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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: +1 -1 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: generate_similarities [remote]

use strict;

my $remote = ((@ARGV == 1) && ($ARGV =~ /remote/i));

if (-s "$FIG_Config::global/queued_similarities")
{
#    &FIG::run("cp $FIG_Config::global/nr $FIG_Config::temp/nr.for.sims");
    print STDERR "copied nr\n";
    my @ids = `cat $FIG_Config::global/queued_similarities`;
#    unlink("$FIG_Config::global/queued_similarities");
    chop @ids;
    &make_fasta_from_ids($fig,"$FIG_Config::temp/fasta.for.sims",\@ids);
    print STDERR "made $FIG_Config::temp/fasta.for.sims\n";

#   &FIG::run("cat $FIG_Config::temp/fasta.for.sims >> $FIG_Config::temp/nr.for.sims");

    my $handle = &pass_blast_request("$FIG_Config::temp/nr.for.sims","$FIG_Config::temp/fasta.for.sims",$remote);
    print STDERR 
    my $file;
    my $n = 1;
    while ($file = &get_blast_output($handle,$remote))
    {
	print STDERR "$file returned as the file\n";
	my $newsims = "$FIG_Config::data/NewSims/newsims.$$";
	&FIG::run("reduce_sims < $file | reformat_sims $FIG_Config::temp/nr.for.sims > $newsims.$n; index_sims $newsims.$n");
	my @tmp = `cut -f1 $newsims.$n | sort -u`;
	chop @tmp;
	$n++;

	my $id;
	foreach $id (@tmp)
	{
	    my $func = &FIG::auto_assign($id);
	    my($f,$c) = split(/\t/,$func);
	    $c = $c ? $c : "";
	    $fig->assign_function($id,"master",$f,$c);
	}
    }
}

sub pass_blast_request {
    my($nr,$input,$remote) = @_;

    my $which = $remote ? "remote" : "local";
    my @tmp = `pass_blast_request.$which $nr $input`;
    chop @tmp;

    return (@tmp == 1) ? $tmp[0] : undef;
}

sub get_blast_output {
    my($handle,$remote) = @_;

    my $which = $remote ? "remote" : "local";
    my @tmp = `get_blast_output.$which $handle`;
    chop @tmp;

    return (@tmp == 1) ? $tmp[0] : undef;
}


sub make_fasta_from_ids {
    my($fig,$file,$ids) = @_;
    my($id,$seq);

    open(TMP,">$file") || die "could not open $file";
    foreach $id (@$ids)
    {
	$seq = $fig->get_translation($id);
	print TMP ">$id\n$seq\n";
    }
    close(TMP);
}

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