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Revision 1.3 - (download) (as text) (annotate)
Tue Jul 18 13:15:15 2006 UTC (13 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 1.2: +13 -12 lines
families.2c should get current function - not family function

use FIG;
my $fig = new FIG;

my $usage = "usage: make_figfams < merged.families > families.2c";

$tmp1 = "$FIG_Config::temp/tmp1.$$";
$tmp2 = "$FIG_Config::temp/tmp2.$$";
open(CLEANED,">$tmp1") || die "could not open $tmp1";

$last = <STDIN>;
while ($last && ($last =~ /^(\S+)\tfig\|\d+\.\d+\.peg\.\d+/))
{
    my @set = ();
    $fam = $1;
    while ($last && ($last =~ /^(\S+)\t(fig\|(\d+\.\d+)\.peg\.\d+)/) && ($1 eq $fam))
    {
	$peg = $2;
	$genome = $3;
	if ($fig->is_prokaryotic($genome) && (! $fig->possibly_truncated($peg)))
	{
	    push(@set,$peg);
	}
	$last = <STDIN>;
    }

    if (@set > 1)
    {
	print CLEANED join("\t",@set),"\n";
    }
}
close(CLEANED);

#&FIG::run("assign_to_close_strains $tmp1 > $tmp2");
#open(NEWFUNCS,"<$tmp2") || die "could not open $tmp2";
#while (defined($_ = <NEWFUNCS>))
#{
#    if ($_ =~ /^(\S+)\t(\S.*\S)/)
#    {
#	$func_of{$1} = $2;
#    }
#}
#close(NEWFUNCS);
unlink($tmp2);

$next_id = 1;
open(SETS,"<$tmp1") || die "could not open $tmp1";
while (defined($_ = <SETS>))
{
    chomp;
    @pegs = split(/\t/,$_);
    my $fam_id = sprintf("FIG%06d", $next_id++);
    foreach $peg (@pegs)
    {
#	$func = $func_of{$peg} ? $func_of{$peg} : $fig->function_of($peg);
	$func = $fig->function_of($peg);
	print join("\t",($fam_id,$peg,$func)),"\n";
    }
}
close(SETS);
unlink($tmp1);

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