Bio::Matrix::PSM::ProtMatrix.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.

SYNOPSIS

    use Bio::Matrix::PSM::ProtMatrix;
    # Create from memory by supplying probability matrix hash both as strings or
    # arrays where the frequencies   Hash entries of the form lN refer to an array
    # of position-specific log-odds scores for amino acid N. Hash entries of the
    # form pN represent the position-specific probability of finding amino acid N.
 
    my %param = (
              'id' => 'A. thaliana protein atp1',
              '-e_val' => $score,
              'lS' => [ '-2', '3', '-3', '2', '-3', '1', '1', '3' ],
              'lF' => [ '-1', '-4', '0', '-5', '0', '-5', '-4', '-4' ],
              'lT' => [ '-1', '1', '0', '1', '-2', '-1', '0', '1' ],
              'lN' => [ '-3', '-1', '-2', '3', '-5', '5', '-2', '0' ],
              'lK' => [ '-2', '0', '-3', '2', '-3', '2', '-3', '-1' ],
              'lY' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-4', '-4' ],
              'lE' => [ '-3', '4', '-3', '2', '-4', '-2', '-3', '2' ],
              'lV' => [ '0', '-2', '1', '-4', '1', '-4', '-1', '-3' ],
              'lQ' => [ '-1', '0', '-2', '3', '-4', '1', '-3', '0' ],
              'lM' => [ '8', '-3', '8', '-3', '1', '-3', '-3', '-3' ],
              'lC' => [ '-2', '-3', '-3', '-4', '-3', '-4', '-3', '-3' ],
              'lL' => [ '1', '-3', '1', '-4', '3', '-4', '-2', '-4' ],
              'lA' => [ '-2', '1', '-2', '0', '-2', '-2', '2', '2' ],
              'lW' => [ '-2', '-4', '-3', '-5', '-4', '-5', '-5', '-5' ],
              'lP' => [ '-3', '-2', '-4', '-3', '-1', '-3', '6', '-3' ],
              'lH' => [ '-2', '-2', '-3', '-2', '-5', '-2', '-2', '-3' ],
              'lD' => [ '-4', '-1', '-3', '1', '-3', '-1', '-3', '4' ],
              'lR' => [ '-2', '-1', '-3', '0', '-4', '4', '-4', '-3' ],
              'lI' => [ '0', '-3', '0', '-4', '6', '-4', '-2', '-2' ],
              'lG' => [ '-4', '-2', '-4', '-2', '-5', '-3', '-1', '-2' ],
              'pS' => [ '0', '33', '0', '16', '1', '12', '11', '25' ],
              'pF' => [ '0', '0', '2', '0', '3', '0', '0', '0' ],
              'pT' => [ '0', '8', '7', '10', '1', '2', '7', '8' ],
              'pN' => [ '0', '0', '2', '13', '0', '36', '1', '4' ],
              'pK' => [ '0', '5', '0', '13', '1', '15', '0', '2' ],
              'pY' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
              'pE' => [ '0', '41', '1', '12', '0', '0', '0', '15' ],
              'pV' => [ '0', '3', '9', '0', '2', '0', '3', '1' ],
              'pQ' => [ '0', '0', '0', '15', '0', '4', '0', '3' ],
              'pM' => [ '100', '0', '66', '0', '2', '0', '0', '0' ],
              'pC' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
              'pL' => [ '0', '0', '8', '0', '25', '0', '4', '0' ],
              'pA' => [ '0', '10', '1', '9', '2', '0', '22', '16' ],
              'pW' => [ '0', '0', '0', '0', '0', '0', '0', '0' ],
              'pP' => [ '0', '0', '0', '0', '3', '1', '45', '0' ],
              'pH' => [ '0', '0', '0', '0', '0', '0', '1', '0' ],
              'pD' => [ '0', '0', '1', '7', '2', '2', '0', '22' ],
              'pR' => [ '0', '0', '0', '3', '0', '27', '0', '0' ],
              'pI' => [ '0', '0', '3', '0', '59', '1', '2', '3' ],
              'pG' => [ '0', '0', '0', '1', '0', '0', '4', '1' ],
    );
 
    my $matrix = Bio::Matrix::PSM::ProtMatrix( %param );
 
 
    my $site = Bio::Matrix::PSM::ProtMatrix->new(%param);
    # Or get it from a file:
    use Bio::Matrix::PSM::IO;
    my $psmIO = Bio::Matrix::PSM::IO->new(-file => $file, -format => 'psi-blast');
    while (my $psm = $psmIO->next_psm) {
       #Now we have a Bio::Matrix::PSM::Psm object, 
       # see Bio::Matrix::PSM::PsmI for details
       #This is a Bio::Matrix::PSM::ProtMatrix object now
       my $matrix = $psm->matrix;   
    }
 
    # Get a simple consensus, where alphabet is:
    # {A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V,}
    # choosing the highest probability or N if prob is too low
    my $consensus = $site->consensus;
 
    # Retrieving and using regular expressions:
    my $regexp = $site->regexp;
    my $count = grep($regexp,$seq);
    my $count = ($seq=~ s/$regexp/$1/eg);
    print "Motif $mid is present $count times in this sequence\n";
 
 

DESCRIPTION

ProtMatrix is designed to provide some basic methods when working with position scoring (weight) matrices related to protein sequences. A protein PSM consists of 20 vectors with 20 frequencies (one per amino acid per position). This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequencies where the frequency is {0..a} and a=1. This is the way MEME compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count).

