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Revision 1.3 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 2005 UTC (14 years, 4 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 1.2: +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;

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);
}


my $fig = new FIG;

my $outfile = "tstout";
print "Writing output to $outfile\n";

my $end = time;
my $start = $end - 100 * 86400;
#$start= 0;
my($annos) = $fig->annotations_made_fast(['633.1'], $start, $end);

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

my(@clist, @flist);
my $count;

my %contig_names;

open(F, ">$outfile");

print F "#gff-version\t3\n";

print F "#seed\tanno_start\t" . iso_time($start) . "\n";
print F "#seed\tanno_end\t" . iso_time($end) . "\n";
for my $genome_anno (@$annos)
{
    my($genome, $gpegs) = @$genome_anno;

    for my $peg (sort { &FIG::by_fig_id($a, $b) } keys(%$gpegs))
    {
	my $alist = $gpegs->{$peg};

	#
	# Create notes for the annos.
	#

	my @notes;
	for my $ent (@$alist)
	{
	    my($peg, $time, $who, $anno) = @$ent;

	    my $nbody = "$time:$who:$anno";
	    push(@notes, uri_escape($nbody));
	}

	my $ntxt = "anno=" . join(",", @notes);

	my($contigs, $fasta) = $w->gff3_for_feature($peg, undef, $ntxt);

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

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

    print F "#seed\tgenome_md5\t$genome\t" . $fig->genome_md5sum($genome) . "\n";

    # 
    # We don't need contig checksums.
    #
    # for my $cname (sort keys %contig_names)
    # {
    #	print F "#seed\tcontig_md5\t$genome\t$cname\t" . $fig->contig_md5sum($genome, $cname) . "\n";
    # }
}



$w->write_gff3(\*F, '83333.1', \@clist, \@flist);

close(F);

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