sub getSeqfromfasta2lmers
{
    my $file = shift;
    my @seqs= ();

    open INFILE, "<$file" or die "$0:  Can't open file $file: $!";
    my $in = Bio::SeqIO->new(-format => 'fasta',
                         -noclose => 1 ,
                         -fh => \*INFILE);

    while ( my $seq = $in->next_seq() ) {
    push @seqs, $seq->seq();
    } #end while
    return @seqs;
}

##</code><code>##

my $nofseq   = scalar( getSeqfromfasta2lmers( $file ) );

##</code><code>##

        my @input_seqs          = getSeqfromfasta2lmers($file);

##</code><code>##

        my $ip                  = @input_seqs;

##</code><code>##

sub getSeqfromfasta2lmers {
    my $file = shift;
    ## Use a lexical file handle so thaty the file is closed automatically
    open my fh, "<$file" or die "$0:  Can't open file $file: $!";
    my $in = Bio::SeqIO->newFH( -format => 'fasta', -fh => $fh );
    return <$in>; ### MUST BE CALLED IN A LIST CONTEXT!!!!
}

##</code><code>##

## Get the sequences.
my @input_seqs = getSeqfromfasta2lmers($file);
## And a count of them
my $nofseq      = @input_seqs;

##</code><code>##

sub main_process {
....
## Just reusing the array from outside the loop/sub will save a lot of time
## and some space.

## DELETE    my @input_seqs          = getSeqfromfasta2lmers($file);

## This doesn't appear to be used anywhere, but if I missed it and it is
## replace references to $ip with $nofseq

## DELETE    my $ip                  = @input_seqs;

##</code><code>##

sub getlmersfromseq {
    my  ($seqsarr,$l)= @_;
    my  @lmers;

    @lmers = map {substrings $_, $l} @{$seqsarr};
    my @uniq_lmers = uniq @lmers;
    return @uniq_lmers;
}

##</code><code>##

sub getlmersfromseq {
    my  ($seqsarr,$l)= @_;
    return uniq map {substrings $_, $l} @{$seqsarr};
}

##</code><code>##

sub gen_param {
    my ( $file, $file_neg, $nofseq ) = @_;
    my @param_groups;

    foreach my $wlen ( 8, 15, 20 ) {
        foreach my $fract ( 0.8, 0.5 ) {
            foreach my $q ( $nofseq, $nofseq * 1.5 ) {
                push @param_groups, {
                    file              => $file,
                    file_neg          => $file_neg,
                    submt_len         => 5,
                    submt_d           => 1,
                    e                 => 0,
                    W_size            => $wlen,
                    lp                => $fract * $wlen,
                    support_threshold => $q,
                    min_inst_lower    => $q,
                    min_inst_upper    => ( 3 * $q ),
                    polyTA_lim        => 0.8,
                    poly_lim          => 0.8,
                };
            }   
        } 
    }
    return @param_groups;
}

##</code><code>##

$hash{ 'some complicated key' } = [@matches];

##</code><code>##

$hash{ 'some complicated key' } = \@matches; 

##</code><code>##

    my $output = main_process( @{$_}{
        qw/ file file_neg submt_len submt_d e W_size lp support_threshold min_inst_lower min_inst_upper polyTA_lim poly_lim /
    });
    $result{ 'ParamGroup' . $count++ } = $output;

##</code><code>##

    }    # -----  end foreach $mcands  -----
    return;
}