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$ cat -n process_files.pl
     1  #!/usr/bin/perl
     2  use strict;
     3
     4  # Set the file names
     5  my $search_file = "file1";
     6  my $data_file = "file2";
     7  my $temp_file = "file1.tmp";
     8
     9  # $sf = The search file; the file from where the search terms are read.
    10  # $df = The data file; the file to be scanned with the search term to fetch
    11  #       values of AF and FDP
    12  # $tf = The temporary file; where the final results are stored temporarily.
    13  #       After all processing is done, you can either move or copy the temp file
    14  #       to the search file. This is much safer than in-place editing of search
    15  #       file.
    16  open(my $sf, "<", $search_file) or die "Can't open $search_file: $!";
    17  open(my $df, "<", $data_file) or die "Can't open $data_file: $!";
    18  open(my $tf, ">", $temp_file) or die "Can't open $temp_file: $!";
    19
    20  # Loop through the search file
    21  while (<$sf>) {
    22      chomp(my $line1 = $_);
    23      # For each line in the search file, extract the search term, which is
    24      # the second "word" from left.
    25      (my $search_term) = $line1 =~ /^\S+\s+(\S+).*$/;
    26
    27      # Initialize AF and FDP to zero-length strings. If the search term is
    28      # not found in data file, we use this fact to print "NOT DETECTED".
    29      my ($af, $fdp) = ("", "");
    30
    31      # Now loop through the data file looking for the search term.
    32      while (<$df>) {
    33          chomp(my $line2 = $_);
    34          # If the search term was found in a particular line of data file,
    35          # set AF and FDP values and stop processing the data file.
    36          if ($line2 =~ /$search_term/) {
    37              ($af, $fdp) = $line2 =~ /AF=(.*?);.*FDP=(.*?);/;
    38              last;
    39          }
    40      }
    41
    42      # If AF and FDP were set, print their values, else "NOT DETECTED".
    43      if ($af eq "" and $fdp eq "") {
    44          print $tf "$line1 NOT DETECTED\n";
    45      } else {
    46          print $tf "$line1 READS=[$fdp] AF=[$af]\n";
    47      }
    48
    49      # Now rewind; set the pointer back to the beginning of data file.
    50      # For the next search term, we will start searching from the top of the
    51      # data file.
    52      seek($df, 0, 0);
    53  }
    54
    55  close($sf) or die "Can't close $search_file: $!";
    56  close($df) or die "Can't close $data_file: $!";
    57  close($tf) or die "Can't close $temp_file: $!";
    58
    59  # At this point, we have the original file "file1" and a temp file "file1.tmp"
    60  # with the desired output. The following statements retain a backup of the
    61  # original file.
    62  my $sf_orig = "file1.orig";
    63  rename($search_file, $sf_orig) or die "Can't rename $search_file to $sf_orig: $!";
    64  rename($temp_file, $search_file) or die "Can't rename $temp_file to $search_file: $!";
    65

$
$ perl process_files.pl
$
$ cat file1
AKT1 c.49G>A p.E17K NOT DETECTED
AKT1 c.155T>G p.L52R NOT DETECTED
APC c.4033G>T p.E1345* READS=[1999] AF=[0.248124]
EGFR c.2237_2255delAATTAAGAGAAGCAACATCinsT p.E746_S752delinsV READS=[1963] AF=[0.0,0.0,0.0,0.139582]

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