Hello much smarter people than I! I have a code due tomorrow for my bioinformatics class and I'm almost done, but I keep getting the error "Can't use string "analysis" as HASH ref while strict refs in use at analysis.pm at line 17." I posted my main code (Perl-1.pl) and then my class/objects (analysis.pm). Any help would be appreciated (and fast!) It's kinda long, but I put a comment where line 17 and the problem is. Thanks # Here is Perl-1:

#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
use analysis;

my $filename=<>;
my %seqhash=();
my $sequence='';
my $seqname='';
my $seq_no=0;


my $stream = Bio::SeqIO->new(-file => $filename,
                             -format => 'GenBank');
while (my $seqObj = $stream->next_seq() ) {
    my  $seq  = $seqObj->seq();
    my $display_id  = $seqObj->display_id;
    
    $seqhash{$sequence}=$seq;
    $seqhash{$seqname}=$display_id;
    ++$seq_no;
    
    foreach my $key (keys %seqhash)
  {
    print "\n\nSeq No.".$seq_no.":=".$seqhash{$seqname}; 
    my $nucleotides=analysis->nucleotide_count($seqhash{seqname},$seq)
+;
    print "Amino Acid = ";
    my $aminoacid=analysis->aminoanalysis($seqhash{seqname},$seq);
  }

}
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#and here is analysis.pm:

package analysis;
use strict;

sub new {
  my $class = shift;
  my $self = bless {}, $class;
  my $seqname=shift;
  my $sequence=shift;
  $self->{_seqname}=$seqname;
  $self->{_sequence}=$sequence;
  return $self;
}


sub nucleotide_count{
  my ($self)=shift;
  my $seqname=$self->{_seqname};      #SOMETHING WRONG HERE!
  my $sequence=$self->{_sequence};
  my $count_of_A=0;
        my $count_of_T=0;
        my $count_of_C=0;
        my $count_of_G=0;
        my $count_of_N=0;
        $self=~s/\s//g;
        my @seq=split(//,$self);
        
        for (my $index=0; $index<$#seq+1; $index++)
        {
           
           if ($seq [$index] eq 'A') {
            ++$count_of_A; 
           }
           elsif ($seq [$index] eq 'C') {
            ++$count_of_C;
           }
           elsif ($seq [$index] eq 'G') {
            ++$count_of_G;
           }
           elsif ($seq [$index] eq 'T') {
            ++$count_of_T;
           }
           elsif ($seq [$index] eq 'N') {
            ++$count_of_N;
           }
           else
           {
            print "In your sequence, there is at least one invalid cha
+racter!\n";
            print "Valid characters are A(a), T(t), G(g), C(c) and N(n
+).\n";}
        }
        
        my $GC_content=(($count_of_G+$count_of_C)/($count_of_A+$count_
+of_C+$count_of_G+$count_of_T))*100;
        print "\n"."A = $count_of_A\n";
        print "C = $count_of_C\n";
        print "G = $count_of_G\n";
        print "T = $count_of_T\n";
        print "N = $count_of_N\n";
        print "GC content="."$GC_content"."%"."\n";

}

sub aminoanalysis {
  my ($self)=shift;
  my $seqname=$self->{_seqname};
  my $sequence=$self->{_sequence};
  my(%genetic_code) = (
    'TCA' => 'S',    # Serine
    'TCC' => 'S',    # Serine
    'TCG' => 'S',    # Serine
    'TCT' => 'S',    # Serine
    'TTC' => 'F',    # Phenylalanine
    'TTT' => 'F',    # Phenylalanine
    'TTA' => 'L',    # Leucine
    'TTG' => 'L',    # Leucine
    'TAC' => 'Y',    # Tyrosine
    'TAT' => 'Y',    # Tyrosine
    'TAA' => '_',    # Stop
    'TAG' => '_',    # Stop
    'TGC' => 'C',    # Cysteine
    'TGT' => 'C',    # Cysteine
    'TGA' => '_',    # Stop
    'TGG' => 'W',    # Tryptophan
    'CTA' => 'L',    # Leucine
    'CTC' => 'L',    # Leucine
    'CTG' => 'L',    # Leucine
    'CTT' => 'L',    # Leucine
    'CCA' => 'P',    # Proline
    'CCC' => 'P',    # Proline
    'CCG' => 'P',    # Proline
    'CCT' => 'P',    # Proline
    'CAC' => 'H',    # Histidine
    'CAT' => 'H',    # Histidine
    'CAA' => 'Q',    # Glutamine
    'CAG' => 'Q',    # Glutamine
    'CGA' => 'R',    # Arginine
    'CGC' => 'R',    # Arginine
    'CGG' => 'R',    # Arginine
    'CGT' => 'R',    # Arginine
    'ATA' => 'I',    # Isoleucine
    'ATC' => 'I',    # Isoleucine
    'ATT' => 'I',    # Isoleucine
    'ATG' => 'M',    # Methionine
    'ACA' => 'T',    # Threonine
    'ACC' => 'T',    # Threonine
    'ACG' => 'T',    # Threonine
    'ACT' => 'T',    # Threonine
    'AAC' => 'N',    # Asparagine
    'AAT' => 'N',    # Asparagine
    'AAA' => 'K',    # Lysine
    'AAG' => 'K',    # Lysine
    'AGC' => 'S',    # Serine
    'AGT' => 'S',    # Serine
    'AGA' => 'R',    # Arginine
    'AGG' => 'R',    # Arginine
    'GTA' => 'V',    # Valine
    'GTC' => 'V',    # Valine
    'GTG' => 'V',    # Valine
    'GTT' => 'V',    # Valine
    'GCA' => 'A',    # Alanine
    'GCC' => 'A',    # Alanine
    'GCG' => 'A',    # Alanine
    'GCT' => 'A',    # Alanine
    'GAC' => 'D',    # Aspartic Acid
    'GAT' => 'D',    # Aspartic Acid
    'GAA' => 'E',    # Glutamic Acid
    'GAG' => 'E',    # Glutamic Acid
    'GGA' => 'G',    # Glycine
    'GGC' => 'G',    # Glycine
    'GGG' => 'G',    # Glycine
    'GGT' => 'G',    # Glycine
);
  
my @seq=split(//,$self);
my $aa='';
for (my $index=0; $index<$#seq-2; $index+=3)
{
    my $codon=$seq[$index].$seq[$index].$seq[$index+2];
    $aa.= $codon;
    
    if ($aa=$genetic_code{$codon})
    {
    
    
    print "$genetic_code{$codon}";
    }

    else
    { print "_";
    }

}



}


1;
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