examples/liveseq/change_gene.pl

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