Shell Programming and Scripting

#read_1
AWEAWQQRZZZQWQQWZ
#read_2
ZZAQWRQTWQQQWADSADZZZ
#read_3
POGZZZZZZADWRR
.
.

#read_1 3
#read_1 1
#read_2 2
#read_2 3
#read_3 6
.
.

#!/usr/bin/perl 

$/ = ">";


while (<>) {
	next if $. ==  1;
	chomp;

	my($header,@other) =  split(/\n/,$_);
	$sequence = join"",@other;

	my @letters = split"",$sequence;
	$seqlength = length $sequence;
	$counter = 0;

	foreach $base (@letters) {
		$counter++ if $base eq 'Z';
	}
	print ">$header\t$counter\n";	
	
}

[home@user]perl count.pl input_file.txt > input_file.stats
[home@user]cat input_file.stats
#read_1 4
#read_2 5
#read_3 6
.
.

perl -l -0043 -ne '/(.*)\n(.*)/;$h=$1;$s=$2;while($s=~/Z+/g){print "#$h " . length $&}' input_file.txt

-0[octal/hexadecimal] 

specifies the input record separator ($/ ) as an octal or hexadecimal number.

/(.*)\n(.*)/