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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 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 1.1: +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;
use strict;
use Data::Dumper;
use URI::Escape;
use POSIX;


#
# usage: export_subsystem_as_gff subsystem_name
#

sub iso_time
{
    my($t) = @_;

    my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($t);

    return POSIX::strftime("%Y-%m-%dT%H:%M:%S",
			  $sec, $min, $hour, $mday, $mon, $year);
}

if (@ARGV != 1)
{
    die "Usage: $0 subsystem_name\n";
}

my $ssa = shift @ARGV;

$ssa =~ s/ /_/g;

my $fig = new FIG;

#
# Open the subsystem, and retrieve the assignment-annotations for
# the pegs that are in it.
#

my $sub = $fig->get_subsystem($ssa);


for my $genome ($sub->get_genomes())
{
    my(@clist, @flist, %contig_names);

    my $w = $fig->get_gff_writer(outputtype => ['cds'],
				 linelength => 78,
				 with_assignments => 0,
				 with_aliases => 1);


    my $gidx = $sub->get_genome_index($genome);
    my $row = $sub->get_row($gidx);

    for my $cell (@$row)
    {
	next unless $cell;

	for my $peg (@$cell)
	{
	    my @aliases = $fig->feature_aliases($peg);
	    my @loc = $fig->feature_location($peg);
	    my $type = $fig->ftype($peg);
	    my @feature_annos;

	    my $group = $FIG_Config::group;
	    $group = 'FIG' unless $group;

	    #
	    # Create the notes text for the annotation.
	    #
	    my $ntxt = '';

	    #
	    # For a subsystem peg, we generate an annotation stating that the
	    # annotation is an assignment based on subsystem membership.

	    my $assign = $fig->function_of($peg);

	    push(@feature_annos, [$peg, time, "subsystem", "Set $group function to\n$assign"]);


	    if (@feature_annos)
	    {
		my @notes;
	
		for my $ent (@feature_annos)
		{
		    my($peg, $time, $who, $anno) = @$ent;
		    
		    my $nbody = "$time:$who:$anno";
		    push(@notes, uri_escape($nbody));
		}
		
		$ntxt = "anno=" . join(",", @notes);
	    }

	    #
	    # Create the GFF for this feature.
	    my($contigs, $fasta) = $w->gff3_for_feature($peg, undef, $ntxt, \@aliases, \@loc);

	    map { $contig_names{$_}++ } keys(%$contigs);

	    push(@clist, $contigs);
	    push(@flist, $fasta);
	}
    }

    open(my $outfh, ">sub.$genome.gff");
    my $gdir = "$FIG_Config::organisms/$genome";

    my $project = &FIG::file_head("$gdir/PROJECT", 1);
    chomp($project);

    print $outfh "#gff-version\t3\n";
    print $outfh "#seed\tgenome\t$genome\t" . $fig->genus_species($genome) . "\n";
    print $outfh "#seed\tgenome_md5\t$genome\t" . $fig->genome_md5sum($genome) . "\n";
    print $outfh "#seed\ttaxonomy\t" . $fig->taxonomy_of($genome) . "\n";
    print $outfh "#seed\tproject\t$project\n";

    $w->write_gff3($outfh, '', \@clist, \@flist);

    close($outfh);
}



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