When creating the object the constructor will check for positions that equal 0. If such is found it will increase the count for all positions by one and recalculate the frequency. Potential bug - if you are using frequencies and one of the positions is 0 it will change significantly. However, you should never have frequency that equals 0.

Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest.

Summary of the methods I use most frequently (details bellow):

    iupac - return IUPAC compliant consensus as a string
    score - Returns the score as a real number
    IC - information content. Returns a real number
    id - identifier. Returns a string
    accession - accession number. Returns a string
    next_pos - return the sequence probably for each letter, IUPAC
          symbol, IUPAC probability and simple sequence
    consenus letter for this position. Rewind at the end. Returns a hash.
    pos - current position get/set. Returns an integer.
    regexp - construct a regular expression based on IUPAC consensus.
          For example AGWV will be [Aa][Gg][AaTt][AaCcGg]
    width - site width
    get_string - gets the probability vector for a single base as a string.
    get_array - gets the probability vector for a single base as an array.
    get_logs_array - gets the log-odds vector for a single base as an array.
 
 

New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with:

    my $str=$matrix->get_compressed_freq('A');
 or
 
    my $str=$matrix->get_compressed_logs('A');
 
 

Loading from a database should be done with new, but is not yet implemented. However you can still uncompress such string with:

    my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM
 
 

or

    my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - James Thompson

Email tex@biosysadmin.com

APPENDIX

new

  Title    : new
  Usage    : my $site = Bio::Matrix::PSM::ProtMatrix->new( 
                %probs,
                %logs,
                -IC    => $ic,
                -e_val => $score, 
                -id    => $mid
                -model => \%model
             );
  Function : Creates a new Bio::Matrix::PSM::ProtMatrix object from memory
  Throws   : If inconsistent data for all vectors (all 20 amino acids) is
                provided, if you mix input types (string vs array) or if a
                position freq is 0.
  Example  :
  Returns  : Bio::Matrix::PSM::ProtMatrix object
  Args     : Hash references to log-odds scores and probabilities for
             position-specific scoring info, e-value (optional), information
             content (optional), id (optional), model for background distribution
             of proteins (optional).
 
 

alphabet

  Title    : Returns an array (or array reference if desired) to the alphabet 
  Usage    :
  Function : Returns an array (or array reference) containing all of the
             allowable characters for this matrix.
  Throws   :
  Example  :
  Returns  : Array or arrary reference.
  Args     :
 
 

_calculate_consensus

  Title    : _calculate_consensus
  Usage    :
  Function : Calculates the consensus sequence for this matrix. 
  Throws   :
  Example  :
  Returns  :
  Args     :
 
 

next_pos

  Title    : next_pos
  Usage    :
  Function : Retrives the next position features: frequencies for all 20 amino
             acids, log-odds scores for all 20 amino acids at this position,
             the main (consensus) letter at this position, the probability
             for the consensus letter to occur at this position and the relative
             current position as an integer.
  Throws   :
  Example  :
  Returns  : hash (or hash reference) (pA,pR,pN,pD,...,logA,logR,logN,logD,aa,prob,rel)
             - pN entries represent the probability for amino acid N
             to be at this position
             - logN entries represent the log-odds score for having amino acid
             N at this position
             - aa is the consensus amino acid
             - prob is the probability for the consensus amino acid to be at this 
             position
             - rel is the relative index of the current position (integer)
  Args      : none
 
 

curpos

  Title    : curpos
  Usage    :
  Function : Gets/sets the current position. 
  Throws   :
  Example  :
  Returns  : Current position (integer).
  Args     : New position (integer).
 
 

e_val

  Title    : e_val
  Usage    :
  Function : Gets/sets the e-value
  Throws   :
  Example  :
  Returns  : 
  Args     : real number
 
 

IC

  Title    : IC
  Usage    :
  Function : Position-specific information content.
  Throws   :
  Example  :
  Returns  : Information content for current position.
  Args     : Information content for current position.
 
