examples/liveseq/change_gene.pl

   1 #!/usr/bin/perl
   2 # $Id$
   3
   4 use strict;
   5 use Bio::LiveSeq::IO::BioPerl;
   6 use Bio::LiveSeq::Mutator;
   7 use Bio::LiveSeq::Mutation;
   8 use Bio::Variation::IO;
   9
  10 if ($#ARGV < 1) { # one argument input
  11     print <<USAGE;
  12
  13 LiveSeq::Mutator example by Joseph Insana
  14
  15 Arguments: filename containing embl entry, gene_name
  16            It will create that Bio::LiveSeq::Gene and print out some
  17            basic informations about it.
  18            It will then issue mutations and print results
  19
  20 Usage:     change_gene.pl filename genename
  21
  22 Example:   change_gene.pl ../../t/data/ar.embl AR
  23 USAGE
  24 exit;
  25 } else {
  26
  27     my $filename=$ARGV[0];
  28     my $loader=Bio::LiveSeq::IO::BioPerl->load(-file => "$filename");
  29
  30     my $gene_name=$ARGV[1];
  31     my $gene=$loader->gene2liveseq(-gene_name => $gene_name,
  32                                    -getswissprotinfo => 0);
  33
  34     print STDERR "Gene: ",$gene->name,"\n";
  35     print STDERR "    Moltype: ", $gene->get_DNA->alphabet,  "\n";
  36     print STDERR "    Features:\n";
  37     print STDERR $gene->printfeaturesnum();
  38     print STDERR "    Gene has boundaries ",$gene->upbound," - ",$gene->downbound,"\n";
  39     print STDERR "    Gene has maxtranscript with start ",$gene->maxtranscript->start,
  40           " end ",$gene->maxtranscript->end," strand ",$gene->maxtranscript->strand,"\n";
  41     print STDERR "    DNA  has boundaries ",$gene->get_DNA->start," - ",$gene->get_DNA->end,"\n";
  42     print STDERR "\n";
  43
  44     print STDERR "Now issuing mutations to the gene....\n";
  45
  46     my $mutation = new Bio::LiveSeq::Mutation (-seq =>'A',
  47                                        -pos => 64
  48                                        );
  49     my $mutate = Bio::LiveSeq::Mutator->new(-gene => $gene,
  50                                          -numbering => "coding"
  51                                          );
  52     $mutate->add_Mutation($mutation);
  53     my $results=$mutate->change_gene();
  54     print "\n";
  55     if ($results) {
  56         my $out = Bio::Variation::IO->new( '-format' => 'flat');
  57         $out->write($results);
  58     }
  59 }