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

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

Please upload the actual file somewhere and post a link. It will be useful to test and to see the solution in an acton. — Miroslav Popov
– Miroslav Popov, Commented Aug 18, 2019 at 14:48

brian d foy · Accepted Answer · 2019-08-18 15:39:00Z

4

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

answered Aug 18, 2019 at 15:39

brian d foy

134k31 gold badges214 silver badges613 bronze badges

Sign up to request clarification or add additional context in comments.

2 Comments

Tina Sharma Over a year ago

Thank you so much for your reply. This code is working but the problem is now I want to compare column values like if column 2nd and 3rd has Resistant value than column 1st will be filled by MDR and if both are susceptible than column Ist will be filled by susceptible.

Dave Cross Over a year ago

@TinaSharma: If you have further questions, then it probably makes sense to post them separately.

Collectives™ on Stack Overflow

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

1 Answer 1

2 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

2 Comments

Your Answer

Sign up or log in

Post as a guest

Related