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how to compare rows in csv file with perl

genetist
Novice

Jul 24, 2013, 10:01 PM

Post #1 of 2 (366 views)

how to compare rows in csv file with perl	Can't Post

Hi to all,

my data looks like this

Code pedigree A B C D E F X X1 -/- -/- -/- C/C A/A -/- Y Y1 C/C C/C A/A A/A A/A A/A

here i want to compare X1 with Y1 from coulmn A to F, if they match exactly then i would like call them as mono else poly but either of X1 or Y1 contains any of these characters -/-,z/z across all columns i would like to consider them as mono even though second row contains different characters.Please see my attached file for better understanding there i worked above procedure clearly. Now i want to compare other rows of data from A to F (I have data of 16 rows below the Y1 in my attached file) to Y1 values from A to F with the rest of values in that coulmn( upto 16 cells in pedigree column) if they match then my score will be 1 else 0, then i would like to make sum from only columns contains POLY tag. I did some basic work for this in perl and i structed some where can any one please help to solve this. This ia my code,

use strict;
use warnings;
my $file = 'perl.csv';
open my $info, $file or die "Could not open $file: $!";

while( my $line = <$info>) {
print $line;
last if $. == 19;
}
close $info;

please see my attached file for better understanding my problem and i may not explained you my problem very well,

any help would be greately appreciated

Genetist

Laurent_R
Enthusiast / Moderator

Jul 24, 2013, 11:23 PM

Post #2 of 2 (364 views)

Re: [genetist] how to compare rows in csv file with perl [In reply to]	Can't Post

The next thing you need to do is to split your $line into an array or into individual variables:

Code

while( my $line = <$info>) { 
my @fields = split / /, $line; 
print $line; 
last if $. == 19; 
}

Now, the @fields array containts the individual fields, you can compare $fields[0] with $fields[7] or whatever you need.

Or this;

Code

while( my $line = <$info>) { 
my ($a, $b, $c, $d, $e, $f, ...) = split / /, $line; 
print $line; 
last if $. == 19; 
}

Same thing, you can now compare $a with $f, or whatever you need.

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