Bio::Matrix::PSM::IO::meme - PSM meme parser implementation

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Matrix::PSM::IO::meme - PSM meme parser implementation

SYNOPSIS

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See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers

DESCRIPTION

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Parser for meme.

FEEDBACK

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Mailing Lists

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

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 Bugs

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 Kirov

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Email skirov@utk.edu

APPENDIX

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new

 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_coordinates

 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!

next_psm

 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

_parseMatrix

 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_logs

 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

_parseInstance

 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
BioPerl documentation Contained in the BioPerl distribution. 
#---------------------------------------------------------



# Let the code begin...
package Bio::Matrix::PSM::IO::meme;
use Bio::Matrix::PSM::InstanceSite;
use Bio::Matrix::PSM::SiteMatrix;
use Bio::Matrix::PSM::Psm;
use vars qw(@HEADER);
use strict;

use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO);

@Bio::Matrix::PSM::IO::meme::HEADER = qw(e_val sites IC width);


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;
    $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 {
    #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
}


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);
}


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);
}


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;
}

				
			

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