Parsing Tab Delimited File into an array - perl

Question

I am attempting to read a CSV into an array in a way that I can access each column in a row. However when I run the following code with the goal of printing a specific column from each row, it only outputs empty lines.
#set command line arguments
my ($infi, $outdir, $idcol) = #ARGV;
#lead file of data to get annotations for
open FILE, "<", $infi or die "Can't read file '$infi' [$!]\n";
my #data;
foreach my $row (<FILE>){
chomp $row;
my #cells = split /\t/, $row;
push #data, #cells;
}
#fetch genes
foreach (#data){
print "#_[$idcol]\n";
# print $geneadaptor->fetch_by_dbID($_[$idcol]);
}
With a test input of
a b c
1 2 3
d e f
4 5 6
I think the issue here isn't so much loading the file, but in treating the resulting array. How should I be approaching this problem?

Answer 1

First of all you need to push #data, \#cells, otherwise you will get all the fields concatenated into a single list.
Then you need to use the loop value in the second for loop.
foreach (#data){
print $_->[$idcol], "\n";
}
#_ is a completely different variable from $_ and is unpopulated here.
You should also consider using
while (my $row = <FILE>) { ... }
to read your file. It reads only a single line at a time whereas for will read the entire file into a list of lines before iterating over it.

Answer 2

I recommend to avoid parsing the CSV file directly and using the Text::CSV module.
use Text::CSV;
use Carp;
#set command line arguments
my ($infi, $outdir, $idcol) = #ARGV;
my $csv = Text::CSV->new({
sep_char => "\t"
});
open(my $fh, "<:encoding(UTF-8)", $infi) || croak "can't open $infi: $!";
# Uncomment if you need to skip header line
# <$fh>;
while (<$fh>) {
if ($csv->parse($_)) {
my #columns = $csv->fields();
print "$columns[0]\t$columns[1]\t$columns[2]\n";
} else {
my $err = $csv->error_input;
print "Failed to parse line: $err";
}
}
close $fh;