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Revision 1.5 - (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 1.4: +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;

$usage = "usage: build_protein_families Sources";

(
 ($sources = shift @ARGV)
)
    || die $usage;

&FIG::verify_dir("$FIG_Config::temp/ProteinFamilies");
&FIG::verify_dir("$FIG_Config::temp/ProteinFamilies/previous");
&FIG::run("cp $FIG_Config::global/ProteinFamilies/local* $FIG_Config::global/ProteinFamilies/id.map $FIG_Config::temp/ProteinFamilies/previous");
&FIG::run("build_syn $sources $FIG_Config::temp/ProteinFamilies/syn$$");
&FIG::run("make_fam_tabs $sources $FIG_Config::temp/ProteinFamilies/syn$$ $FIG_Config::global/ProteinFamilies");
&load_idmaps($sources);
#unlink("/tmp/syn$$");
&FIG::run("load_protein_families");




sub load_idmaps {
 my $sources=shift;
 opendir(SOURCES, $sources) || die "Can't open $sources while trying to load id.maps";
 my @idmaps = map { "$sources/$_/id.map" } grep { ($_ !~ /^\./) && (-s "$sources/$_/id.map") } readdir(SOURCES);
 open(OUT, ">$FIG_Config::global/ProteinFamilies/id.map") || die "Can't open $FIG_Config::global/ProteinFamilies/id.map for writing";
 foreach my $file (@idmaps)
 {
  open(IN, $file) || die "can't open $idmaps";
  while (<IN>)
  {
   my @line=split /\t/;
   unless ($#line==1)
   {
    print STDERR "Error reading the data at $_ in $dir/$f/id.map\n";
    next;
   }
   if (length($line[0])>32 || length($line[1])>32)
   {
    print STDERR "One of the entries in $_ from  $dir/$f/id.map is too long. Each piece can only be 32 characters\n";
    next;
   }
   print OUT $_;
  }
 }
}
  
  
  
  


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