Bio::Matrix::PSM::IO meme
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Summary
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
Package variables
Globals (from "use vars" definitions)
@HEADER
Included modules
Bio::Matrix::PSM::InstanceSite
Bio::Matrix::PSM::Psm
Bio::Matrix::PSM::SiteMatrix
strict
Inherit
Bio::Matrix::PSM::IO Bio::Matrix::PSM::PsmHeader
Synopsis
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers
Description
Parser for meme.
Methods
newDescriptionCode
_parse_coordinatesDescriptionCode
headerDescriptionCode
next_psmDescriptionCode
_parseMatrixDescriptionCode
_parse_logsDescriptionCode
_parseInstanceDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', 
						 -file=>$file);
 Function: Associates a file with the appropriate parser
 Throws  : Throws if the file passed is in HTML format or 
           if the MEME header cannot be found.
 Example :
 Args    : hash
 Returns : "Bio::Matrix::PSM::$format"->new(@args);
_parse_coordinatescodeprevnextTop
 Title   : _parse_coordinates
 Usage   :
 Function:
 Throws  :
 Example : Internal stuff
 Returns :
 Args    :
headercodeprevnextTop
 Title   : header
 Usage   :  my %header=$psmIO->header;
 Function:  Returns the header for the MEME file
 Throws  :
 Example : Fetching all the sequences included in the MEME analysis, 
           being parsed
           my %header=$psmIO->header;
            foreach my $seqid (@{$header{instances}}) {
               my $seq=$db->get_Seq_by_acc($id);
               #Do something with the sequence
            }
            where $db might be Bio::DB:GenBank object, see
 Returns : Hash with three keys: instances, weights and lengths, which
           should be self-explenatory. Each value is an array
           reference. Each array element corresponds to the same
           element in the other two arrays. So $header{instances}->[$i]
           will refer to the same sequence in the motif file as
           $header{weights}->[$i] and $header{lengths}->[$i]
 Args    :  none
 Notes   :  OBSOLETE!
next_psmcodeprevnextTop
 Title   : next_psm
 Usage   : my $psm=$psmIO->next_psm();
 Function: Reads the next PSM from the input file, associated with this object
 Throws  : Throws if the format is inconsistent with the rules for MEME 3.0.4:
            no SUMMARY Section present or some keywords are missing/altered.
 Example :
 Returns : Bio::Matrix::PSM::Psm object
 Args    : none
_parseMatrixcodeprevnextTop
 Title   : _parseMatrix
 Usage   :
 Function: Parses the next site matrix information in the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  hash as for constructing a SiteMatrix object (see SiteMatrixI)
 Args    :  string
_parse_logscodeprevnextTop
 Title   : _parse_logs
 Usage   :
 Function: Parses the next site matrix log values in the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  array of array refs
 Args    :  string
_parseInstancecodeprevnextTop
 Title   : _parseInstance
 Usage   :
 Function:  Parses the next sites instances from the meme file
 Throws  :
 Example :  Internal stuff
 Returns :  Bio::Matrix::PSM::InstanceSite object
 Args    :  none
Methods code
newdescriptionprevnextTop
sub new {
    my($class, @args)=@_;
    my $self = $class->SUPER::new(@args);
    my ($file)=$self->_rearrange(['FILE'], @args);
    my ($query,$tr1)=split(/\./,$file,2);
    $self->{file} = $file;
    $self->{query}= $query;
    $self->{end}  = 0;
    $self->{_strand}=0; #This we'll need to see if revcom option is used
    $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now
    #Skip header
    my $line;
    while (my $line=$self->_readline) {
	$self->throw('Cannot parse HTML, please use text output\n') if ($line=~/<HEAD>/); #Should start parsing HTML output, not a bug deal
	chomp($line);
	if ($line=~"^ALPHABET") {
	    $self=_parse_coordinates($self);
	    last;
	}
	push @{$self->{unstructured}},$line unless (($line=~/\*{10,}/) || ($line eq ''));
    }
    $self->_initialize;
    return $self;
}
_parse_coordinatesdescriptionprevnextTop
sub _parse_coordinates {
    my $self=shift;
    $self->_readline;
    $self->_readline;
    my $line=$self->_readline;
    while ($line !~ /^\*{10,}/ ) {
	chomp $line;
	$line =~ s/\s+/,/g;
	my ($id1,$w1,$l1,$id2,$w2,$l2)=split(/,/,$line);
	push @{$self->{hid}},$id1;
	$self->{weight}->{$id1}=$w1;
	$self->{length}->{$id1}=$l1;
	if ($id2) {
	    push @{$self->{hid}},$id2;
	    $self->{weight}->{$id2}=$w2;
	    $self->{length}->{$id2}=$l2;
	}
	$line=$self->_readline;
    }
    return $self;
}
headerdescriptionprevnextTop
sub header {
    my $self=shift;
    my @instances=@{$self->{_inst_name}};
    my @weights=@{$self->{_inst_weight}};
    my @lengths=@{$self->{_inst_coord}};
    return (instances=>\@instances,weights=>\@weights,lengths=>\@lengths);
}
next_psmdescriptionprevnextTop
sub next_psm {
    #Parses the next prediction and returns a psm objects
    my $self=shift;
    return if ($self->{end});
    my ($endm,$line,$instances,$tr,$width,$motif_id,$sites,$e_val,$id,$ic,$lA,$lC,$lG,$lT);
    while (defined( $line = $self->_readline) ) {
#Check if revcom is enabled, not very original check....
  $self->{_strand}=1 if (($line=~/^Sequence name/) && ($line=~/Strand/));
	if ($line=~ m/\sSite\s/) {
	    $instances= $self->_parseInstance;
	}
	#Here starts the next motif
	if ( ($line=~/width/) && ($line=~/sites/)) {
	    chomp($line);
	    $line=~s/[\t\s=]+/,/g;
	    $line=~s/\t/,/g;
	    #Parsing the general information for this prediction
	    ($tr,$motif_id,$tr,$width,$tr,$sites,
	     $tr,$tr,$tr,$e_val)=split(/,/,$line);
	    $self->{id}=$self->{query} . $motif_id;
	}
	if ($line =~ /content/i) {
	    $line=$self->_readline;
	    chomp($line);
	    $line=~s/[\)\(]//g;
	    ($ic)=split(/\s/,$line);
	}
        #Last info-prob matrix data
	if ($line=~/position-specific\s+scoring matrix/) {
		($lA,$lC,$lG,$lT)=_parse_logs($self);
	}
	if ($line=~/^letter-probability\smatrix/) {
	    my %matrix_dat=$self->_parseMatrix($motif_id);
	    my $psm= Bio::Matrix::PSM::Psm->new(%matrix_dat, 
					       -instances=>$instances, 
					       -e_val=>$e_val,
					       -IC=>$ic, 
					       -width=>$width, 
					       -sites=>$sites,
						   -lA=>$lA,
						   -lC=>$lC,
						   -lG=>$lG,
						   -lT=>$lT,
						   );
	    return $psm;
	}
	if ($line=~"SUMMARY OF MOTIFS") {
	    $self->{end}=1;
	    return;
	}
	$endm=1 if ($line=~/^Time\s/); 
    }
	if ($endm) { #End of file found, end of current motif too, but not all predictions were made as requested (No summary)
	    $self->{end}=1;
            warn "This MEME analysis was terminated prematurely, you may have less motifs than you requested\n";
	    return;
	}
    $self->throw("Wrong format\n"); # Multiple keywords not found, probably wrong format
}
_parseMatrixdescriptionprevnextTop
sub _parseMatrix {
    my ($self,$id)=@_;
    my (@pA,@pC,@pG,@pT);
    my $i=0;
    my $line = $self->_readline;
    #Most important part- the probability matrix
    do {
	chomp $line;
	last if ($line eq '');
  $line=~s/^\s+//;
	$line=~s/\s+/,/g;
	($pA[$i],$pC[$i],$pG[$i],$pT[$i])=split(/,/,$line);
	$i++;
	$line=$self->_readline;
    } until $line =~ /\-{10,}/;
    return (-pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,-id=>$id);
}
_parse_logsdescriptionprevnextTop
sub _parse_logs {
    my $self=shift;
    my (@lA,@lC,@lG,@lT);
    my $i=0;
    $self->_readline;   $self->_readline;
    my $line = $self->_readline;
    #Most important part- the probability matrix
    do {
	chomp $line;
	last if ($line eq '');
  $line=~s/^\s+//;
	$line=~s/\s+/,/g;
	($lA[$i],$lC[$i],$lG[$i],$lT[$i])=split(/,/,$line);
	$i++;
	$line=$self->_readline;
    } until $line =~ /\-{10,}/;
    
