How can I normalize my results in perl with foreach control structure? - perl

Question

I have this output:
10dvex2_miRNA_ce.out.data|6361
10dvex2_miRNA_ce.out.data|6361
10dvex2_misc_RNA_ce.out.data|0
10dvex2_rRNA_ce.out.data|239
with this script in Perl:
#!/usr/bin/perl
use warnings;
use strict;
open(MYINPUTFILE, $ARGV[0]); # open for input
my #lines = <MYINPUTFILE>; # read file into list
my $count = 0;
print "Frag"."\t"."ncRNA"."\t"."Amount"."\n";
foreach my $lines (#lines){
my $pattern = $lines;
$pattern =~ s/(.*)dvex\d_(.*)_(.*).(out.data)\|(.*)/$1 $2 $3 $5/g;
$count += $5;
print $1."\t".$2.$3."\t".$5."\n";
}
close(MYINPUTFILE);
exit;
I extract this information:
Frag ncRNA Amount
10 miRNAce 6361
10 misc_RNAce 0
10 rRNAce 239
but in the Amount column I want to report those numbers divided by the total result (6600). In this case I want this output:
Frag ncRNA Amount
10 miRNAce 0.964
10 misc_RNAce 0
10 rRNAce 0.036
My problem is extract the TOTAL result in the loop...to normalize this data. Some ideas?

Answer 1

Perhaps the following will be helpful:
use strict;
use warnings;
my ( %hash, $total, %seen, #array );
while (<>) {
next if $seen{$_}++;
/(\d+).+?_([^.]+).+\|(\d+)$/;
$hash{$1}{$2} = $3;
$total += $3;
}
print "Frag\tncRNA\tAmount\n";
while ( my ( $key1, $val1 ) = each %hash ) {
while ( my ( $key2, $val2 ) = each %$val1 ) {
my $frac = $val2 / $total == 0 ? 0 : sprintf( '%.3f', $val2 / $total );
push #array, "$key1\t$key2\t$frac\n";
}
}
print map { $_->[0] }
sort { $b->[1] <=> $a->[1] }
map { [ $_, (split)[2] ] }
#array;
Output from your data set:
Frag ncRNA Amount
10 miRNA_ce 0.964
10 rRNA_ce 0.036
10 misc_RNA_ce 0
Identical lines are skipped, and then the required elements are captured from each line. A running total is kept for the subsequent calculation. Your desired output showed sorting from high to low, which is why each record is pushed onto #array. However, if sorting isn't necessary, you can just print that line and omit the Schwartzian transform on #array.
Hope this helps!

Answer 2

To do this you will need two passes over the data.
#! /usr/bin/env perl
use warnings;
use strict;
print join("\t",qw'Frag ncRNA Amount'),"\n";
my #data;
my $total = 0;
# parse the lines
while( <> ){
my #elem = /(.+?)(?>dvex)\d_(.+)_([^._]+)[.]out[.]data[|](d+)/;
next unless #elem;
# running total
$total += $elem[-1];
# combine $2 and $3
splice #elem, 1, 2, $2.$3; # $elem[1].$elem[2];
push #data, \#elem;
}
# print them
for( #data ){
my #copy = #$_;
$copy[-1] = $copy[-1] / $total;
$copy[-1] = sprintf('%.3f', $copy[-1]) if $copy[-1];
print join("\t",#copy),"\n";
}