Bio::Matrix::PSM SiteMatrix
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Summary
Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a
position scoring matrix (or position weight matrix) and log-odds
Package variables
No package variables defined.
Inherit
Bio::Matrix::PSM::SiteMatrixI Bio::Root::Root
Synopsis
  use Bio::Matrix::PSM::SiteMatrix;
# Create from memory by supplying probability matrix hash
# both as strings or arrays
# where the frequencies $a,$c,$g and $t are supplied either as
# arrayref or string. Accordingly, lA, lC, lG and lT are the log
# odds (only as arrays, no checks done right now)
my ($a,$c,$g,$t,$score,$ic, $mid)=@_;
#or
my ($a,$c,$g,$t,$score,$ic,$mid)=('05a011','110550','400001',
'100104',0.001,19.2,'CRE1');
#Where a stands for all (this frequency=1), see explanation bellow
my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,
-lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l,
-IC=>$ic,-e_val=>$score, -id=>$mid);
my $site=Bio::Matrix::PSM::SiteMatrix->new(%param);
#Or get it from a file:
use Bio::Matrix::PSM::IO;
my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');
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::SiteMatrix object now
my $matrix=$psm->matrix;
}
# Get a simple consensus, where alphabet is {A,C,G,T,N}, # choosing the character that both satisfies a supplied or default threshold # frequency and is the most frequenct character at each position, or N. # So for the position with A, C, G, T frequencies of 0.5, 0.25, 0.10, 0.15, # the simple consensus character will be 'A', whilst for 0.5, 0.5, 0, 0 it # would be 'N'. my $consensus=$site->consensus; # Get the IUPAC ambiguity code representation of the data in the matrix. # Because the frequencies may have been pseudo-count corrected, insignificant # frequences (below 0.05 by default) are ignored. So a position with # A, C, G, T frequencies of 0.5, 0.5, 0.01, 0.01 will get the IUPAC code 'M', # while 0.97, 0.01, 0.01, 0.01 will get the code 'A' and # 0.25, 0.25, 0.25, 0.25 would get 'N'. my $iupac=$site->IUPAC; # Getting/using regular expression (a representation of the IUPAC string) 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
SiteMatrix is designed to provide some basic methods when working with position
scoring (weight) matrices, such as transcription factor binding sites for
example. A DNA PSM consists of four vectors with frequencies {A,C,G,T}. This is
the minimum information you should provide to construct a PSM object. The
vectors can be provided as strings with frequenciesx10 rounded to an int, going
from {0..a} and 'a' represents the maximum (10). This is like MEME's 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 you can ask the constructor to make a simple pseudo
count correction by adding a number (typically 1) to all positions (with the
-correction option). After adding the number the frequencies will be
calculated. Only use correction when you supply counts, not frequencies.
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 yest 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
Methods
newDescriptionCode
_calculate_consensusDescriptionCode
calc_weightDescriptionCode
next_posDescriptionCode
curposDescriptionCode
e_valDescriptionCode
ICDescriptionCode
accession_numberDescriptionCode
consensusDescriptionCode
widthDescriptionCode
sitesDescriptionCode
IUPACDescriptionCode
_to_IUPACDescriptionCode
_to_consDescriptionCode
get_stringDescriptionCode
get_arrayDescriptionCode
get_logs_arrayDescriptionCode
idDescriptionCode
regexpDescriptionCode
regexp_arrayDescriptionCode
_compress_arrayDescriptionCode
_uncompress_stringDescriptionCode
get_compressed_freqDescriptionCode
get_compressed_logsDescriptionCode
sequence_match_weightDescriptionCode
get_all_vectorsDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $site=Bio::Matrix::PSM::SiteMatrix->new(-pA=>$a,-pC=>$c,
-pG=>$g,-pT=>$t,
-IC=>$ic,
-e_val=>$score,
-id=>$mid);
Function: Creates a new Bio::Matrix::PSM::SiteMatrix object from memory
Throws : If inconsistent data for all vectors (A,C,G and T) is
provided, if you mix input types (string vs array) or if a
position freq is 0.
