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Revision 1.3 - (download) (as text) (annotate)
Sat Aug 23 23:39:22 2008 UTC (11 years, 2 months ago) by golsen
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, 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, HEAD
Changes since 1.2: +16 -13 lines
Move writing of assignment annotation from a case-by-case basis (and it
was missing in several key places) to the FIG::assign_function.

Modify the code in each of the calling locations to not make duplicate
annotations.

At the same time, remove (most) of the instances of making different
calls to assign_function depending on the user name.  assign_function
treats everyone as master (but writes an annotation with the real user
name).

#
# Copyright (c) 2003-2008 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 = "usage: assign_to_unchanged Date User < assignments";

(
 ($date = shift @ARGV) &&
 ($user = shift @ARGV)
)
    || die $usage;

if ($user =~ /master:(.*)/)
{
    $userR = $1;
}
else
{
    $userR = $user;
}

while ($_ = <STDIN>)
{
    chop;
    ($peg,$new) = split(/\t/,$_);
    $func = $fig->function_of($peg);
    if ($new ne $func)
    {
        @ann = $fig->feature_annotations($peg,1);
        for ($i=0; ($i < @ann) && (! &later_assignment($ann[$i],$date)); $i++) {}
        if ($i == @ann)
        {
            #  Everyone is master, and assign_function makes annotation.
            #
            # if ($user =~ /master:(.*)/)
            # {
            #     if ($ENV{'VERBOSE'}) { print STDERR "making assignment: $peg\t$new\n"; }
            #     $fig->assign_function($peg,$user,$new,"");
            #     $fig->add_annotation($peg,$userR,"Set master function to\n$new\n");
            # }
            # else
            # {

            if ($ENV{'VERBOSE'}) { print STDERR "making assignment: $peg\t$new\n"; }
            $fig->assign_function($peg,$user,$new,"");

            # $fig->add_annotation($peg,$user,"Set function to\n$new\n");
        }
    }
}

sub later_assignment {
    my($ann,$date) = @_;
    my($ts,$mm,$dd,$yyyy,$epoch_date);

    (undef,$ts,undef,$annotation) = @$ann;
    if ($date =~ /^(\d{1,2})\/(\d{1,2})\/(\d{4})$/)
    {
        my($mm,$dd,$yyyy) = ($1,$2,$3);
        $epoch_date = &Time::Local::timelocal(0,0,0,$dd,$mm-1,$yyyy-1900,0,0,0);
    }
    elsif ($date =~ /^\d+$/)
    {
        $epoch_date = $date;
    }
    else
    {
        $epoch_date = 0;
    }
    return ($epoch_date <= $ts);
}

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