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Revision 1.2 - (download) (as text) (annotate)
Mon May 7 00:43:26 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
Changes since 1.1: +1 -1 lines
add computation of alignments to building FIGFAMS

# usage: filter_figfams < families.2c > filtered.families.2c

use PHOB;

use FIGO;
$figO = new FIGO;

use FIGO;
$figO = new FIGO;

$x = <STDIN>;
while ($x && ($x =~ /^(\S+)/))
{
    $curr = $1;
    @set = ();
    while ($x && ($x =~ /^(\S+)\t(\S+)/) && ($1 eq $curr))
    {
        push(@set,$2);
        $x = <STDIN>;
    }
    &process($figO,$curr,\@set);
}

sub process {
    my($figO,$fam,$set) = @_;

    my @ok = ();
    foreach $peg (@$set)
    {
        $pegO = new FeatureO($figO,$peg);
	if     ($pegO->possibly_truncated)
	{
	    print STDERR "truncated\t$fam\t$peg\n";
	}
	elsif  ($pegO->possible_frameshift)
	{
	    print STDERR "frameshift\t$fam\t$peg\n";
	}
	else
	{
	    push(@ok,[$peg,'',$pegO->prot_seq]);
	}
    }

    if (@ok > 1)
    {
	my @good_fams = &PHOB::alignable_subsets( seqs => \@ok );
	for ($i=0; ($i < @good_fams); $i++)
	{
	    my $fam1 = ($i == 0) ? $fam : "$fam.$i";
	    foreach my $seq (@{$good_fams[$i]})
	    {
		$pegO = new FeatureO($figO,$seq->[0]);
		print join("\t",($fam1,$pegO->id,$pegO->function_of)),"\n";
	    }
	}
    }
}


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