Returns : Bio::Matrix::PSM::SiteMatrix object
Args : -pA => vector with the frequencies or counts of A
-pC => vector for C
-pG => vector for G
-pt => vector for T
-lA => vector for the log of A
-lC => vector for the log of C
-lG => vector for the log of G
-lT => vector for the log of T
-IC => real number, the information content of this matrix
-e_val => real number, the expect value
-id => string, an identifier
-width => int, width of the matrix in nucleotides
-sites => int, the number of sites that went into this matrix
-model => hash ref, background frequencies for A, C, G and T
-correction => number, the number to add to all positions to achieve
psuedo count correction (default 0: no correction)
NB: do not use correction when your input is
frequences!
-accession_number => string, an accession number
Vectors can be strings of the frequencies where the frequencies are multiplied by 10 and rounded to the nearest whole number, and where 'a' is used to denote the maximal frequency 10. There should be no punctuation (spaces etc.) in the string. For example, 'a0501'. Alternatively frequencies or counts can be represented by an array ref containing the counts, frequencies or logs as any kind of number.
_calculate_consensuscodeprevnextTop
 Title   : _calculate_consensus
Function: Internal stuff
calc_weightcodeprevnextTop
 Title   : calc_weight
Usage : $obj->calc_weight({A=>0.2562, C=>0.2438, G=>0.2432, T=>0.2568});
Function: Recalculates the PSM (or weights) based on the PFM (the frequency
matrix) and user supplied background model.
Throws : if no model is supplied
Returns : n/a
Args : reference to a hash with background frequencies for A,C,G and T
next_poscodeprevnextTop
 Title   : next_pos
Usage :
Function: Retrives the next position features: frequencies for A,C,G,T, the
main letter (as in consensus) and the probabilty for this letter to
occur at this position and the current position
Returns : hash (pA,pC,pG,pT,logA,logC,logG,logT,base,prob,rel)
Args : none
curposcodeprevnextTop
 Title   : curpos
Usage :
Function: Gets/sets the current position. Converts to 0 if argument is minus
and to width if greater than width
Returns : integer
Args : integer
e_valcodeprevnextTop
 Title   : e_val
Usage :
Function: Gets/sets the e-value
Returns : real number
Args : none to get, real number to set
ICcodeprevnextTop
 Title   : IC
Usage :
Function: Get/set the Information Content
Returns : real number
Args : none to get, real number to set
accession_numbercodeprevnextTop
 Title   : accession_number
Function: Get/set the accession number, this will be unique id for the
SiteMatrix object as well for any other object, inheriting from
SiteMatrix
Returns : string
Args : none to get, string to set
consensuscodeprevnextTop
 Title   : consensus
Usage :
Function: Returns the consensus
Returns : string
Args : (optional) threshold value 1 to 10, default 5
'5' means the returned characters had a 50% or higher presence at
their position
widthcodeprevnextTop
 Title   : width
Usage :
Function: Returns the length of the sites in used to make this matrix
Returns : int
Args : none
sitescodeprevnextTop
 Title   : sites
Usage :
Function: Get/set the number of sites that were used to make this matrix
Returns : int
Args : none to get, int to set
IUPACcodeprevnextTop
 Title   : IUPAC
Usage :
Function: Returns IUPAC compliant consensus
Returns : string
Args : optionally, also supply a whole number (int) of 1 or higher to set
the significance level when considering the frequencies. 1 (the
default) means a 0.05 significance level: frequencies lower than
0.05 will be ignored. 2 Means a 0.005 level, and so on.
_to_IUPACcodeprevnextTop
 Title   : _to_IUPAC
Usage :
Function: Converts a single position to IUPAC compliant symbol.
For rules see the implementation
Returns : char, real number
Args : real numbers for frequencies of A,C,G,T (positional)
optionally, also supply a whole number (int) of 1 or higher to set the significance level when considering the frequencies. 1 (the default) means a 0.05 significance level: frequencies lower than 0.05 will be ignored. 2 Means a 0.005 level, and so on.
