[Bio] / FigKernelScripts / FFB2_make_subsys_based_families.pl Repository:
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revision 1.2, Mon Jul 12 19:30:27 2010 UTC revision 1.3, Mon Nov 22 17:41:30 2010 UTC
# Line 20  Line 20 
20    
21  use FIG;  use FIG;
22  use strict;  use strict;
23    use Getopt::Long;
24    
25    # usage: FFB2_make_subsys_based_families > subsys.based.families
26    
27  my $fig = new FIG;  my $fig = new FIG;
28    
29  # usage: FFB2_make_subsys_based_families > subsys.based.families  my $function_override_file;
30    
31    my $rc = GetOptions("functions=s" => \$function_override_file);
32    
33    ($rc && @ARGV == 0) ||
34        die "Usage: FFB2_make_subsys_based_families [-functions function-overrides] > subsys.based.families\n";
35    
36    my %fn_override;
37    if (defined($function_override_file))
38    {
39        open(FN, "<", $function_override_file) or die "Cannot open $function_override_file: $!";
40        while (<FN>)
41        {
42            chomp;
43    
44            my($id, $fn) = split(/\t/);
45            $fn_override{$id} = $fn;
46        }
47        close(FN);
48    }
49    
50    
51  my $pairsF = "$FIG_Config::temp/peg-func.$$";  my $pairsF = "$FIG_Config::temp/peg-func.$$";
52  #open(TMP1,"pegs_in_subsystems | cut -f2,3 | sort -u | function_of |")  #open(TMP1,"pegs_in_subsystems | cut -f2,3 | sort -u | function_of |")
# Line 60  Line 83 
83  {  {
84      my($role, $peg, $func) = @$row;      my($role, $peg, $func) = @$row;
85    
86        $func = $fn_override{$peg} if defined($fn_override{$peg});
87    
88  #while (<TMP1>)  #while (<TMP1>)
89  #{  #{
90  #    chomp;  #    chomp;

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