branch-1-6/examples/contributed/rebase2list.pl

   1 #!/usr/bin/perl
   2 # Generate an enzyme list for RestrictionEnzyme.pm from rebase
   3 # From Ryan Brinkman
   4
   5 my $strider = $ARGV[0]; #commercial_version_rebase_strider_format
   6
   7 open (FILEIN,"$strider") or die "can't open $strider: $!\n";
   8
   9 while (<FILEIN>){
  10    chomp;
  11    if ( /^[A-Z]\S+,\S+/ ){
  12       ($enzyme,$cutsite)=split(',');
  13       if ($cutsite =~ m#/#){
  14          $match=$-[0];
  15       }
  16       ($seqfixed=$cutsite) =~ s/\///g;
  17       $seqfixed=uc $seqfixed;
  18       print " \'$enzyme\'\t=> \'".$seqfixed." ".$match."\'\,\n";
  19    }
  20 }
  21
  22