[Bio] / FigKernelScripts / assign_with_no_sims.pl Repository:
ViewVC logotype

View of /FigKernelScripts/assign_with_no_sims.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (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 1.1: +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.
#

# usage: assign_with_no_sims Failed [auto assign parms] < fasta > assignments

use FIG;

$| = 1;

(($input = shift @ARGV) &&
 ($failed = shift @ARGV)
)
    || die "usage: assign_with_no_sims Input Failed > assignments";
$args = join(" ",@ARGV);

&FIG::run("generate_input_for_auto_assignments < $input > tmp$$.1");

open(TMP1,"<tmp$$.1") 
    || die "could not open tmp$$.1";

while ($line = <TMP1>)
{
    @set = ($line);
    for ($i=0; ($i < 9) && ($line = <TMP1>); $i++) 
    {
	push(@set,$line);
    }
    open(TMP2,">tmp$$.2") || die "could not open tmp$$.2";
    foreach $_ (@set)
    {
	print TMP2 $_;
    }
    close(TMP2);

    if (system("auto_assign $args < tmp$$.2 2> tmp$$.3 | make_calls > tmp$$.4") != 0)
    {
	system "cat tmp$$.2 >> $failed";
	print STDERR "auto assign failed\n";
    }
    @tmp = `grep \"blast failed\" tmp$$.3`;

    if (@tmp > 0)
    {
	system "cat tmp$$.2 >> $failed";
	print STDERR "blast failed\n";
    }
    else
    {
	foreach $_ (`cat tmp$$.4`)
	{
	    print $_;
	}
    }
}
unlink("tmp$$.1","tmp$$.2","tmp$$.3","tmp$$.4");

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3