TFBS
MatrixSet
TFBS::Matrix::Set - an agregate class representing a set of matrix patterns, containing methods for manipulating the set as a whole
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# creation of a TFBS::MatrixSet object
# let @list_of_matrix_objects be a list of TFBS::Matrix::* objects
###################################
# Create a TFBS::MatrixSet object:
my $matrixset = TFBS::MatrixSet->new(); # creates an empty set
$matrixset->add_Matrix(@list_of_matrix_objects); #add matrix objects to set
$matrixset->add_Matrix($matrixobj); # adds a single matrix object to set
# or, same as above:
my $matrixset = TFBS::MatrixSet->new(@list_of_matrix_objects, $matrixobj);
###################################
#
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TFBS::MatrixSet is an aggregate class storing a set of TFBS::Matrix::* subclass objects, and providing methods form manipulating those sets as a whole. TFBS::MatrixSet objects are created <I>de novo<I> or returned by some database (TFBS::DB::*) retrieval methods.
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Methods description
Title : Iterator
Usage : my $matrixset_iterator =
$matrixset->Iterator(-sort_by =>'total_ic');
while (my $matrix_object = $matrix_iterator->next) {
# do whatever you want with individual matrix objects
}
Function: Returns an iterator object that can be used to go through
all members of the set
Returns : an iterator object (currently undocumentened in TFBS -
but understands the 'next' method)
Args : -sort_by # optional - currently it accepts
# 'ID' (alphabetically)
# 'name' (alphabetically)
# 'class' (alphabetically)
# 'total_ic' (numerically, decreasing order)
-reverse # optional - reverses the default sorting order if true
Title : add_matrix
Usage : $matrixset->add_matrix(@list_of_matrix_objects);
Function: Adds matrix objects to matrixset
Returns : object reference (usually ignored)
Args : one or more TFBS::Matrix::* objects
Title : add_matrix
Usage : $matrixset->add_matrix(@list_of_matrixset_objects);
Function: Adds to the matrixset matrix objects contained in one or
more other matrixsets
Returns : object reference (usually ignored)
Args : one or more TFBS::MatrixSet objects
Title : search_aln
Usage : my $site_pair_set = $matrixset->search_aln(%args)
Function: Scans a pairwise alignment of nucleotide sequences
with the pattern represented by the PWM: it reports only
those hits that are present in equivalent positions of both
sequences and exceed a specified threshold score in both, AND
are found in regions of the alignment above the specified
conservation cutoff value.
It works only if all matrix object in $matrixset understand
search_aln method (currently only TFBS::Matrix::PWM objects do)
Returns : a TFBS::SitePairSet object
Args : # you must specify either one of the following three:
-file, # the name of the alignment file in Clustal
format
#or
-alignobj # a Bio::SimpleAlign object
# (more accurately, a Bio::PrimarySeqobject or a
# subclass thereof)
#or
-alignstring # a multi-line string containing the alignment
# in clustal format
#############
-threshold, # minimum score for the hit, either absolute
# (e.g. 11.2) or relative (e.g. "75%")
# OPTIONAL: default "80%"
-window, # size of the sliding window (inn nucleotides)
# for calculating local conservation in the
# alignment
# OPTIONAL: default 50
-cutoff # conservation cutoff (%) for including the
# region in the results of the pattern search
# OPTIONAL: default "70%"
-subpart # subpart of the alignment to search, given as e.g.
