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revision 1.1, Wed Nov 30 08:44:26 2005 UTC revision 1.3, Mon Dec 5 18:56:37 2005 UTC
# Line 1  Line 1 
1  # -*- perl -*-  # -*- perl -*-
2    #
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    #
18    
19    
20  use strict;  use strict;
21  use Carp;  use Carp;
# Line 92  Line 109 
109  close(TMP);  close(TMP);
110  # print STDERR "$0;\n", Dumper($relabel);  # print STDERR "$0;\n", Dumper($relabel);
111    
112  system "$FIG_Config::ext_bin/clustalw -infile=$file.fasta -align "  system "$FIG_Config::ext_bin/clustalw -infile=$file.fasta -align -outorder=aligned > /dev/null";
      . ( $tree ? "-tree " : "" )  
      . "-outorder=aligned > /dev/null";  
113  if ( -s "$file.aln" && open( ALIGN, "<$file.aln" ) )  if ( -s "$file.aln" && open( ALIGN, "<$file.aln" ) )
114  {  {
115      print <ALIGN>;      print <ALIGN>;
116      close( ALIGN );      close( ALIGN );
117  }  }
118    
119  if ( $tree )  if ( $tree && -s "$file.aln" )
120  {  {
121            system "$FIG_Config::ext_bin/clustalw -infile=$file.aln -tree > /dev/null";
122      my $treetext = "";      my $treetext = "";
123      my $tree1;      my $tree1;
124      if ( ( -s "$file.ph"  && open( TREE, "<$file.ph"  ) )      if ( ( -s "$file.ph"  && open( TREE, "<$file.ph"  ) )
# Line 133  Line 149 
149  }  }
150    
151  unlink("$file.fasta","$file.aln","$file.dnd");  unlink("$file.fasta","$file.aln","$file.dnd");
152  -s "$file.ph" and unlink("$file.ph");  # -s "$file.ph" and unlink("$file.ph");
153    
154  1;  1;

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