) (annotate)
Tue Nov 9 22:14:29 2010 UTC (9 years ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, 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, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
New FIGfam merge code.

use lib 'FigKernelPackages';
use CorrTableEntry;
use Correspondence;
use strict;
use SeedEnv;

$ENV{SAS_SERVER} = 'PSEED';

my $sap = SAPserver->new();

my @genomes;
while (<>)
{
    if (/(\d+\.\d+)/)
    {
	push(@genomes, $1);
    }
}

for my $i (0..$#genomes)
{
    my $genome1 = $genomes[$i];

    for my $j ($i + 1..$#genomes)
    {
	my $genome2 = $genomes[$j];

	my $corr = $sap->gene_correspondence_map(-genome1 => $genome1,
						 -genome2 => $genome2,
						 -fullOutput => 1);

	for my $tuple (@$corr)
	{
	    bless $tuple, 'CorrTableEntry';
	    if (Correspondence::entry_meets_criteria($sap, $tuple,
						     -bbhRequired => 1,
						     -minCoverage1 => 0.7,
						     -minCoverage2 => 0.7,
						     -contextSize => 5,
						    ))
	    {
		print $tuple->id1, "\t", $tuple->id2, "\n";
	    }
	}
    }
}

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