How to extract row data from a csv file using perl? - csv

Question

I have a csv file like
Genome Name,Resistance_phenotype,Amikacin,Gentamycin,Aztreonam
AB1,,Susceptible,Resistant,Resistant
AB2,,Susceptible,Susceptible,Susceptible
AB3,,Resistant,Resistant,NA
I need to fill 2nd column i.e. Resistant phenotype with MDR, XDR and susceptible. for which I have to match antibiotic resistance profile like if in first row gentamycin & antreanam both are resistant the 2nd column will be filled with MDR and in 3nd row if all 3 are susceptible the 2nd column of 3rd row will be filled with susceptible.
I have written a code mentioned below which only display columns of the csv file. I got stuck what to do further.
#!/usr/bin/perl
use strict;
use warnings;
my $file = 'text.csv';
my #data;
open(my $fh, '<', $file) or die "Can't read file '$file' [$!]\n";
while (my $line = <$fh>) {
chomp $line;
my #fields = split(/,/, $line);
print $fields[0], "\n";
#print $fields[1], "\n";
}
close $file;
Genome Name,Resistance_phenotype,Amikacin,Gentamycin,Aztreonam
AB1,MDR,Susceptible,Resistant,Resistant
AB2,Susceptible,Susceptible,Susceptible,Susceptible
AB3,MDR,Resistant,Resistant,NA

Answer 1

Use the Text::CSV_XS module. Read a line, assign the right value to the that column, then print it again. In your sample code, you were only writing one column instead of all of them; the module will handle all of that for you:
use Text::CSV_XS;
my $csv = Text::CSV_XS->new;
# replace *DATA and *STDOUT with whatever filehandles you want
# to read then write.
while( my $row = $csv->getline(*DATA) ) {
$row->[1] = 'Some value';
$csv->say( *STDOUT, $row );
}
__DATA__
Genome Name,Resistance_phenotype,Amikacin,Gentamycin,Aztreonam
AB1,,Susceptible,Resistant,Resistant
AB2,,Susceptible,Susceptible,Susceptible
AB3,,Resistant,Resistant,NA
The output is:
"Genome Name","Some value",Amikacin,Gentamycin,Aztreonam
AB1,"Some value",Susceptible,Resistant,Resistant
AB2,"Some value",Susceptible,Susceptible,Susceptible
AB3,"Some value",Resistant,Resistant,NA