 

accession_number

  Title    : accession_number
  Usage    :
  Function: accession number, this will be unique id for the ProtMatrix object as
             well for any other object, inheriting from ProtMatrix.
  Throws   :
  Example  :
  Returns  : New accession number (string)
  Args     : Accession number (string)
 
 

consensus

  Title    : consensus
  Usage    :
  Function : Returns the consensus sequence for this PSM.
  Throws   : if supplied with thresold outisde 5..10 range
  Example  :
  Returns  : string
  Args     : (optional) threshold value 5 to 10 (corresponds to 50-100% at each position
 
 

get_string

  Title   : get_string
  Usage   :
  Function: Returns given probability vector as a string. Useful if you want to
             store things in a rel database, where arrays are not first choice
  Throws  : If the argument is outside {A,C,G,T}
  Example :
  Returns : string
  Args    : character {A,C,G,T}
 
 

width

  Title    : width
  Usage    :
  Function : Returns the length of the site
  Throws   :
  Example  :
  Returns  : number
  Args     :
 
 

get_array

  Title    : get_array
  Usage    :
  Function : Returns an array with frequencies for a specified amino acid.
  Throws   :
  Example  :
  Returns  : Array representing frequencies for specified amino acid.
  Args     : Single amino acid (character).
 
 

get_logs_array

  Title    : get_logs_array
  Usage    :
  Function : Returns an array with log_odds for a specified base
  Throws   :
  Example  :
  Returns  : Array representing log-odds scores for specified amino acid.
  Args     : Single amino acid (character).
 
 

id

  Title    : id
  Usage    :
  Function : Gets/sets the site id
  Throws   :
  Example  :
  Returns  : string
  Args     : string
 
 

regexp

  Title    : regexp
  Usage    :
  Function : Returns a case-insensitive regular expression which matches the
             IUPAC convention.  X's in consensus sequence will match anything.     
  Throws   :
  Example  :
  Returns  : string
  Args     : Threshold for calculating consensus sequence (number in range 0-100
             representing a percentage). Threshold defaults to 20.
 
 

regexp_array

  Title    : regexp_array
  Usage    :
  Function : Returns an array of position-specific regular expressions.
              X's in consensus sequence will match anything.      
  Throws   :
  Example  :
  Returns  : Array of position-specific regular expressions.
  Args     : Threshold for calculating consensus sequence (number in range 0-100
             representing a percentage). Threshold defaults to 20.
  Notes    : Simply calls regexp method in list context.
 
 

_compress_array

  Title    : _compress_array
  Usage    :
  Function :  Will compress an array of real signed numbers to a string (ie vector of bytes)
              -127 to +127 for bi-directional(signed) and 0..255 for unsigned ;
  Throws   :
  Example  :  Internal stuff
  Returns  :  String
  Args     :  array reference, followed by max value and direction (optional, defaults to 1),
              direction of 1 is unsigned, anything else is signed.
 
 

_uncompress_string

  Title    : _uncompress_string
  Usage    :
  Function :   Will uncompress a string (vector of bytes) to create an array of real
                   signed numbers (opposite to_compress_array)
  Throws   :
  Example  :   Internal stuff
  Returns  :   string, followed by max value and direction (optional, defaults to 1),
               direction of 1 is unsigned, anything else is signed.
  Args     :   array
 
 

get_compressed_freq

  Title    : get_compressed_freq
  Usage    :
  Function:   A method to provide a compressed frequency vector. It uses one byte to
              code the frequence for one of the probability vectors for one position.
              Useful for relational database. Improvment of the previous 0..a coding.
  Throws   :
  Example  :   my $strA=$self->get_compressed_freq('A');
  Returns  :   String
  Args     :   char
 
 

sequence_match_weight

  Title    : sequence_match_weight
  Usage    :
  Function :   This method will calculate the score of a match, based on the PSM
               if such is associated with the matrix object. Returns undef if no
               PSM data is available.
  Throws   :   if the length of the sequence is different from the matrix width
  Example  :   my $score=$matrix->sequence_match_weight('ACGGATAG');
  Returns  :   Floating point
  Args     :   string
 
 

_to_IUPAC

  Title   : _to_IUPAC
  Usage   :
  Function: Converts a single position to IUPAC compliant symbol and returns its probability.
             Currently returns the most likely amino acid/probability combination.
  Throws  :
  Example :
  Returns : char, real number representing an amino acid and a probability.
  Args    : real numbers for all 20 amino acids (ordered by alphabet contained
             in $self->{_alphabet}, minimum probability threshold.
 
 

_to_cons

  Title   : _to_cons
  Usage   :
  Function: Converts a single position to simple consensus character and returns
             its probability. Currently just calls the _to_IUPAC subroutine. 
  Throws  :
  Example :
  Returns : char, real number
  Args    : real numbers for A,C,G,T (positional)
 
 

get_all_vectors

  Title    : get_all_vectors
  Usage    :
  Function :  returns all possible sequence vectors to satisfy the PFM under
              a given threshold
  Throws   :  If threshold outside of 0..1 (no sense to do that)
  Example  :  my @vectors = $self->get_all_vectors(4);
  Returns  :  Array of strings
  Args     :  (optional) floating