# -subpart => { relative_to => 1,
# start => 140,
# end => 180 }
# where start and end are coordinates in the
# sequence indicated by relative_to (1 for the
# 1st sequence in the alignment, 2 for the 2nd)
# OPTIONAL: by default searches entire alignment
-conservation
# conservation profile, a TFBS::ConservationProfile
# OPTIONAL: by default the conservation profile is
# computed internally on the fly (less efficient)
Title : search_seq
Usage : my $siteset = $matrixset->search_seq(%args)
Function: scans a nucleotide sequence with all patterns represented
stored in $matrixset;
It works only if all matrix objects in $matrixset understand
search_seq method (currently only TFBS::Matrix::PWM objects do)
Returns : a TFBS::SiteSet object
Args : # you must specify either one of the following three:
-file, # the name od a fasta file (single sequence)
#or
-seqobj # a Bio::Seq object
# (more accurately, a Bio::PrimarySeqobject or a
# subclass thereof)
#or
-seqstring # a string containing the sequence
-threshold, # minimum score for the hit, either absolute
# (e.g. 11.2) or relative (e.g. "75%")
# OPTIONAL: default "80%"
Title : size
Usage : my $number_of_matrices = $matrixset->size;
Function: gets the number of matrix objects in the $matrixset
(i.e. the size of the set)
Returns : a number
Args : none
Methods code
sub Iterator
{ my ($self, %args) = @_;
return TFBS::_Iterator::_MatrixSetIterator->new($self->{matrix_list},
$args{'-sort_by'},
$args{'-reverse'}
);}
sub _bsearch
{ my ($self,%args) = @_; ##the rest of @_ goes to _to_seqob;
my @PWMs;
## prepare the sequence
my $seqobj = $self->_to_seqobj(%args);
$seqobj->{_pdl_matrix} = _seq_to_pdlmatrix($seqobj);
## prepare the PWMs
$self->reset();
while (my $pwm = $self->next() ) {
push @PWMs,$pwm;
}
## do the analysis
my $hitlist = TFBS::SiteSet->new();
foreach my $pwm (@PWMs) {
my $threshold = ($args{-threshold} or $pwm->{minscore});
$hitlist->add_siteset($pwm->bsearch(-seqobj=>$seqobj,
-threshold =>$threshold ));
}
delete $seqobj->{_pdl_matrix};
return $hitlist;
}
sub _csearch
{ my ($self, %args) = @_;
my $PWM_SEARCH = '/home/httpd/cgi-bin/CONSITE/bin/pwm_searchPFF';
## DIRTY - stick tmp file name to seq object
my $seqobj = $self->_to_seqobj(%args);
($seqobj->{_fastaFH}, $seqobj->{_fastafile}) = tmpnam();
## we need $fastafile below
my $seqFH = Bio::SeqIO->newFh(-fh=>$seqobj->{_fastaFH}, -format=>"Fasta");
print $seqFH $seqobj;
## iterate through pwms
my @PWMs;
$self->reset();
while (my $pwm = $self->next() ) {
push @PWMs,$pwm;
}
## do the analysis
my $hitlist = TFBS::SiteSet->new();
foreach my $pwm (@PWMs) {
my $threshold = ($args{-threshold} or $pwm->{minscore});
$hitlist->add_siteset($pwm->search_seq(-seqobj=>$seqobj,
-threshold =>$threshold ));
}
delete $seqobj->{_fastaFH};
delete $seqobj->{_fastafile};
return $hitlist;}
sub _search
{ my ($self, %args) = @_;
## DIRTY - stick tmp file name to seq object
my $seqobj = $self->_to_seqobj(%args);
($seqobj->{_fastaFH}, $seqobj->{_fastafile}) = tmpnam();
## we need $fastafile below
my $outstream = Bio::SeqIO->new(-file=>">".$seqobj->{_fastafile}, -format=>"Fasta");
my $subseqobj;
if(my $subpart = $args{-subpart}) {
my $subseq_start = $subpart->{-start};
my $subseq_end = $subpart->{-end};
unless($subseq_start and $subseq_end) {
$self->throw("Option -subpart missing suboption -relative_to, -start or -end");
}
$subseqobj = Bio::Seq->new(-seq => $seqobj->subseq($subseq_start, $subseq_end),
-id => $seqobj->id);
}
$outstream->write_seq($subseqobj or $seqobj);
$outstream->close;
## iterate through pwms
my @PWMs;
