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Revision 1.6 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
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, caBIG-05Apr06-00, 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, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.5: +17 -0 lines
Add license words.

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

use FIG;
my $fig = new FIG;

# usage: aliases_of < PEG > PEG-ALIASES
#

%tag_order = ( gene => 1,
	       sp   => 2,
	       nr   => 3,
	       uni  => 4,
	       kegg => 5,
	       gi   => 6
	     );

while (defined($_ = <STDIN>))
{
    while ($_ =~ /(fig\|\d+\.\d+\.peg\.\d+)/g)
    {
	if (! $seen{$1})
	{
	    push(@pegs,$1);
	    $seen{$1} = 1;
	}
    }
}

foreach $peg (@pegs)
{
    @tagged_aliases = grep { $_->[1] ne "misc" } map { [$_,&type_alias($_)] } $fig->feature_aliases($peg);
    foreach $x (@tagged_aliases)
    {
	$types{$x->[1]} = 1;
    }
    $tags{$peg} = [@tagged_aliases];
}

@types = sort { $tag_order{$a} <=> $tag_order{$b} } keys(%types);
for ($i=0; ($i < @types); $i++)
{
    $col_of{$types[$i]} = $i+2;
}
@hdrs = ("PEG","Organism",@types);
print join("\t",@hdrs),"\n";

$cols = 2 + @types;
foreach $peg ( sort { &FIG::by_fig_id($a,$b) } @pegs)
{
    $tags = $tags{$peg};
    @row = ();
    for ($i=0; ($i < $cols); $i++)
    {
	$row[$i] = "";
    }
    foreach $x (@$tags)
    {
	($alias,$type) = @$x;

	$col = $col_of{$type};
	if (! $row[$col])
	{
	    $row[$col] = $alias;
	}
	else
	{
	    $row[$col] .= ",$alias";
	}
    }
    $row[0] = $peg;
    $row[1] = $fig->org_of($peg);
    print join("\t",@row),"\n";
}

sub type_alias {
    my($alias) = @_;

    if (($alias =~ /^([^|]+)\|\S+$/) && defined($tag_order{$1}))
    {
	return $1;
    }
    elsif ($alias =~ /^[NXYZA]P_/)
    {
	return "nr";
    }
    elsif (($alias =~ /^[a-zA-Z]{3,4}$/) || ($alias =~ /^[a-zA-Z]{1,3}\d+$/))
    {
	return "gene";
    }
    return "misc";
}

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