_to_conscodeprevnextTop
 Title   : _to_cons
Usage :
Function: Converts a single position to simple consensus character and returns
its probability. For rules see the implementation
Returns : char, real number
Args : real numbers for A,C,G,T (positional), and optional 5th argument of
threshold (as a number between 1 and 10, where 5 is default and
means the returned character had a 50% or higher presence at this
position)
get_stringcodeprevnextTop
 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}
Returns : string
Args : character {A,C,G,T}
get_arraycodeprevnextTop
 Title   : get_array
Usage :
Function: Returns an array with frequencies for a specified base
Returns : array
Args : char
get_logs_arraycodeprevnextTop
 Title   : get_logs_array
Usage :
Function: Returns an array with log_odds for a specified base
Returns : array
Args : char
idcodeprevnextTop
 Title   : id
Usage :
Function: Gets/sets the site id
Returns : string
Args : string
regexpcodeprevnextTop
 Title   : regexp
Usage :
Function: Returns a regular expression which matches the IUPAC convention.
N will match X, N, - and .
Returns : string
Args : none (works at the threshold last used for making the IUPAC string)
regexp_arraycodeprevnextTop
 Title   : regexp_array
Usage :
Function: Returns a regular expression which matches the IUPAC convention.
N will match X, N, - and .
Returns : array
Args : none (works at the threshold last used for making the IUPAC string)
To do : I have separated regexp and regexp_array, but
maybe they can be rewritten as one - just check what should be returned
_compress_arraycodeprevnextTop
 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
Returns : String
Args : array reference, followed by an max value and direction (optional,
default 1-unsigned),1 unsigned, any other is signed.
_uncompress_stringcodeprevnextTop
 Title   : _uncompress_string
Usage :
Function: Will uncompress a string (vector of bytes) to create an array of
real signed numbers (opposite to_compress_array)
Returns : string, followed by an max value and
direction (optional, default 1-unsigned), 1 unsigned, any other is signed.
Args : array
get_compressed_freqcodeprevnextTop
 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.
Example : my $strA=$self->get_compressed_freq('A');
Returns : String
Args : char
get_compressed_logscodeprevnextTop
 Title   : get_compressed_logs
Usage :
Function: A method to provide a compressed log-odd vector. It uses one byte to
code the log value for one of the log-odds vectors for one position.
Example : my $strA=$self->get_compressed_logs('A');
Returns : String
Args : char
sequence_match_weightcodeprevnextTop
 Title   : sequence_match_weight
Usage :
Function: This method will calculate the score of a match, based on the PWM
if such is associated with the matrix object. Returns undef if no
PWM 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
get_all_vectorscodeprevnextTop
 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=$self->get_all_vectors(4);
Returns : Array of strings
Args : (optional) floating
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my $consensus;
    # Too many things to rearrange, and I am creating simultanuously >500 
# such objects routinely, so this becomes performance issue
my %input; while (@args) { (my $key = shift @args) =~ s/-//g; #deletes all dashes (only dashes)!
$input{$key} = shift @args; } $self->{_position} = 0; $self->{IC} = $input{IC}; $self->{e_val} = $input{e_val}; $self->{width} = $input{width}; $self->{logA} = $input{lA}; $self->{logC} = $input{lC}; $self->{logG} = $input{lG}; $self->{logT} = $input{lT}; $self->{sites} = $input{sites}; $self->{id} = $input{id} || 'null'; $self->{correction} = $input{correction} || 0; $self->{accession_number} = $input{accession_number}; return $self unless (defined($input{pA}) && defined($input{pC}) && defined($input{pG}) && defined($input{pT})); # This should go to _initialize?
