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sub getSeqfromfasta2lmers
{
...
    } #end while
    return @seqs;
}

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

        my @input_seqs          = getSeqfromfasta2lmers($file);

        my $ip                  = @input_seqs;

sub getSeqfromfasta2lmers {
    my $file = shift;
...
    my $in = Bio::SeqIO->newFH( -format => 'fasta', -fh => $fh );
    return <$in>; ### MUST BE CALLED IN A LIST CONTEXT!!!!
}

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

sub main_process {
....
...
## replace references to $ip with $nofseq

## DELETE    my $ip                  = @input_seqs;

sub getlmersfromseq {
    my  ($seqsarr,$l)= @_;
...
    my @uniq_lmers = uniq @lmers;
    return @uniq_lmers;
}

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

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

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

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

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

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