released/pIRS.old/pIRS_simulator/extra/make_pure_ref_genome.pl

   1 #!/usr/bin/perl
   2 use strict;
   3
   4 #usage: remove the N bases in the sequence, to get a pure sequnence used for simulation
   5
   6
   7 my $ori_len = 0;
   8 my $pure_len = 0;
   9 my $loss_rate = 0;
  10
  11 $/=">";<>;$/="\n";
  12 while (<>) {
  13         my $title = $_;
  14         my $seq_name = $1 if($title =~ /^(\S+)/);
  15
  16         $/=">";
  17         my $seq=<>;
  18         chomp $seq;
  19         $/="\n";
  20
  21         $seq =~ s/\s//g;
  22         $ori_len = length($seq);
  23         $seq =~ s/[^acgtACGT]//g;
  24         $seq = uc($seq);
  25         $pure_len = length($seq);
  26
  27         Display_seq(\$seq);
  28         print ">$title$seq";
  29 }
  30
  31 $loss_rate = ($ori_len - $pure_len) / $ori_len if($ori_len);
  32
  33 print STDERR "ori_len:$ori_len\tpure_len:$pure_len\tloss_rate:$loss_rate\n";
  34
  35
  36
  37 #display a sequence in specified number on each line
  38 #usage: disp_seq(\$string,$num_line);
  39 #               disp_seq(\$string);
  40 #############################################
  41 sub Display_seq{
  42         my $seq_p=shift;
  43         my $num_line=(@_) ? shift : 50; ##set the number of charcters in each line
  44         my $disp;
  45
  46         $$seq_p =~ s/\s//g;
  47         for (my $i=0; $i<length($$seq_p); $i+=$num_line) {
  48                 $disp .= substr($$seq_p,$i,$num_line)."\n";
  49         }
  50         $$seq_p = ($disp) ?  $disp : "\n";
  51 }
  52 #############################################
  53