# Check for input type- no mixing alllowed, throw ex
if (ref($input{pA}) =~ /ARRAY/i ) { $self->throw("Mixing matrix data types not allowed: C is not reference") unless(ref($input{pC})); $self->throw("Mixing matrix data types not allowed: G is not reference") unless (ref($input{pG})); $self->throw("Mixing matrix data types not allowed: T is not reference") unless (ref($input{pT})); $self->{probA} = $input{pA}; $self->{probC} = $input{pC}; $self->{probG} = $input{pG}; $self->{probT} = $input{pT}; } else { $self->throw("Mixing matrix data types not allowed: C is reference") if (ref($input{pC})); $self->throw("Mixing matrix data types not allowed: G is reference") if (ref($input{pG})); $self->throw("Mixing matrix data types not allowed: T is reference") if (ref($input{pT})); $self->{probA} = [split(//,$input{pA})]; $self->{probC} = [split(//,$input{pC})]; $self->{probG} = [split(//,$input{pG})]; $self->{probT} = [split(//,$input{pT})]; for (my $i=0; $i<= @{$self->{probA}}+1; $i++) { # we implictely assume these are MEME-style frequencies x 10, so
# 'a' represents the 'maximum', 10. Other positions can actually
# add up to over 10 due to rounding, but I don't think that is a
# problem?
if (${$self->{probA}}[$i] and ${$self->{probA}}[$i] eq 'a') { ${$self->{probA}}[$i]='10'; } if (${$self->{probC}}[$i] and ${$self->{probC}}[$i] eq 'a') { ${$self->{probC}}[$i]='10'; } if (${$self->{probG}}[$i] and ${$self->{probG}}[$i] eq 'a') { ${$self->{probG}}[$i]='10'; } if (${$self->{probT}}[$i] and ${$self->{probT}}[$i] eq 'a') { ${$self->{probT}}[$i]='10'; } } } # Check for position with 0 for all bases, throw exception if so
for (my $i=0;$i <= $#{$self->{probA}}; $i++) { if ((${$self->{probA}}[$i] + ${$self->{probC}}[$i] + ${$self->{probG}}[$i] + ${$self->{probT}}[$i]) == 0) { $self->throw("Position meaningless-all frequencies are 0"); } # apply psuedo-count correction to all values - this will result in
# very bad frequencies if the input is already frequences and a
# correction value as large as 1 is used!
if ($self->{correction}) { ${$self->{probA}}[$i] += $self->{correction}; ${$self->{probC}}[$i] += $self->{correction}; ${$self->{probG}}[$i] += $self->{correction}; ${$self->{probT}}[$i] += $self->{correction}; } # (re)calculate frequencies
my $div= ${$self->{probA}}[$i] + ${$self->{probC}}[$i] + ${$self->{probG}}[$i] + ${$self->{probT}}[$i]; ${$self->{probA}}[$i]=${$self->{probA}}[$i]/$div;
${$self->{probC}}[$i]=${$self->{probC}}[$i]/$div;
${$self->{probG}}[$i]=${$self->{probG}}[$i]/$div;
${$self->{probT}}[$i]=${$self->{probT}}[$i]/$div;
} # Calculate the logs
if ((!defined($self->{logA})) && ($input{model})) { $self->calc_weight($input{model}); } # Make consensus, throw if any one of the vectors is shorter
$self->_calculate_consensus; return $self;
}
_calculate_consensusdescriptionprevnextTop
sub _calculate_consensus {
    my $self=shift;
    my ($lc,$lt,$lg)=($#{$self->{probC}},$#{$self->{probT}},$#{$self->{probG}});
    my $len=$#{$self->{probA}};
    $self->throw("Probability matrix is damaged for C: $len vs $lc") if ($len != $lc);
    $self->throw("Probability matrix is damaged for T: $len vs $lt") if ($len != $lt);
    $self->throw("Probability matrix is damaged for G: $len vs $lg") if ($len != $lg);
    for (my $i=0; $i<$len+1; $i++) {
        #*** IUPACp values not actually used (eg. by next_pos)
(${$self->{IUPAC}}[$i],${$self->{IUPACp}}[$i])=_to_IUPAC(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i]); (${$self->{seq}}[$i], ${$self->{seqp}}[$i]) = _to_cons(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i]); } return $self;
}
calc_weightdescriptionprevnextTop
sub calc_weight {
    my ($self, $model) = @_;
    my %model;
    $model{probA}=$model->{A};
    $model{probC}=$model->{C};
    $model{probG}=$model->{G};
    $model{probT}=$model->{T};
    foreach my $let (qw(probA probC probG probT)) {
      my @str;
      $self->throw('You did not provide valid model\n') unless (($model{$let}>0) && ($model{$let}<1));
      foreach my $f (@{$self->{$let}}) {
        my $w=log($f)-log($model{$let});
        push @str,$w;
      }
      my $llet=$let;
      $llet=~s/prob/log/;
$self->{$llet}=\@str; } return $self;
}
next_posdescriptionprevnextTop
sub next_pos {
    my $self = shift;
    $self->throw("instance method called on class") unless ref $self;
    my $len=@{$self->{seq}};
    my $pos=$self->{_position};
