perl/etc/WoodyMiaoLin/PbeBefore2015/convert_fasta_to_nexus.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 my $i = shift;
   6 my $o = shift;
   7
   8 open my $i1, "<", "$i";
   9 open O, ">", "$o";
  10
  11 my $nchar;
  12 my %dna = %{&readfasta($i1)};
  13 close $i1;
  14 my $ntax = keys %dna;
  15
  16 print O "#NEXUS
  17 BEGIN DATA;
  18 Dimensions ntax=$ntax nchar=$nchar;
  19 Format datatype=DNA gap=- missing=?;
  20 Matrix\n";
  21
  22 foreach (sort keys %dna) {
  23         print O "$_\t$dna{$_}\n";
  24 }
  25 print O ";\nEND;\n";
  26 close O;
  27
  28 sub readfasta {
  29         my $in = $_[0];
  30         my %fa;
  31         while (<$in>) {
  32                 $/ = ">";
  33                 my $seq = <$in>;
  34                 chomp $seq;
  35                 $seq =~ s/\s//g;
  36                 $/ = "\n";
  37                 $nchar = length $seq unless $nchar;
  38                 s/>//;
  39                 /^(\S+)\s/;
  40                 $fa{$1} = $seq;
  41         }
  42         return \%fa;
  43 }