/usr/share/doc/bioperl/examples/contributed/rebase2list.pl is in bioperl 1.6.901-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #!/usr/bin/perl
# Generate an enzyme list for RestrictionEnzyme.pm from rebase
# From Ryan Brinkman
my $strider = $ARGV[0]; #commercial_version_rebase_strider_format
open (FILEIN,"$strider") or die "can't open $strider: $!\n";
while (<FILEIN>){
chomp;
if ( /^[A-Z]\S+,\S+/ ){
($enzyme,$cutsite)=split(',');
if ($cutsite =~ m#/#){
$match=$-[0];
}
($seqfixed=$cutsite) =~ s/\///g;
$seqfixed=uc $seqfixed;
print " \'$enzyme\'\t=> \'".$seqfixed." ".$match."\'\,\n";
}
}
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