perl read file from specified line thru the end - perl

Question

I'm new with perl. I'm trying to read a large comma separate file, split and grab only some columns. I could create it with some internet help, but I'm struggling to change to code to start reading from a specific line thru the end of the file.
my need is open file start reading on line 12, split ',' grab column 0,2,10,11 and concatenate those needed columns with '\t'.
here is my code
#!/usr/bin/perl
my $filename = 'file_to_read.csv';
open(FILER, $filename) or die "Could not read $filename.";
open(FILEW, ">$filename.txt") || die "couldn't create the file\n";
while(<FILER>) {
chomp;
my #fields = split(',', $_);
print FILEW "$fields[0]\t$fields[3]\t$fields[10]\t$fields[11]\n";
}
close FILER;
close FILEW;
here is the file example:
[Header]
GSGT Version: X
Processing Date:12/01/2010 7:20 PM
Content:
Num SNPs:
Total SNPs:
Num Samples:
Total Samples:
Sample:
[Data]
SNP Name,Chromosome,Pos,GC Score,Theta,R,X,Y,X Raw,Y Raw,B Allele Freq,Log R Ratio,Allele1 - TOP,Allele2 - TOP
1:10001102-G-T,1,10001102,0.4159,0.007,0.477,0.472,0.005,6281,126,0.0000,-0.2581,A,A
1:100011159-T-G,1,100011159,0.4259,0.972,0.859,0.036,0.822,807,3648,0.9942,-0.0304,C,C
1:10002775-GA,1,10002775,0.4234,0.977,1.271,0.043,1.228,809,5140,0.9892,0.0111,G,G

Answer 1

Rather than skipping until a specific line number, which may vary from file to file, it is best to keep track of the current section of the file marked by [Header], [Data] etc.
This solution keeps a state variable $section which is updated to the current section name every time a [Section] label is encountered in the file. Everything from the Data section is summarised and printed
A similar thing could be done with the column headers, using names instead of numbers to select the fields to be output, but I have chosen to keep the complexity down instead
use strict;
use warnings 'all';
use feature 'say';
my $filename = 'file_to_read.csv';
open my $fh, '<', $filename or die qq{Unable to open "$filename" for input: $!};
my $section = "";
while ( <$fh> ) {
next unless /\S/; # Skip empty lines
if ( $section eq 'Data' ) { # Skip unless we're in the [Data] section
chomp;
my #fields = split /,/;
say join ',', #fields[0,3,10,11];
}
elsif ( /\[(\w+)\]/ ) {
$section = $1;
}
}
output
SNP Name,GC Score,B Allele Freq,Log R Ratio
1:10001102-G-T,0.4159,0.0000,-0.2581
1:100011159-T-G,0.4259,0.9942,-0.0304
1:10002775-GA,0.4234,0.9892,0.0111

Answer 2

please assign a variable to count the lines processed like my $line_count = 0;
and inside the beginning of while loop increment the varialbe $line_count++;
and skip if the line count is below 12 ie , next if $line_count > 12;