#--------------------------------------------------------- # $Id: meme.pm 16123 2009-09-17 12:57:27Z cjfields $ =head1 NAME Bio::Matrix::PSM::IO::meme - PSM meme parser implementation =head1 SYNOPSIS See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers =head1 DESCRIPTION Parser for meme. =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # 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); =head2 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::$format"->new(@args); =cut sub new { my($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=~//); #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; } =head2 _parse_coordinates Title : _parse_coordinates Usage : Function: Throws : Example : Internal stuff Returns : Args : =cut 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 $self; } =head2 header Title : header Usage : my %header=$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! =cut 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); } =head2 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 =cut 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; } $self->throw("Wrong format\n"); # Multiple keywords not found, probably wrong format } =head2 _parseMatrix Title : _parseMatrix Usage : Function: Parses the next site matrix information in the meme file Throws : Example : Internal stuff Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI) Args : string =cut sub _parseMatrix { my ($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); } =head2 _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 =cut 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); } =head2 _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 =cut 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;