# $Id: mast.pm 16123 2009-09-17 12:57:27Z cjfields $ =head1 NAME Bio::Matrix::PSM::IO::mast - PSM mast parser implementation =head1 SYNOPSIS See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM parsers =head1 DESCRIPTION Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches, than to PSM themselves. =head1 TO DO Section III should be parsed too, otherwise no real sequence is available, so we supply 'NNNNN....' as a seq which is not right. =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 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Matrix::PSM::IO::mast; use Bio::Matrix::PSM::InstanceSite; use Bio::Matrix::PSM::Psm; use Bio::Root::Root; use strict; use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO); =head2 new Title : new Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast', -file=>$file); Function: Associates a file with the appropriate parser Throws : Throws if the file passed is in HTML format or if some criteria for the file format are not met. Example : Returns : psm object, associated with a file with matrix file Args : hash return : "Bio::Matrix::PSM::$format"->new(@args); =cut sub new { my($class, @args)=@_; my $self = $class->SUPER::new(@args); my (%instances,@header,$n); my ($file)=$self->_rearrange(['FILE'], @args); $self->{file} = $file; $self->{_factor}=1; $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now $self->{_end}=0; undef $self->{hid}; return $self if ($file=~/^>/);#Just writing my $buf=$self->_readline; $self->throw('Cannot parse HTML format yet') if ($buf =~/^/); # this should probably be moved to its own function while ( defined($buf=$self->_readline)) { chomp($buf); if ($buf=~/DATABASE AND MOTIFS/) { while ($buf=$self->_readline) { if ($buf=~/DATABASE/) { $buf=~s/^[\s\t]+//; chomp $buf; ($n,$self->{_dbname},$self->{_dbtype})=split(/\s/,$buf); $self->{_dbtype}=~s/[\(\)]//g; } if ($buf=~/MOTIFS/) { $buf=~s/^[\s\t]+//; chomp $buf; ($n,$self->{_mrsc},$self->{_msrctype})=split(/\s/,$buf); $self->{_msrctype}=~s/[\(\)]//g; last; } } if ($self->{_msrctype} ne $self->{_dbtype}) {#Assume we have protein motifs, nuc DB (not handling opp.) $self->{_factor}=3; $self->{_mixquery}=1; } } if ($buf=~m/MOTIF WIDTH BEST POSSIBLE MATCH/) { $self->_readline; while (defined($buf=$self->_readline)) { last if ($buf!~/\w/); $buf=~s/\t+//g; $buf=~s/^\s+//g; my ($id,$width,$seq)=split(/\s+/,$buf); push @{$self->{hid}},$id; $self->{length}->{$id}=$width; $self->{seq}->{$id}=$seq; } next; } if ($buf=~m/section i:/i) { $self->_readline; $self->_readline; $self->_readline; %instances=_get_genes($self); $self->{instances}=\%instances; if (!(%instances)) { $self->warn ("Your MAST analysis did not find any matches satisfying the current threshold.\nSee MAST documentation for more information.\n"); return $self; #The header might be useful so we return the object, not undef } next; } if ($buf=~m/section ii:/i) { $self->_readline; $self->_readline; $self->_readline; last; } $buf=~s/[\t+\s+]/ /g; push @header,$buf unless (($buf=~/\*{10,}/)||($buf!~/\w/)); } $self->throw('Could not read Section I, probably wrong format, make sure it is not HTML, giving up...') if !(%instances); $self->warn( "This file might be an unreadable version, proceed with caution!\n") if (!grep(/\s+MAST\s+version\s+3/,@header)); $self->{unstructured} = \@header; $self->_initialize; return $self; } # Get the file header and put store it as a hash, which later we'll use to create # the header for each Psm. See Bio::Matrix::PSM::PsmI for header function. sub _get_genes { my $self=shift; my %llid; my $ok=0; my $i=0; my %instances; while (my $line=$self->_readline) { last if ($line=~/^[\s\t*]/); # Well, ids can be nearly anything...??? chomp($line); $i++; next if ($line eq ''); $line=~s/\s+/,/g; my ($id,$key,$eval,$len)=split(/,/,$line); unless ($len) { warn "Malformed data found: $line\n"; next; } $instances{$id}=Bio::Matrix::PSM::InstanceSite->new(-id=>$id, -desc=>$key, -score=>$eval, -width=>$len, -seq=>'ACGT'); } return %instances; } =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 there ara format violations in the input file (checking is not very strict with all drivers). Example : Returns : Bio::Matrix::PSM::Psm object Args : none =cut sub next_psm { my $self=shift; return if ($self->{_end}==1); my (@lmotifsm,%index,$eval,$scheme,$sid); %index= %{$self->{length}}; my (@instances,%instances); my $line=$self->_readline; $line=~s/[\t\n]//; if ($line =~ /\*{10,}/) { #Endo of Section II if we do only section II $self->{_end}=1; return ; } do { if ($line!~/^\s/) { ($sid,$eval,$scheme)=split(/\s+/,$line,3); } else { $scheme .=$line; } $line=$self->_readline; $line=~s/[\t\n]//; } until ($line!~/^\s/); my $pos=1; $scheme=~s/\s+//g; $scheme=~s/\n//g; my @motifs=split(/_/,$scheme); while (@motifs) { my $next=shift(@motifs); if (!($next=~/\D/)) { last if (!@motifs); $pos+=$next; next; } my $id=$next; my $score= $id=~m/\[/ ? 'strong' : 'weak' ; my $frame; my $strand = $id =~ m/\-\d/ ? -1 : 1 ; if ($self->{_mixquery}) { $frame = 0 if $id =~ m/\d+a/ ; $frame = 1 if $id =~ m/\d+b/ ; $frame = 2 if $id =~ m/\d+c/ ; } $id=~s/\D+//g; my @s; my $width=$index{$id}; #We don't know the sequence, but we know the length my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq my $instance=Bio::Matrix::PSM::InstanceSite->new ( -id=>"$id\@$sid", -mid=>$id, -accession_number=>$sid, -desc=>"Motif $id occurrance in $sid", -score=>$score, -seq=>$seq, -alphabet => 'dna', -start=>$pos, -strand=>$strand); $instance->frame($frame) if ($self->{_mixquery}); push @instances,$instance; $pos+=$index{$id}*$self->{_factor}; } my $psm= Bio::Matrix::PSM::Psm->new(-instances=> \@instances, -e_val => $eval, -id => $sid); $self->_pushback($line); return $psm; } =head2 write_psm Title : write_psm Usage : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix) my $matrix=$psmin->next_matrix; #Create the stream my $psmio=new(-file=>">psms.mast",-format=>'mast'); $psmio->write_psm($matrix); #Will warn if only PFM data is contained in $matrix, recalculate the PWM #based on normal distribution (A=>0.25, C=>0.25, etc) Function: writes pwm in mast format Throws : Example : Args : SiteMatrix object Returns : =cut sub write_psm { my ($self,$matrix)=@_; # my $idline=">". $matrix->id . "\n"; my $w=$matrix->width; my $header="ALPHABET= ACGT\nlog-odds matrix: alength= 4 w= $w\n"; $self->_print($header); unless ($matrix->get_logs_array('A')) { warn "No log-odds data, available, using normal distribution to recalculate the PWM"; $matrix->calc_weight({A=>0.25, C=>0.25, G=>0.25,T=>0.25}); } while (my %h=$matrix->next_pos) { $self->_print (join("\t",$h{lA},$h{lC},$h{lG},$h{lT},"\n")); } } 1;