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 # REVISION : $Id$
   8 #
   9 # INSTALLATION
  10 #    If you have installed bioperl using the standard
  11 #    makefile system everything should be fine and
  12 #    dandy.
  13 #
  14 #    if not edit the use lib "...." line to point the directory
  15 #    containing your Bioperl modules.
  16 #
  17
  18
  19 use Bio::Seq;
  20 use Bio::SeqIO;
  21
  22 # new sequence from raw memory...
  23 # it is *very* important to get the type right so it
  24 # is translated correctly.
  25
  26 $seq = Bio::Seq->new ( -id => "myseq",
  27                       -seq => "CGCCGAAGAAGCATCGTTAAAGTCTCTCTTCACCCTGCCGTCATGTCTAAGTCAGAGTCTCCT",
  28                       -type => 'Dna');
  29
  30 $seqout = Bio::SeqIO->new('-format' => 'fasta', -fh => \*STDOUT);
  31
  32 # make a reverse complement sequence
  33
  34 $rev = $seq->revcom();
  35
  36 # the actual sequence is here
  37
  38 $actual_bases = $rev->seq();
  39
  40 print "Reversed sequence as a string is [$actual_bases]\n";
  41
  42 # we could also write it as fasta formatted output
  43
  44 $seqout->write_seq($rev);
  45
  46 # make a translation
  47
  48 $trans = $seq->translate();
  49
  50 print "Translated sequence!\n";
  51
  52 $seqout->write_seq($trans);
  53