    return (\@lA,\@lC,\@lG,\@lT);
}
_parseInstancedescriptionprevnextTop
sub _parseInstance {
    my $self = shift;
    my $i=0;
    $self->_readline;
    my ($line,@instance);
    while (defined($line=$self->_readline) ) {
	last if ($line =~ /\-{5}/ );
	chomp($line);
	my @comp=split(/\s+/,$line);
	my ($id,$start,$score,$strand,$s1,$s2,$s3);
	if ( $self->{_strand}) {
	    ($id,$strand,$start,$score,$s1,$s2,$s3)=@comp;
	} else {
	    ($id,$start,$score,$s1,$s2,$s3)=@comp;
	    $strand=1;
	}
  	my $seq= $s1.$s2.$s3;
	if ($seq =~ /[^ACGTacgtNnXx\-\.]/) {
            my $col=$#comp;
	    $self->throw("I have not been able to parse the correct instance sequence: $seq, $col columns\n");
	}
	my $sid = $self->{id} . '@' . $id;
	$instance[$i] = Bio::Matrix::PSM::InstanceSite->new
	    (-mid      => $self->{id}, 
	     -start    => $start, 
	     -score    => $score,
	     -seq      => $seq, 
	     -strand   => $strand,
	     -accession_number => $id, 
	     -primary_id => $sid, 
	     -desc => 'Bioperl MEME parser object' );
	$i++;
    }
    $self->{instances} =\@ instance;
    return\@ instance;
}

				
			

1;
}
General documentation
FEEDBACKTop
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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
APPENDIXTop