Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48001.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48007.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48023.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48033.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48055.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48059.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48061.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48079.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48087.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48101.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48103.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48107.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48131.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48135.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48189.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48219.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48221.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48225.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48235.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48237.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48243.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48247.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48253.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48299.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48351.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48371.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48387.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48391.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48395.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48403.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48423.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48425.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48447.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48451.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48453.
Use of uninitialized value in concatenation (.) or string at sequence_replacement.pl line 56, <TWO> line 48455. 
##</code><code>##

 

#!/usr/bin/perl

use strict;
use warnings;

use Getopt::Long;

#set variables
my ($optHelp, $optFile1, $optFile2, $optList);

#get program options
GetOptions ('h' => \$optHelp, 'a=s' => \$optFile1, 'b=s' => \$optFile2, 'l=s' => \$optList);

# there are better ways to do this but I like this strategy :)
if($optHelp || !$optFile1 || !$optFile2  || !$optList ){
  print "Usege:\n\n";
  print "./program -a file1 -b file2 -l list<.tsv> \n\n";
  print "Note: sequences from file2 are replaced with those in file1 according to the list -l\n\n";
  exit(0);
}

 
#allocate memory (well, more of set variables)
my %hash1 =();
my %list = ();

#open files
open (ONE, "<", $optFile1) or die "$!";
open (TWO, "<", $optFile2) or die "$!";
open (LIST, "<", $optList) or die "$!";

#load list which should look like:
#file1_id <tab> file2_id

while(<LIST>){
  chomp;
  /^(.*?)\t(.*)/;
  $list{$1} = $2; #e
}
close LIST;

#read file one into memory
my $head;
while(<ONE>){
  chomp;
  if(/>(.*)/){$head = $1; next;} #e
  $hash1{$head} .= $_;
}
close ONE;

#replace fasta record from file to with the one in file one if id is set in list file
my $x = 0;
while(<TWO>){
  chomp;
  ## You can play with this if one line fasfa sequence is not what you can use
  if(/>(.*)/){if(defined $list{$1}){print $_. "\n" . $hash1{$list{$1}} . "\n"; $x = 1}else{$x = 0}}  #e
  print $_ . "\n" if $x == 0;  #e
}
close TWO;