    # End reached?
if ($pos<$len) { my $pA=${$self->{probA}}[$pos]; my $pC=${$self->{probC}}[$pos]; my $pG=${$self->{probG}}[$pos]; my $pT=${$self->{probT}}[$pos]; my $lA=${$self->{logA}}[$pos]; my $lC=${$self->{logC}}[$pos]; my $lG=${$self->{logG}}[$pos]; my $lT=${$self->{logT}}[$pos]; my $base=${$self->{seq}}[$pos]; my $prob=${$self->{seqp}}[$pos]; $self->{_position}++; my %seq=(pA=>$pA,pT=>$pT,pC=>$pC,pG=>$pG, lA=>$lA,lT=>$lT,lC=>$lC,lG=>$lG,base=>$base,rel=>$pos, prob=>$prob); return %seq; } else {$self->{_position}=0; return;}
}
curposdescriptionprevnextTop
sub curpos {
    my $self = shift;
    my $prev = $self->{_position};
    if (@_) { $self->{_position} = shift; }
    return $prev;
}
e_valdescriptionprevnextTop
sub e_val {
    my $self = shift;
    my $prev = $self->{e_val};
    if (@_) { $self->{e_val} = shift; }
    return $prev;
}
ICdescriptionprevnextTop
sub IC {
    my $self = shift;
    my $prev = $self->{IC};
    if (@_) { $self->{IC} = shift; }
    return $prev;
}
accession_numberdescriptionprevnextTop
sub accession_number {
    my $self = shift;
    my $prev = $self->{accession_number};
    if (@_) { $self->{accession_number} = shift; }
    return $prev;
}
consensusdescriptionprevnextTop
sub consensus {
    my ($self, $thresh) = @_;
    if ($thresh) {
        my $len=$#{$self->{probA}};
        for (my $i=0; $i<$len+1; $i++) {
            (${$self->{seq}}[$i], ${$self->{seqp}}[$i]) = _to_cons(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i], $thresh);
        }
    }
    my $consensus='';
    foreach my $letter (@{$self->{seq}}) {
        $consensus .= $letter;
    }
    return $consensus;
}
widthdescriptionprevnextTop
sub width {
    my $self = shift;
    my $width=@{$self->{probA}};
    return $width;
}
sitesdescriptionprevnextTop
sub sites {
    my $self = shift;
    if (@_) { $self->{sites} = shift }
    return $self->{sites} || return;
}
IUPACdescriptionprevnextTop
sub IUPAC {
	my ($self, $thresh) = @_;
    if ($thresh) {
        my $len=$#{$self->{probA}};
        for (my $i=0; $i<$len+1; $i++) {
            (${$self->{IUPAC}}[$i],${$self->{IUPACp}}[$i])=_to_IUPAC(${$self->{probA}}[$i], ${$self->{probC}}[$i], ${$self->{probG}}[$i], ${$self->{probT}}[$i], $thresh);
        }
    }
	my $iu=$self->{IUPAC};
	my $iupac='';
	foreach my $let (@{$iu}) {
		$iupac .= $let;
	}
    return $iupac;
}
_to_IUPACdescriptionprevnextTop
sub _to_IUPAC {
	my ($a, $c, $g, $t, $thresh) = @_;
    $thresh ||= 1;
    $thresh = int($thresh);
    $a = sprintf ("%.${thresh}f", $a);
    $c = sprintf ("%.${thresh}f", $c);
    $g = sprintf ("%.${thresh}f", $g);
    $t = sprintf ("%.${thresh}f", $t);
    
    my $total = $a + $c + $g + $t;
    
	return 'A' if ($a == $total);
	return 'G' if ($g == $total);
	return 'C' if ($c == $total);
	return 'T' if ($t == $total);
	my $r=$g+$a;
	return 'R' if ($r == $total);
	my $y=$t+$c;
