[Bio] / FigKernelScripts / align_with_clustal_2.pl Repository:
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revision 1.1, Wed Nov 30 08:44:26 2005 UTC revision 1.2, Wed Nov 30 09:18:08 2005 UTC
# Line 92  Line 92 
92  close(TMP);  close(TMP);
93  # print STDERR "$0;\n", Dumper($relabel);  # print STDERR "$0;\n", Dumper($relabel);
94    
95  system "$FIG_Config::ext_bin/clustalw -infile=$file.fasta -align "  system "$FIG_Config::ext_bin/clustalw -infile=$file.fasta -align -outorder=aligned > /dev/null";
      . ( $tree ? "-tree " : "" )  
      . "-outorder=aligned > /dev/null";  
96  if ( -s "$file.aln" && open( ALIGN, "<$file.aln" ) )  if ( -s "$file.aln" && open( ALIGN, "<$file.aln" ) )
97  {  {
98      print <ALIGN>;      print <ALIGN>;
99      close( ALIGN );      close( ALIGN );
100  }  }
101    
102  if ( $tree )  if ( $tree && -s "$file.aln" )
103  {  {
104            system "$FIG_Config::ext_bin/clustalw -infile=$file.aln -tree > /dev/null";
105      my $treetext = "";      my $treetext = "";
106      my $tree1;      my $tree1;
107      if ( ( -s "$file.ph"  && open( TREE, "<$file.ph"  ) )      if ( ( -s "$file.ph"  && open( TREE, "<$file.ph"  ) )
# Line 133  Line 132 
132  }  }
133    
134  unlink("$file.fasta","$file.aln","$file.dnd");  unlink("$file.fasta","$file.aln","$file.dnd");
135  -s "$file.ph" and unlink("$file.ph");  # -s "$file.ph" and unlink("$file.ph");
136    
137  1;  1;

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