[ensembl-dev] How fetch a prediction matrix using stable ID

[ori]

Hi Sarah, Thank you, I was just worried about the difference. Yes, I am aware of that and I wanted HumVar, that's why I am not specifying anything. By the way, do you know how to prevent the API from closing when it finds an error (for example, the matrix for this ID doesn't exist and then it quits). If I am looping through some IDs, and one of them is not found, the script stops.
Thank you, 
Oriol
Date: Tue, 10 Mar 2015 15:00:58 +0000
From: seh at ebi.ac.uk
To: dev at ensembl.org
Subject: Re: [ensembl-dev] How fetch a prediction matrix using stable ID


  
    
  
  
    

    Hi Oriol,

    
    

    Polyphen (and Sift) results are heavily dependant on sequence
    conservation estimates derived from protein sequence alignments, so
    using different protein databases can result in a substantial number
    of different calls. 

    

    We used the latest protein databases available in November 2013,
    while the PolyPhen website uses databases from December 2011/
    January 2012, so we would expect to see some differences.

    

    
    As you are no doubt aware, Polyphen provides two different scores,
    HumVar and HumDiv. We supply HumVar as default while the PolyPhen
    web site defaults to HumDiv. If you would like to extract HumDiv
    results you can amend your script:

        

        my $matrix_prediction= $matrix_adaptor->
        fetch_polyphen_predictions_by_translation_md5($translation_md5,
        'humdiv');

    

    Best wishes,

    

    Sarah

    

    On 10/03/2015 14:04, ori wrote:

    
    
      
      Hi, 
        I am trying to fetch the prediction matrix for some
            proteins, and then some polyphen predictions for some
            particular aminoacid changes. In Ensembl Help Documentation
            of predicted data, it is found: "Prediction matrices can be
            fetched and manipulated in a user-friendly manner using the
            variation API, specifically using the ProteinFunctionPredictionMatrixAdaptor which allows you to fetch a
            prediction matrix using either a transcript or a translation
            stable ID. This adaptor returns a ProteinFunctionPredictionMatrix object and you can use the get_prediction method to retrieve a
            prediction for a given position and amino acid". 
        

          
        However, I am not able to get my matrix
            using any type of ID. I have been trying
            fetch_polyphen_predictions_by_translation_md5 (using Perl Digest::MD5 to
              get md5_hex), and it returns a matrix, but the predictions
              doesn't match the real ones that polyphen predicts for
              this change (I checked on their website). 
        I would appreciate helps/tips
              to make things easier or to point out where is my mistake.
              Here is so far what I wrote: 
        
              

              
              use warnings;
              use Bio::EnsEMBL::Registry;
              use Digest::MD5 qw(md5 md5_hex md5_base64);
              use Bio::EnsEMBL::Utils::Exception qw(throw warning);
              use
                Bio::EnsEMBL::Variation::ProteinFunctionPredictionMatrix;
              print "Loading Registry...\n";
              my $registry = "Bio::EnsEMBL::Registry";
              $registry->load_registry_from_db( -host =>
                'ensembldb.ensembl.org', -user => 'anonymous');
              print "Correctly Loaded Registry\n";
              my $transcript_adaptor = $registry -> get_adaptor
                ('Human', 'Core', 'Transcript');
              my $matrix_adaptor= $registry-> get_adaptor
                ('Human', 'variation',
                'ProteinFunctionPredictionMatrixAdaptor');
              my $transcript= $transcript_adaptor ->
                fetch_by_stable_id('ENST00000367429');
              my $translation_md5 =
                md5_hex($transcript->translate->seq());
              my $matrix_prediction= $matrix_adaptor->
                fetch_polyphen_predictions_by_translation_md5($translation_md5);
              my ($prediction)  = $matrix_prediction
                ->get_prediction(1, V);
              print "$prediction\n";
              

              
              You will see that the outcome is benign, and it
                should be probably damaging.
              

              
              Thanks for the help, 
              

              
              Oriol
            
      
      

      
      

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