	return 'Y' if ($y == $total);
	my $m=$a+$c;
	return 'M' if ($m == $total);
	my $k=$g+$t;
	return 'K' if ($k == $total);
	my $s=$g+$c;
	return 'S' if ($s == $total);
	my $w=$a+$t;
	return 'W' if ($w == $total);
	my $d=$r+$t;
	return 'D' if ($d == $total);
	my $v=$r+$c;
	return 'V' if ($v == $total);
	my $b=$y+$g;
	return 'B' if ($b == $total);
	my $h=$y+$a;
	return 'H' if ($h == $total);
	return 'N';
}
_to_consdescriptionprevnextTop
sub _to_cons {
	my ($A, $C, $G, $T, $thresh) = @_;
    $thresh ||= 5;
    
    # this multiplication by 10 is just to satisfy the thresh range of 1-10
my $a = $A * 10; my $c = $C * 10; my $g = $G * 10; my $t = $T * 10; return 'N',10 if (($a<$thresh) && ($c<$thresh) && ($g<$thresh) && ($t<$thresh)); return 'N',10 if (($a==$t) && ($a==$c) && ($a==$g)); # threshold could be lower than 50%, so must check is not only over
# threshold, but also the highest frequency
return 'A',$a if (($a>=$thresh) && ($a>$t) && ($a>$c) && ($a>$g)); return 'C',$c if (($c>=$thresh) && ($c>$t) && ($c>$a) && ($c>$g)); return 'G',$g if (($g>=$thresh) && ($g>$t) && ($g>$c) && ($g>$a)); return 'T',$t if (($t>=$thresh) && ($t>$g) && ($t>$c) && ($t>$a)); return 'N',10;
}
get_stringdescriptionprevnextTop
sub get_string {
	my $self=shift;
	my $base=shift;
	my $string='';
	my @prob;
    
	BASE: {
		if ($base eq 'A') {@prob= @{$self->{probA}}; last BASE; }
		if ($base eq 'C') {@prob= @{$self->{probC}}; last BASE; }
		if ($base eq 'G') {@prob= @{$self->{probG}}; last BASE; }
		if ($base eq 'T') {@prob= @{$self->{probT}}; last BASE; }
		$self->throw ("No such base: $base!\n");
	}
    
    foreach  my $prob (@prob) {
        my $corrected = $prob*10;
        my $next=sprintf("%.0f",$corrected);
        $next='a' if ($next eq '10');
        $string .= $next;
    }
    return $string;
}
get_arraydescriptionprevnextTop
sub get_array {
	my $self=shift;
	my $base=uc(shift);
	return  @{$self->{probA}} if ($base eq 'A');
	return  @{$self->{probC}} if ($base eq 'C');
	return  @{$self->{probG}} if ($base eq 'G');
	return  @{$self->{probT}} if ($base eq 'T');
	$self->throw("No such base: $base!\n");
}
get_logs_arraydescriptionprevnextTop
sub get_logs_array {
	my $self=shift;
	my $base=uc(shift);
	return  @{$self->{logA}} if (($base eq 'A')  && ($self->{logA}));
	return  @{$self->{logC}} if (($base eq 'C')  && ($self->{logC}));
	return  @{$self->{logG}} if (($base eq 'G')  && ($self->{logG}));
	return  @{$self->{logT}} if (($base eq 'T')  && ($self->{logT}));
	$self->throw ("No such base: $base!\n") if (!grep(/$base/,qw(A C G T)));
    return;
}
iddescriptionprevnextTop
sub id {
    my $self = shift;
    my $prev = $self->{id};
    if (@_) { $self->{id} = shift; }
    return $prev;
}
regexpdescriptionprevnextTop
sub regexp {
	my $self=shift;
	my $regexp;
	foreach my $letter (@{$self->{IUPAC}}) {
		my $reg;
		LETTER: {
