Below is my script. I have attempted many print statements to work out why it is only accessing the first array element. The pattern match works. The array holds a minimum 40 elements. I have checked and it is full. I have printed each line, and each line prints.
my $index = 0;
open(FILE, "$file") or die "\nNot opening $file for reading\n\n";
open(OUT, ">$final") or die "Did not open $final\n";
while (<FILE>) {
foreach my $barcode (@barcode) {
my @line = <FILE>;
foreach $_ (@line) {
if ($_ =~ /Barcode([0-9]*)\t$barcode[$index]\t$otherarray[$index]/) {
my $bar = $1;
$_ =~ s/.*//;
print OUT ">Barcode$bar"."_"."$barcode[$index]\t$otherarray[$index]";
}
print OUT $_;
}
$index++;
}
}
Okay, lets say the input was:
File:
Barcode001 001 abc
Barcode002 002 def
Barcode003 003 ghi
@barcode holds:
001
002
003
@otherarray holds:
abc
def
ghi
The output result for this script is currently printing only:
Barcode001_001 abc
It should be printing:
>Barcode001_001 abc
>Barcode002_002 def
>Barcode003_003 ghi
Where it should be printing a whole load up to ~40 lines.
Any ideas? There must be something wrong with the way I am accessing the array elements? Or incrementing? Hoping this isn't something too silly! Thanks in advance.
It needs the index because I am trying to match arrays in parallel, as they are ordered. Each line needs to match the corresponding indices of the arrays to each line in the file.
It turns out it was a simple issue as I had suspected being a Monday. I had a colleague go through it with me, and it was the placing of the index:
#my $index = 0; #This means the index is iterated through,
#but for each barcode for one line, then it continues
#counting up and misses the other values, therefore
#repeatedly printing just the first element of the array.
open(FILE, "$file") or die "\nNot opening $file for reading\n\n";
open(OUT, ">$final") or die "Did not open $final\n";
while (<FILE>) {
$index = 0; #New placement of $index for initialising.
foreach my $barcode (@barcode) {
my @line = <FILE>;
foreach $_ (@line) {
if ($_ =~ /Barcode([0-9]*)\t$barcode[$index]\t$otherarray[$index]/) {
my $bar = $1;
$_ =~ s/.*//;
print OUT ">Barcode$bar"."_"."$barcode[$index]\t$otherarray[$index]";
}
print OUT $_;
$index++; #Increment here
}
#$index++;
}
}
Thanks to everyone for their responses, for my original and poorly worded question they would have worked and may be more efficient, but for the purpose of the script and my edited question, it needs to be this way.
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