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revision 1.5, Fri Nov 12 03:48:02 2004 UTC revision 1.6, Wed Feb 9 20:15:42 2005 UTC
# Line 1  Line 1 
1    
2  # -*- perl -*-  # -*- perl -*-
3    
4  use Carp;  use Carp;
# Line 9  Line 10 
10    
11  $| = 1;  $| = 1;
12    
13  $usage = "align_with_clustal [-org] [-func[=user]] [-tree] [-save=Dir] Id1 Id2 ... ";  $usage = "align_with_clustal [-org] [-func[=user]] [-tree] [-UniProt] [-save=Dir] Id1 Id2 ... ";
14    
15  (@ARGV > 1) || die "usage: $usage";  (@ARGV > 1) || die "usage: $usage";
16    
# Line 17  Line 18 
18  my $file     = "$temp_dir/tmp$$";  my $file     = "$temp_dir/tmp$$";
19  my $relabel  = {};  my $relabel  = {};
20  my $save = "";  my $save = "";
21    my $uni_prot = "";
22    
23  while ($ARGV[0] =~ m/^-/)  while ($ARGV[0] =~ m/^-/)
24  {  {
# Line 38  Line 40 
40      {      {
41          $tree = shift @ARGV;          $tree = shift @ARGV;
42      }      }
43        elsif ($ARGV[0] =~ /-UniProt/i)
44        {
45            $uni_prot = 1;
46            shift @ARGV;
47        }
48      else      else
49      {      {
50          $trouble = 1;          $trouble = 1;
# Line 65  Line 72 
72      }      }
73    
74      $label = $id;      $label = $id;
75        if ($uni_prot && ($_ = $fig->to_alias($id,"uni")))  { $label .= " [$_]" }
76      if ($add_org && $org)    { $label .= " [$org]"; }      if ($add_org && $org)    { $label .= " [$org]"; }
77      if ($add_func && $func)  { $label .= " $func"; }      if ($add_func && $func)  { $label .= " $func"; }
78    

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