perl/etc/WoodyMiaoLin/PbeBefore2015/get_samples_with_onlyATP8.pl

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 open I1, "<", "../../../a.mt_haplotype_full_length_tree/b.modified_alignment/haplotype_sampleID.txt";
   6 open I2, "<", "../../a.fromZhangYue/AllPbeATP8_20120315.fasta";
   7 open O, ">", "samples_with_onlyATP8.fasta";
   8
   9 my @s; #sampleIDs with full mt sequence.
  10 while (<I1>) {
  11         /\t(.+)\n/;
  12         my @a = split / /, $1;
  13         push @s, @a;
  14 }
  15 close I1;
  16
  17 while (<I2>) {
  18         $/ = ">";
  19         my $seq = <I2>;
  20         chomp $seq;
  21         $seq =~ s/\s//g;
  22         $/ = "\n";
  23         s/>//;
  24         /^(\S+)\s/;
  25         my $b = $1;
  26         if (!grep(/^$b$/, @s)) {
  27                 print O ">$1\n$seq\n";
  28         }
  29 }
  30 close I2;
  31 close O;