perl - fetch column names from file - perl

Question

I have the following command in my perl script:
my #files = `find $basedir/ -type f -iname '$sampleid*.summary.csv'`; #there are multiple summary.csv files in my basedir. I store them in an array
my $summary = `tail -n 1 $files[0]`; #Each summary.csv contains a header line and a line with data. I fetch here the last line.
chomp($summary);
my #sp = split(/,/,$summary); # I split based on ','
my $gender = $sp[11]; # the values from column 11 are stored in $gender
my $qc = $sp[2]; # the values from column 2 are stored in $gender
Now, I'm experiencing the situation where my *summary.csv files don't have the same number of columns. They do all have 2 lines, where the first line represents the header.
What I want now is not storing the values from column 11 in gender, but I want to store the values from the column 'Gender' in $gender.
How can I achieve this?
First try at solution:
my %hash = ();
my $header = `head -n 1 $files[0]`; #reading the header
chomp ($header);
my #colnames = split (/,/,$header);
my $keyfield = $colnames[#here should be the column with the name 'Gender']
push #{ $hash{$keyfield} };
my $gender = $sp[$keyfield]

Answer 1

You will have to read the header line as well as the data to know what column holds which information. This is done easiest by writing actual Perl code instead of shelling out to various command line utilities. See further below for that solution.
Fixing your solution also requires a hash. You need to read the header line first, store the header fields in an array (as you've already done), and then read the data line. The data needs to be a hash, not an array. A hash is a map of keys and values.
# read the header and create a list of header fields
my $header = `head -n 1 $files[0]`;
chomp ($header);
my #colnames = split (/,/,$header);
# read the data line
my $summary = `tail -n 1 $files[0]`;
chomp($summary);
my %sp; # use a hash for the data, not an array
# use a hash slice to fill in the columns
#sp{#colnames} = split(/,/,$summary);
my $gender = $sp{Gender};
The tricky part here is this line.
#sp{#colnames} = split(/,/,$summary);
We have declared %sp as a hash, but we now access it with a # sigil. That's because we are taking a hash slice, as indicated by the curly braces {}. The slice we take is all elements with the names of the values in #colnames. There is more than one value, so the return value is not a scalar (with a $) any more. There is a list of return values, so the sigil turns to #. Now we use that list on the left hand side (that's called an LVALUE), and assign the result of the split to that list.
Doing it with modern Perl
The following program will use File::Find::Rule to replace your find command, and Text::CSV to read the CSV file. It grabs all the files, then opens one at a time. The header line will be read first, and fed into the Text::CSV object, so that it can then give back a hash reference, which you can use to access every field by name.
I've written it in a way that it will only read one line for each file, as you said there are only two lines per file. You can easily extend that to be a loop.
use strict;
use warnings;
use File::Find::Rule;
use Text::CSV;
my $sampleid;
my $basedir;
my $csv = Text::CSV->new(
{
binary => 1,
sep => ',',
}
) or die "Cannot use CSV: " . Text::CSV->error_diag;
my #files = File::Find::Rule->file()->name("$sampleid*.summary.csv")->in($basedir);
foreach my $file (#files) {
open my $fh, '<', $file or die "Can't open $file: $!";
# get the headers
my #cols = #{ $csv->getline($fh) };
$csv->column_names(#cols);
# read the first line
my $row = $csv->getline_hr($fh);
# do whatever you you want with the row
print "$file: ", $row->{gender};
}
Please note that I have not tested this program.