in reply to mitoprot bioperl code help

This much works on my machine. 
use 5.008;      # Require at least Perl version 5.8
use strict;     # Must declare all variables before using them
use warnings;   # Emit helpful warnings

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

use Bio::PrimarySeq;

my $seq = new Bio::PrimarySeq(
    -seq =>'MIKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
    -primary_id=>'test',
); # a Bio::PrimarySeqI object

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

# run Mitoprot prediction on amino acid sequence
$mitoprot->run();

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

1;

[download]
It gives the following output: 
Input sequence length : 31 aa


                 VALUES OF COMPUTED PARAMETERS

Net charge of query sequence                    :  +1
Analysed region                                 :  28
Number of basic residues in targeting sequence  :   2
Number of acidic residues in targeting sequence :   1
Cleavage site                                   : not predictable
Cleaved sequence                                : 

                         HYDROPHOBIC SCALE USED

                    GES       KD       GVH1       ECS

H17         :      0.365     1.571    -0.153     0.534
MesoH       :     -0.410    -0.410    -0.410    -0.410
MuHd_075    :     16.751     8.794     5.615     2.837
MuHd_095    :     19.407    14.027     7.300     3.693
MuHd_100    :     14.856    12.028     6.718     2.831
MuHd_105    :     17.763    15.164     7.100     3.885
Hmax_075    :      5.017     5.000    -2.544     3.990
Hmax_095    :      8.313    10.762     0.128     3.806
Hmax_100    :      6.100    10.400     0.010     3.710
Hmax_105    :      4.433     8.400    -2.501     3.640

                            PROBABILITY

of export to mitochondria: 0.0001

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Re^2: mitoprot bioperl code help
by cburger (Acolyte) on Mar 21, 2012 at 03:31 UTC

    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!!

[reply]
[d/l]
[select]
      Try removing these lines and seeing if it works: 
        my $rawdata = my $analysis_object->result;
  
  print "rawdata: $rawdata\n";

      [download]
[reply]
[d/l]

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