my $mxit = $self->Iterator();
while (my $pwm = $mxit->next() ) {
push @PWMs,$pwm;
}
## do the analysis
my $hitlist = TFBS::SiteSet->new();
foreach my $pwm (@PWMs) {
my $threshold = ($args{-threshold} or $pwm->{minscore});
$hitlist->add_siteset($pwm->search_seq(-seqobj=>$seqobj,
-threshold =>$threshold,
-subpart=>$args{-subpart}));
}
delete $seqobj->{_fastaFH};
unlink $seqobj->{_fastafile};
delete $seqobj->{_fastafile};
return $hitlist;}
sub _seq_to_pdlmatrix
{ ## not OO - help function for search
my $seqobj = shift;
my $seqstring = uc($seqobj->seq());
my @perlarray;
foreach (qw(A C G T)) {
my $seqtobits = $seqstring;
eval "\$seqtobits =~ tr/$_/1/"; ## curr. letter $_ to 1
eval "\$seqtobits =~ tr/1/0/c"; ## non-1s to 0
push @perlarray, [split("", $seqtobits)];
}
return byte (\@perlarray);
}
sub _to_seqobj
{ my ($self, %args) = @_;
my $seq;
if ($args{-file}) { ## not a Bio::Seq
return Bio::SeqIO->new(-file => $args{-file},
-format => 'fasta',
-moltype => 'dna')->next_seq();
}
elsif ($args{-seqstring}
or $args{-seq})
{ ## I guess it's a string then
return Bio::Seq->new(-seq => ($args{-seqstring} or $args{-seq}),
-id => ($args{-seq_id} or "undefined"),
-moltype => 'dna');
}
elsif ($args{'-seqobj'} and ref($args{'-seqobj'}) =~ /Bio\:\:Seq/) {
## do nothing (maybe check later)
return $args{'-seqobj'};
}
##elsif (ref($format) =~ /Bio\:\:Seq/ and !defined $seq) {
## if only one parameter passed and it's a Bio::Seq
##return $format;
##}
else {
$self->throw ("Wrong parametes passed to search method: ".%args);
}
## CONTINUE HERE TOMORROW
}
sub add_Matrix
{ my ($self, @matrixlist) = @_;
foreach (@matrixlist) {
ref($_) =~ /TFBS::Matrix::/
or $self->throw("Attempted to add an element ".
"that is not a TFBS::Matrix object.");
push @{$self->{matrix_list}}, $_;
push @{$self->{_iterator_list}}, $_;
}
return 1;}
sub add_matrix
{ my ($self, @matrices) = @_;
foreach my $matrix (@matrices) {
$self->throw("Argument to add_matrix_set not a TFBS::Matrix object")
unless $matrix->isa("TFBS::Matrix");
}
push @{$self->{matrix_list}}, @matrices;
return $self;}
sub add_matrix_set
{ my ($self, @sets) = @_;
foreach my $matrixset (@sets) {
$self->throw("Argument to add_matrix_set not a TFBS::Matrixset object")
unless $matrixset->isa("TFBS::MatrixSet");
push @{$self->{matrix_list}}, @{$matrixset->{matrix_list}};
}}
sub new
{ my ($caller, @matrices) = shift;
my $self = bless {matrix_list =>[]}, ref($caller) || $caller;
$self->add_matrix(@matrices) if @matrices;
return $self;}
sub next
{ my ($self) = @_;
$self->warn("next: Deprecated method use Iterator instead.");
if (my $next_matrix = shift (@{$self->{_iterator_list}})) {
return $next_matrix;
}
else {
$self->reset;
return undef;
}}
sub reset
{ my ($self) = @_;
$self->warn("reset: Deprecated method use Iterator instead.");
@{$self->{_iterator_list}} = @{$self->{matrix_list}};}
sub search_aln
{ my ($self, %args) = @_;
my $mxit = $self->Iterator();
my $sitepairset = TFBS::SitePairSet->new;
my $aln = TFBS::Matrix::_Alignment->new(%args);
while (my $mx = $mxit->next) {
my $singleset = $mx->search_aln(%args,
-alignment_setup => $aln);
$sitepairset->add_site_pair_set($singleset);
}
return $sitepairset;}
sub search_seq
{ my ($self, %args) = @_;
$self->_search(%args);}
sub size
{ scalar @{ $_[0]->{matrix_list} };}
sub sort_by_name
{ my ($self) = @_;
$self->warn("sort_by_name: Deprecated method use Iterator instead.");
@{$self->{matrix_list}} = sort { uc($a->{name}) cmp uc ($b->{name}) }
@{$self->{matrix_list}};
$self->reset();}
General documentation