mitoprot bioperl code help

cburger has asked for the wisdom of the Perl Monks concerning the following question:

Hi I'm new to bioperl and am trying to use the bioperl mitoprot wrapper to search protein sequences for mitochondrial target sequences. I tried the test code provided on the wiki link with Spombe fasta file. however I still have problems when it is supposed to read through a whole fasta file. it stops after the first sequence and doesn't go through the whole file. Any idea why? When I leave out the mitprot code part - and just print the id's it reads the whole file.

#!/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');
# my  $seqobj = $inputstream->next_seq();


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 again!

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Re: mitoprot bioperl code help by onelesd (Pilgrim) on Mar 20, 2012 at 18:20 UTC
This line: `my $mitoprot->run();` should probably read: `$mitoprot->run();`	[reply] [d/l] [select]
Re: mitoprot bioperl code help by molecules (Monk) on Mar 20, 2012 at 18:26 UTC
Add the line `use strict;` at the beginning of your code. After you do this, then you'll get an error message telling you that you tried to declare `$mitoprot` again (i.e. using `my`). It's at this line: `my $mitoprot->run();`	[reply] [d/l] [select]
Re: mitoprot bioperl code help by molecules (Monk) on Mar 20, 2012 at 18:53 UTC
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	[reply] [d/l]
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]
Re^3: mitoprot bioperl code help by molecules (Monk) on Mar 21, 2012 at 15:50 UTC
Try removing these lines and seeing if it works: `my $rawdata = my $analysis_object->result; print "rawdata: $rawdata\n";` [download]	[reply] [d/l]
Re: mitoprot bioperl code help by molecules (Monk) on Mar 20, 2012 at 18:38 UTC
You also need to create `$analysis_object` somehow.	[reply] [d/l]


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