			if ($letter eq 'A') { $reg='[Aa]'; last LETTER; }
			if ($letter eq 'C') { $reg='[Cc]'; last LETTER; }
			if ($letter eq 'G') { $reg='[Gg]'; last LETTER; }
			if ($letter eq 'T') { $reg='[Tt]'; last LETTER; }
			if ($letter eq 'M') { $reg='[AaCcMm]'; last LETTER; }
			if ($letter eq 'R') { $reg='[AaGgRr]'; last LETTER; }
			if ($letter eq 'W') { $reg='[AaTtWw]'; last LETTER; }
			if ($letter eq 'S') { $reg='[CcGgSs]'; last LETTER; }
			if ($letter eq 'Y') { $reg='[CcTtYy]'; last LETTER; }
			if ($letter eq 'K') { $reg='[GgTtKk]'; last LETTER; }
			if ($letter eq 'V') { $reg='[AaCcGgVv]'; last LETTER; }
			if ($letter eq 'H') { $reg='[AaCcTtHh]'; last LETTER; }
			if ($letter eq 'D') { $reg='[AaGgTtDd]'; last LETTER; }
			if ($letter eq 'B') { $reg='[CcGgTtBb]'; last LETTER; }
			$reg='\S';
		}
		$regexp .= $reg;
	}
    return $regexp;
}
regexp_arraydescriptionprevnextTop
sub regexp_array {
	my $self=shift;
	my @regexp;
	foreach my $letter (@{$self->{IUPAC}}) {
		my $reg;
		LETTER: {
			if ($letter eq 'A') { $reg='[Aa]'; last LETTER; }
			if ($letter eq 'C') { $reg='[Cc]'; last LETTER; }
			if ($letter eq 'G') { $reg='[Gg]'; last LETTER; }
			if ($letter eq 'T') { $reg='[Tt]'; last LETTER; }
			if ($letter eq 'M') { $reg='[AaCcMm]'; last LETTER; }
			if ($letter eq 'R') { $reg='[AaGgRr]'; last LETTER; }
			if ($letter eq 'W') { $reg='[AaTtWw]'; last LETTER; }
			if ($letter eq 'S') { $reg='[CcGgSs]'; last LETTER; }
			if ($letter eq 'Y') { $reg='[CcTtYy]'; last LETTER; }
			if ($letter eq 'K') { $reg='[GgTtKk]'; last LETTER; }
			if ($letter eq 'V') { $reg='[AaCcGgVv]'; last LETTER; }
			if ($letter eq 'H') { $reg='[AaCcTtHh]'; last LETTER; }
			if ($letter eq 'D') { $reg='[AaGgTtDd]'; last LETTER; }
			if ($letter eq 'B') { $reg='[CcGgTtBb]'; last LETTER; }
			$reg='\S';
		}
		push @regexp,$reg;
	}
    return @regexp;
}
_compress_arraydescriptionprevnextTop
sub _compress_array {
	my ($array,$lm,$direct)=@_;
	my $str;
	return  unless(($array) && ($lm));
	$direct=1 unless ($direct);
	my $k1= ($direct==1) ? (255/$lm) : (127/$lm);
	foreach my $c (@{$array}) {
		$c=$lm if ($c>$lm);
		$c=-$lm if (($c<-$lm) && ($direct !=1));
    $c=0 if (($c<0) && ($direct ==1));
		my $byte=int($k1*$c);
    $byte=127+$byte if ($direct !=1);#Clumsy, should be really shift the bits
my $char=chr($byte); $str.=$char; } return $str;
}
_uncompress_stringdescriptionprevnextTop
sub _uncompress_string {
	my ($str,$lm,$direct)=@_;
	my @array;
	return unless(($str) && ($lm));
	$direct=1 unless ($direct);
	my $k1= ($direct==1) ? (255/$lm) : (127/$lm);
	foreach my $c (split(//,$str)) {
		my $byte=ord($c);
		$byte=$byte-127 if ($direct !=1);#Clumsy, should be really shift the bits
my $num=$byte/$k1;
push @array,$num; } return @array;
}
get_compressed_freqdescriptionprevnextTop
sub get_compressed_freq {
	my $self=shift;
	my $base=shift;
	my $string='';
	my @prob;
	BASE: {
