fasta_length

#!/usr/bin/perl

# returns the length of each fasta entry, one length per line of output
# written by Lex Nederbragt
# lex.nederbragt@bio.uio.no
# October 2009

use strict;
use warnings;

# my %seq;

$/=">"; # set the record separator to the '>' symbol
		# this forces each sequence into $_
		# note however, that each sequence ENDS with the '>' symbol
		# and that the first 'entry' (record) is consisting of ONLY the '>' symbol

<>;		# remove the empty first 'sequence'
while (<>){
	chomp;	# remove the trailing '>' symbol
	my @lines = split(/\n/,$_);	# split the entry into individual lines based on the newline character
	my $header = shift @lines;	# the header is the first line (now without the '>' symbol)
	my $seq = join "", @lines;

#	print sequences concatenated
	print length $seq; print "\n";

#	build a hash of sequences
#	$seq{join "", @lines}=$header;
}
$/="\n"; # reset the record separator