#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Long;

# Declare variables
my @nucs;
my @data;
my $GC_counter;
my $sequence;

# Define defaults for variables
my $fasta="";
my $winlen="";
my $increment="";

parseArgs();   # subroutine to call GetOptions

# Open the fasta file, read it in, pass only sequences to @data
open( FASTA, $fasta ) || die "Doh! Can't open $fasta: $!n";
while( my $seq = <FASTA> ){
chomp $seq;

    if( $seq =~ /^>/ ){
    next;
    }elsif( $seq =~ /^s*$/ ){
    next;
    }elsif( $seq =~ /^s*#/ ){
    next;
    }else{
    $data .= $seq;
    }
}
close FASTA;

# subroutine to call sliding_window and calculate GC content of each
# sliding window
sliding_window();

exit;


###########################SUBROUTINES##################################

sub parseArgs{
#Message to print if mandatory variables not declared
my $usage ="nUsage: $0 --fasta /path/to/*.fasta --winlen <integer> --increment <integer> [options]

Mandatory options:
--fasta       -  path to the first input file (fasta) in .fasta or .fsa format
--winlen      -  specify size of the sliding window
--increment   -  specify increment length for the sliding window
n";

my $options = GetOptions
    (
    'fasta=s{1,1}'      =>  $fasta,
    'winlen=i{1,1}'     =>  $winlen,
    'increment=i{1,1}'  =>  $increment,
    );

    if ( $fasta eq "" ){ die "nnDoh!: fasta input file must be specified!nn$usagen"};
    if ( $winlen eq "" ){die "nnDoh!: length of sliding window must be specifiednn$usagen"};
    if ( $increment eq "" ){die "nnDoh!: increment length must be specifiednn$usagen"};

};

#########################################################################

sub sliding_window{

    my $start = 0;
    while( $start < length( $data ) ){;
        my $sequence = substr( $data, $start, $winlen );

            if( $start == 0 ){
                print $start + 1, "t";
            }else{
                print $start, "t";
            }

        # calls the subroutine getGC to calculate %GC content
        getGC( $sequence );
        $start = $start + $increment;

    }
}

#########################################################################

sub getGC{

    my $sequence = $_[0];
    my $GC_counter = 0;
    my @nucs = split( //, $sequence );

    for ( my $i = 0; $i < @nucs; $i++ ){
        if( $nucs[$i] =~ /G|C/g ){
            $GC_counter++;
        }
    }
    printf ( "%.2f%%n", ( $GC_counter / $winlen ) * 100);
}

#########################################################################

push ( @data, $seq );
        @nucs = split ( //, $_ );

substr outside of string at ./slidingWindowGC.pl line 76.
76         my $sequence = substr( @nucs, $increment, $winlen );

Use of uninitialized value $sequence in print at ./slidingWindowGC.pl line 87.