examples/generate_random_seq.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use vars qw($USAGE);
   4
   5 # random sequence generator #
   6 # -c=1 option will cause prot sequences to be built
   7 # using vertebrate aa frequencies,
   8 # with option -a putting a 1st methionine residues on. Frequencies are
   9 # calculated from the NCBI human RefSeq protein sequences
  10 # -c and -a only affect protein sequences
  11 # -a only works in conjunction with -c
  12 # -n number of random sequences, default = 1
  13
  14 use Bio::PrimarySeq;
  15 use Bio::SeqIO;
  16 use Getopt::Long;
  17 my ($length,$type,$filename,$comp,$met);
  18
  19 $USAGE = 'usage: generate_random_seq.pl --length=1000 --type=dna --filename=/tmp/test.seq --number=50';
  20
  21 my %alphabets = ( 'dna' => [qw(C A G T)],
  22                   'rna' => [qw(C A G U)],
  23                   'prot'=> [qw( A C D E F G H I K L M N P Q R S T V W Y)],
  24               );
  25 # make random num from 1-10000. numbers in this array reflect the frequency,
  26 # e.g., a random number from 1.744 = A, 745-991 = C etc;
  27 my @aa_frequencies = qw(744 991 1398 2017 2378 3104 3349 3726 4239 5273 5443
  28                         5749 6410 6848 7455 8263 8760 9340 9488 9713 10000);
  29 my $number = 1;
  30
  31 &GetOptions
  32   (
  33    'l|length:s'          => \$length,
  34    't|type|m|alphabet:s' => \$type,
  35    'f|file|filename:s'   => \$filename,
  36    'c|composition:s'     => \$comp,
  37    'a|methionine:s'      => \$met,
  38    'n|number:s'          => \$number
  39   );
  40
  41 assert ( $type && defined ($alphabets{lc $type}),
  42          $USAGE);
  43 assert ( $length && $length =~ /^\d+$/, $USAGE );
  44
  45 foreach my $num (1..$number) {
  46    my $sequence = "";
  47    my $alphabet = $alphabets{lc $type};
  48    my $sspace = scalar @$alphabet;
  49    if (!$comp || $type ne 'prot') {
  50       foreach ( 1..$length ) {
  51          $sequence .= $alphabet->[ int rand($sspace) ];
  52       }
  53    }elsif ($type eq 'prot') {
  54       $sequence = build_seq($length, \@aa_frequencies);
  55    }
  56    my $seq =  Bio::PrimarySeq->new(-seq        => $sequence,
  57                                    -display_id => 'randomseq'.$num);
  58    my %args = (-format => 'fasta');
  59    if( $filename ) { $args{-file} = ">>$filename" }
  60    my $seqio = Bio::SeqIO->new(%args);
  61    $seqio->write_seq($seq);
  62 }
  63
  64 sub assert { die $_[1] unless( $_[0] ); }
  65
  66 sub build_seq {
  67    #takes seqlen and ref to frequency data as parameters
  68    my ($len, $pf)  = @_;
  69    my $str = ($met)?'M':'';
  70    my $i = ($met)?1:0;
  71    for ($i..$len-1) {
  72       my $aa = int(rand (10000)) ;
  73       my $j = 0;
  74       while ($pf->[$j] < $aa && $j <19) {
  75          $j++;
  76       }
  77       $str .= $alphabets{'prot'}[$j];
  78    }
  79    print "str is $str\n";
  80    return $str;
  81 }