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Revision 1.1 - (download) (as text) (annotate)
Thu Nov 15 14:30:50 2007 UTC (12 years, 6 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
redone FIGfam stuff

### #!/usr/bin/perl

use FF;
use FFs;

$usage = "usage: test_placement Data Dir Process < PEGs";

(
 ($data = shift @ARGV) &&
 ($dir  = shift @ARGV) &&
 ($proc = shift @ARGV)
)
    || die $usage;

my $figfams = new FFs($data);

opendir(DIR,"$dir") || die "could not open $dir";
@files = grep { $_ =~ /^\d/ } readdir(DIR);
closedir(DIR);

foreach $file (@files)
{
    open(FILE,"<$dir/$file") || die "could not open $dir/$file";
    while (defined($_ = <FILE>))
    {
	if ($_ =~ /^(fig\|\d+\.\d+\.peg\.\d+)/)
	{
#	    $seen{$1} = 1;
	}
    }
    close(FILE);
}

open(OUT,">>$dir/$proc") || die "could not open $dir/$proc";
$| = 1;
while (defined($_ = <STDIN>))
{
    if (($_ =~ /^(fig\|\d+\.\d+\.peg\.\d+)/) && (! $seen{$1}))
    {
	$peg = $1;
	my $pseq = $figfams->seq_of($peg);
	if ($pseq)
	{
	    my($got,undef) = $figfams->place_in_family($pseq,undef,undef,$peg);
	    my $fam_id = $got ? $got->family_id : "";
	    print OUT join("\t",($peg,$fam_id)),"\n";
	}
    }
}

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