Bio::Matrix::PSM::IO
meme
Summary
Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
Package variables
Globals (from "use vars" definitions)
@HEADER
Included modules
Inherit
Synopsis
See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers
Description
Parser for meme.
Methods
Methods description
Title : new
Usage : my $psmIO = new Bio::Matrix::PSM::IO(-format=>'meme',
-file=>$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::$format"->new(@args); |
Title : _parse_coordinates
Usage :
Function:
Throws :
Example : Internal stuff
Returns :
Args : |
Title : header
Usage : my %header=$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
Notes : OBSOLETE! |
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;
$self->_initialize_io(@args) || warn "Did you intend to use STDIN?";
my $line;
while (my $line=$self->_readline) {
$self->throw('Cannot parse HTML, please use text output\n') if ($line=~/<HEAD>/);
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;
$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;} | 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
{
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) ) {
$self->{_strand}=1 if (($line=~/^Sequence name/) && ($line=~/Strand/));
if ($line=~ m/\sSite\s/) {
$instances= $self->_parseInstance;
}
if ( ($line=~/width/) && ($line=~/sites/)) {
chomp($line);
$line=~s/[\t\s=]+/,/g;
$line=~s/\t/,/g;
($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);
}
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 $psm= new Bio::Matrix::PSM::Psm(%matrix_dat,
-instances=>$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) {
$self->{end}=1;
warn "This MEME analysis was terminated prematurely, you may have less motifs than you requested\n";
return;
}
$self->throw("Wrong format\n");
} | sub _parseMatrix
{ my ($self,$id)=@_;
my (@pA,@pC,@pG,@pT);
my $i=0;
my $line = $self->_readline;
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);} | sub _parse_logs
{ my $self=shift;
my (@lA,@lC,@lG,@lT);
my $i=0;
$self->_readline; $self->_readline;
my $line = $self->_readline;
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);} | 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] = new Bio::Matrix::PSM::InstanceSite
(-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;} | General documentation
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