#!/usr/bin/perl


# To redirect the output of your program to a file called hw1.out,
# run it with the following command:
#
#       -> ./hw1_1.pl > hw1_1.out
#
# You can then diff the results with my output with the following command:
#
#       -> diff ~stacia/ws05/hw1_1.out hw1_1.out
#
# If this command returns nothing, the two files are identical. Note that
# diff is sensitive to whitespace.

$prefix = "/home/faculty/stacia/ws05/data/metazoa/";
opendir(METAZOA,"$prefix") || die "Couldn't open dir: $!";
@ALL_FILES = readdir(METAZOA);
closedir(METAZOA);

foreach $file (@ALL_FILES){
  if($file =~ /.*\.gbk/) {
    open(I,$prefix . $file) || die "Couldn't open file: $!";
    while(<I>) {
      if(/DEFINITION\s+(\S.*\S)\s+mitochon/) {
        print "$1, ";
      }
      if(/\/gene="COX1"/ && $last =~ /gene\s+(\S+)/) {
        print "$1";
      }  
       
      $last = $_;  #save, in case the next line indicates that this is the COX-I gene
       
    }
    print "\n";
    close(I);
  } 
}