Thanks all for the help, I got it to run on the test file. I'm trying now to get it reading through a whole fasta file. But it stops after the first sequence and doesn't go through the whole file. Any idea why? 


#!/usr/bin/perl-w
use strict;

  use Bio::Tools::Analysis::Protein::Mitoprot;

  use Bio::PrimarySeq;
  use Bio::SeqIO;
  
my  $inputstream = Bio::SeqIO->new(-file => "myseq2.fa",-format => 'Fa
+sta');



while (my $seqobj = $inputstream->next_seq){   
    # print the sequence   
    print ">";
    print $seqobj->id,"\n";
    
    my $seq= $seqobj-> seq;
    my $id= $seqobj->id;
   

      my $seq = new Bio::PrimarySeq(-seq=>$seq, -primary_id=>$id); 
     
     
     my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new(-seq 
+=> $seq); # sequence must be  >!5aa long and start with an M.

    $mitoprot->run();

  die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED
+/;

  print $mitoprot->result;     # print raw prediction to STDOUT



 
  my $rawdata = my $analysis_object->result;
  
  print "rawdata: $rawdata\n"; 
  
  ## ....................................................
    
   
} # close while

[download]

here is the output I get with error message : 

 
>SPAC212.11.1



Input sequence length : 1887 aa


                 VALUES OF COMPUTED PARAMETERS

Net charge of query sequence                    : -14
Analysed region                                 :   5
Number of basic residues in targeting sequence  :   0
Number of acidic residues in targeting sequence :   0
Cleavage site                                   : not predictable
Cleaved sequence                                : 

                         HYDROPHOBIC SCALE USED

                    GES       KD       GVH1       ECS

H17         :      1.776     1.635     0.456     0.701
MesoH       :     -0.097     0.599    -0.205     0.261
MuHd_075    :      8.891     2.722     0.982     0.422
MuHd_095    :     40.686    26.860    12.359     9.439
MuHd_100    :     45.583    25.681    12.613     9.543
MuHd_105    :     45.113    22.080    11.556     8.739
Hmax_075    :      1.867     9.625    -1.365     2.660
Hmax_095    :     15.800    20.400     3.835     6.380
Hmax_100    :     16.000    20.300     3.835     6.190
Hmax_105    :     15.600    15.600     2.796     5.250

                            PROBABILITY

of export to mitochondria: 0.5284
Can't call method "result" on an undefined value at test.pl line 36, <
+GEN0> line 1.

[download]

Thanks!!

In reply to Re^2: mitoprot bioperl code help by cburger
in thread mitoprot bioperl code help by cburger

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