Bio::Matrix::PSM::IO meme
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
Package variables
Globals (from "use vars" definitions)
Included modules
Bio::Matrix::PSM::IO Bio::Matrix::PSM::PsmHeader
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers
Parser for meme.
Methods description
newcode    nextTop
 Title   : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
Function: Associates a file with the appropriate parser
Throws : Throws if the file passed is in HTML format or
if the MEME header cannot be found.
Example :
Args : hash
Returns : "Bio::Matrix::PSM::$format"->new(@args);
 Title   : _parse_coordinates
Usage :
Throws :
Example : Internal stuff
Returns :
Args :
 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
 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
 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
 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
 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
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;
sub _parse_coordinates {
    my $self=shift;
    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;
	if ($id2) {
	    push @{$self->{hid}},$id2;
    return $self;
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);
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); $line=~s/[\t\s=]+/,/g;
#Parsing the general information for this prediction
($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; } $self->throw("Wrong format\n"); # Multiple keywords not found, probably wrong format
sub _parseMatrix {
    my ($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 ''); $line=~s/^\s+//;
($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);
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 ''); $line=~s/^\s+//;
($lA[$i],$lC[$i],$lG[$i],$lT[$i])=split(/,/,$line); $i++; $line=$self->_readline; } until $line =~ /\-{10,}/; return (\@lA,\@lC,\@lG,\@lT);
sub _parseInstance {
    my $self = shift;
    my $i=0;
    my ($line,@instance);
    while (defined($line=$self->_readline) ) {
	last if ($line =~ /\-{5}/ );
	my @comp=split(/\s+/,$line);
	my ($id,$start,$score,$strand,$s1,$s2,$s3);
	if ( $self->{_strand}) {
	} else {
  	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' );
    $self->{instances} =\@ instance;
    return\@ instance;


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AUTHOR - Stefan KirovTop