		if ($base eq 'A') {
      @prob= @{$self->{probA}} unless (!defined($self->{probA}));
      last BASE;
    }
  		if ($base eq 'G') {
      @prob= @{$self->{probG}} unless (!defined($self->{probG}));
      last BASE;
    }
  		if ($base eq 'C') {
      @prob= @{$self->{probC}} unless (!defined($self->{probC}));
      last BASE;
    }
  		if ($base eq 'T') {
      @prob= @{$self->{probT}} unless (!defined($self->{probT}));
      last BASE;
    }
		$self->throw ("No such base: $base!\n");
	}
	my $str= _compress_array(\@prob,1,1);
    return $str;
}
get_compressed_logsdescriptionprevnextTop
sub get_compressed_logs {
	my $self=shift;
	my $base=shift;
	my $string='';
	my @prob;
	BASE: {
		if ($base eq 'A') {@prob= @{$self->{logA}} unless (!defined($self->{logA})); last BASE; }
		if ($base eq 'C') {@prob= @{$self->{logC}} unless (!defined($self->{logC})); last BASE; }
		if ($base eq 'G') {@prob= @{$self->{logG}} unless (!defined($self->{logG})); last BASE; }
		if ($base eq 'T') {@prob= @{$self->{logT}} unless (!defined($self->{logT})); last BASE; }
		$self->throw ("No such base: $base!\n");
	}
	return _compress_array(\@prob,1000,2);
}
sequence_match_weightdescriptionprevnextTop
sub sequence_match_weight {
    my ($self,$seq)=@_;
    return unless ($self->{logA});
    my $width=$self->width;
    $self->throw ("I can calculate the score only for sequence which are exactly my size for $seq, my width is $width\n") unless (length($seq)==@{$self->{logA}});
    $seq = uc($seq);
    my @seq=split(//,$seq);
    my $score = 0;
    my $i=0;
    foreach my $pos (@seq) {
        my $tv = 'log'.$pos;
        $self->warn("Position ".($i+1)." of input sequence has unknown (ambiguity?) character '$pos': scores will be wrong") unless defined $self->{$tv};
        $score += defined $self->{$tv} ? $self->{$tv}->[$i] : 0;
        $i++;
    }
    return $score;
}
get_all_vectorsdescriptionprevnextTop
sub get_all_vectors {
	my $self=shift;
	my $thresh=shift;
    $self->throw("Out of range. Threshold should be >0 and 1<.\n") if (($thresh<0) || ($thresh>1));
    my @seq=split(//,$self->consensus($thresh*10));
    my @perm;
    for my $i (0..@{$self->{probA}}) {
        push @{$perm[$i]},'A' if ($self->{probA}->[$i]>$thresh);
        push @{$perm[$i]},'C' if ($self->{probC}->[$i]>$thresh);
        push @{$perm[$i]},'G' if ($self->{probG}->[$i]>$thresh);
        push @{$perm[$i]},'T' if ($self->{probT}->[$i]>$thresh);
        push @{$perm[$i]},'N' if  ($seq[$i] eq 'N');
    }
    my $fpos=shift @perm;
    my @strings=@$fpos;
    foreach my $pos (@perm) {
        my @newstr;
        foreach my $let (@$pos) {
            foreach my $string (@strings) {
                my $newstring = $string . $let;
                push @newstr,$newstring;
            }
        }
        @strings=@newstr;
    }
	return @strings;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _