Add script that demonstrates reverse_tranlate_best()

svn path=/bioperl-live/trunk/; revision=15087

examples/popgen/parse_calc_stats.pl

@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 # Author: Jason Stajich, jason@bioperl.org
 # $Id$
-# $Revision$
+# $Revision: 6576 $
 
 use strict;
 

examples/tools/reverse-translate.pl

@@ -0,0 +1,60 @@
+#!/usr/bin/perl -w
+# $Id$
+
+=head1 NAME
+
+reverse-translate.pl
+
+=head1 DESCRIPTION
+
+Reverse-translates a nucleotide sequence using the most frequent codons.
+Requires an input sequence file and a nucleotide sequence file containing 
+one sequence comprised of one or more ORFs. This file supplies the codon
+frequency data and will be parsed starting at the first triplet in the sequence.
+
+=head1 OPTIONS
+
+  -i   Input sequence, amino acid
+  -c   Input sequence, nucleotide ORFs
+
+Example:
+
+ reverse-translate.pl -i ~/bioperl-live/t/data/cysprot.fa -c ~/bioperl-live/t/data/HUMBETGLOA.fa 
+
+=cut
+
+use strict;
+use Bio::SeqIO;
+use Bio::Tools::CodonTable;
+use Bio::Tools::SeqStats;
+use Bio::CodonUsage::Table;
+use Getopt::Long;
+
+my ($codonFile,$seqFile);
+
+GetOptions( "c=s" => \$codonFile,
+            "i=s" => \$seqFile );
+
+die "Need input sequence and file containing coding regions"
+  if ( !$codonFile || !$seqFile );
+
+my $codonIn = Bio::SeqIO->new(-file => $codonFile,
+										-format => 'fasta');
+
+my $codonSeq = $codonIn->next_seq;
+
+my $codonStats = Bio::Tools::SeqStats->count_codons($codonSeq);
+
+my $codonUsage = Bio::CodonUsage::Table->new(-data => $codonStats );
+
+my $codonTable = Bio::Tools::CodonTable->new;
+
+my $seqIn = Bio::SeqIO->new(-file => $seqFile);
+
+my $seq = $seqIn->next_seq;
+
+my $rvSeq = $codonTable->reverse_translate_best($seq,$codonUsage);
+
+print $rvSeq,"\n";
+
+__END__