examples/rev_and_trans.pl

   1 #!/usr/bin/perl
   2
   3 # PROGRAM  : rev_and_trans.pl
   4 # PURPOSE  : Simple driver for Bio::Seq revcom and translate
   5 # AUTHOR   : Ewan Birney birney@sanger.ac.uk
   6 # CREATED  : Tue Oct 27 1998
   7 #
   8 # INSTALLATION
   9 #    If you have installed bioperl using the standard
  10 #    makefile system everything should be fine and
  11 #    dandy.
  12 #
  13 #    if not edit the use lib "...." line to point the directory
  14 #    containing your Bioperl modules.
  15 #
  16
  17
  18 use Bio::Seq;
  19 use Bio::SeqIO;
  20
  21 # new sequence from raw memory...
  22 # it is *very* important to get the type right so it
  23 # is translated correctly.
  24
  25 $seq = Bio::Seq->new ( -id => "myseq",
  26                       -seq => "CGCCGAAGAAGCATCGTTAAAGTCTCTCTTCACCCTGCCGTCATGTCTAAGTCAGAGTCTCCT",
  27                       -type => 'Dna');
  28
  29 $seqout = Bio::SeqIO->new('-format' => 'fasta', -fh => \*STDOUT);
  30
  31 # make a reverse complement sequence
  32
  33 $rev = $seq->revcom();
  34
  35 # the actual sequence is here
  36
  37 $actual_bases = $rev->seq();
  38
  39 print "Reversed sequence as a string is [$actual_bases]\n";
  40
  41 # we could also write it as fasta formatted output
  42
  43 $seqout->write_seq($rev);
  44
  45 # make a translation
  46
  47 $trans = $seq->translate();
  48
  49 print "Translated sequence!\n";
  50
  51 $seqout->write_seq($trans);
  52