Please help with a shell script of the following. I need count number of consistent variables in each lane (col1) across samples (col2). For example, since all the values (col4) of lane1 variable 1 accross all theree samples are the sample, variable1 is counted towards a consistent variable. Similarly, lane 2 variables 2 and 3 are both inconsistent.
lane1 sample1 variable1 ab lane1 sample2 variable1 ab lane1 sample3 variable1 ab lane1 sample1 variable2 cd lane1 sample2 variable2 cd lane1 sample3 variable2 cd lane1 sample1 variable3 gh lane1 sample2 variable3 ab lane1 sample3 variable3 gh lane2 sample1 variable1 ac lane2 sample2 variable1 ac lane2 sample3 variable1 ac lane2 sample1 variable2 gt lane2 sample2 variable2 gt lane2 sample3 variable2 ac lane2 sample1 variable3 ga lane2 sample2 variable3 ga lane2 sample3 variable3 ac
Output
Number of consistent and inconsistent variables accross all three samples
#Consistent #Inconsistent lane1 2 1 lane2 1 2
Answer
Perl solution:
#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };
my %values;
while (<>) {
next if /^$/; # Skip empty lines
my ($lane, $sample, $var, $val) = split;
die "Duplicate $lane $sample $varn" if $values{$lane}{$var}{$val}{$sample};
$values{$lane}{$var}{$val}{$sample} = 1;
}
my %results;
for my $lane (keys %values) {
for my $var (keys %{ $values{$lane} }) {
my $count = keys %{ $values{$lane}{$var} };
if (1 == $count) {
++$results{$lane}{consistent};
} else {
++$results{$lane}{inconsistent};
}
}
say join "t", $lane, @{ $results{$lane} }{qw{ consistent inconsistent }};
}