c_cpp/etc/KaKs_Calculator/parseFastaIntoAXT.pl

   1 #!/usr/local/perl
   2 if(@ARGV!=1) {
   3         die ("Usage: [Fasta file with aligned pairwise sequences]\n");
   4 }
   5 print "*****************************************************************
   6 Function: Parse fasta file with aligned pairwise sequences into AXT file
   7 Reference: Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 2006 , 4:259-263.
   8 Web Link: Documentation, example and updates at <http://code.google.com/p/kaks-calculator>
   9 *****************************************************************
  10 \n";
  11
  12 print "Input file = $ARGV[0]\n";
  13 print "Opening the input file...\n";
  14 unless (open (MYFILE, $ARGV[0])) {
  15     die ("Cannot open file\n");
  16 }
  17 @array = <MYFILE>;
  18 chomp @array;
  19
  20 $count = 0;
  21 @seq = ();
  22 @name = ();
  23 $tmp_seq = "";
  24
  25 print "Reading sequences";
  26 while ($count < @array) {
  27         print ".";
  28         if(index($array[$count], ">")==0) {
  29                 push(@name, substr($array[$count], 1, length($array[$count])-1));
  30                 if ($tmp_seq ne "") {
  31                         push(@seq, $tmp_seq);
  32                         $tmp_seq = "";
  33                 }
  34         }
  35         else {
  36                 $tmp_seq .= $array[$count];
  37         }
  38         $count++;
  39
  40         if ($count==@array) {
  41            push(@seq, $tmp_seq);
  42         }
  43
  44 }
  45
  46 print "\nFormatting AXT sequences...\n";
  47 $output  = join("-", @name)."\n";
  48 $output .= join("\n", @seq)."\n";
  49 $output .= "\n";
  50
  51 $outfile = $ARGV[0].".axt";
  52 print "Outputing AXT file: $outfile\n";
  53 open(OUTFILE, ">$outfile");
  54 print OUTFILE ($output);
  55
  56 print "\nMission accomplished.\n";