Bio/Matrix/PSM/IO/mast.pm

   1
   2 =head1 NAME
   3
   4 Bio::Matrix::PSM::IO::mast - PSM mast parser implementation
   5
   6 =head1 SYNOPSIS
   7
   8 See Bio::Matrix::PSM::IO for detailed documentation on how to
   9 use PSM parsers
  10
  11 =head1 DESCRIPTION
  12
  13 Parser for mast. This driver unlike meme or transfac for example is
  14 dedicated more to PSM sequence matches, than to PSM themselves.
  15
  16 =head1 TO DO
  17
  18 Section III should be parsed too, otherwise no real sequence is
  19 available, so we supply 'NNNNN....' as a seq which is not right.
  20
  21 =head1 FEEDBACK
  22
  23 =head2 Mailing Lists
  24
  25 User feedback is an integral part of the evolution of this
  26 and other Bioperl modules. Send your comments and suggestions preferably
  27 to one of the Bioperl mailing lists. Your participation is much appreciated.
  28
  29   bioperl-l@bioperl.org                  - General discussion
  30   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  31
  32 =head2 Support
  33
  34 Please direct usage questions or support issues to the mailing list:
  35
  36 I<bioperl-l@bioperl.org>
  37
  38 rather than to the module maintainer directly. Many experienced and
  39 reponsive experts will be able look at the problem and quickly
  40 address it. Please include a thorough description of the problem
  41 with code and data examples if at all possible.
  42
  43 =head2 Reporting Bugs
  44
  45 Report bugs to the Bioperl bug tracking system to help us keep track
  46 the bugs and their resolution.  Bug reports can be submitted via the
  47 web:
  48
  49   https://github.com/bioperl/bioperl-live/issues
  50
  51 =head1 AUTHOR - Stefan Kirov
  52
  53 Email skirov@utk.edu
  54
  55 =head1 APPENDIX
  56
  57 The rest of the documentation details each of the object
  58 methods. Internal methods are usually preceded with a _
  59
  60 =cut
  61
  62 # Let the code begin...
  63 package Bio::Matrix::PSM::IO::mast;
  64 use Bio::Matrix::PSM::InstanceSite;
  65 use Bio::Matrix::PSM::Psm;
  66 use Bio::Root::Root;
  67 use strict;
  68
  69 use base qw(Bio::Matrix::PSM::PsmHeader Bio::Matrix::PSM::IO);
  70
  71 =head2 new
  72
  73  Title   : new
  74  Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast',
  75                                                                                -file=>$file);
  76  Function: Associates a file with the appropriate parser
  77  Throws  : Throws if the file passed is in HTML format or if
  78            some criteria for the file
  79            format are not met.
  80  Example :
  81  Returns : psm object, associated with a file with matrix file
  82  Args    : hash
  83  return  : "Bio::Matrix::PSM::$format"->new(@args);
  84
  85 =cut
  86
  87
  88 sub new {
  89     my($class, @args)=@_;
  90     my $self = $class->SUPER::new(@args);
  91     my (%instances,@header,$n);
  92     my ($file)=$self->_rearrange(['FILE'], @args);
  93     $self->{file} = $file;
  94     $self->{_factor}=1;
  95     $self->_initialize_io(@args) || warn "Did you intend to use STDIN?"; #Read only for now
  96     $self->{_end}=0;
  97     undef $self->{hid};
  98     return $self if ($file=~/^>/);#Just writing
  99     my $buf=$self->_readline;
 100         $self->throw('Cannot parse HTML format yet') if ($buf =~/^<HTML>/);
 101     # this should probably be moved to its own function
 102     while ( defined($buf=$self->_readline)) {
 103         chomp($buf);
 104         if ($buf=~/DATABASE AND MOTIFS/) {
 105                 while ($buf=$self->_readline) {
 106                         if ($buf=~/DATABASE/) {
 107                                         $buf=~s/^[\s\t]+//;
 108                                         chomp $buf;
 109                                         ($n,$self->{_dbname},$self->{_dbtype})=split(/\s/,$buf);
 110                                         $self->{_dbtype}=~s/[\(\)]//g;
 111                         }
 112                         if ($buf=~/MOTIFS/) {
 113                                         $buf=~s/^[\s\t]+//;
 114                                         chomp $buf;
 115                                         ($n,$self->{_mrsc},$self->{_msrctype})=split(/\s/,$buf);
 116                                         $self->{_msrctype}=~s/[\(\)]//g;
 117                                         last;
 118                         }
 119                 }
 120                 if ($self->{_msrctype} ne $self->{_dbtype}) {#Assume we have protein motifs, nuc DB (not handling opp.)
 121                         $self->{_factor}=3;
 122                         $self->{_mixquery}=1;
 123                 }
 124         }
 125         if ($buf=~m/MOTIF WIDTH BEST POSSIBLE MATCH/) {
 126             $self->_readline;
 127             while (defined($buf=$self->_readline)) {
 128                 last if ($buf!~/\w/);
 129                 $buf=~s/\t+//g;
 130                 $buf=~s/^\s+//g;
 131                 my ($id,$width,$seq)=split(/\s+/,$buf);
 132                 push @{$self->{hid}},$id;
 133                 $self->{length}->{$id}=$width;
 134                 $self->{seq}->{$id}=$seq;
 135             }
 136             next;
 137         }
 138         if ($buf=~m/section i:/i) {
 139             $self->_readline;
 140             $self->_readline;
 141             $self->_readline;
 142             %instances=_get_genes($self);
 143             $self->{instances}=\%instances;
 144         if (!(%instances)) {
 145                 $self->warn ("Your MAST analysis did not find any matches satisfying the current threshold.\nSee MAST documentation for more information.\n");
 146                 return $self; #The header might be useful so we return the object, not undef
 147         }
 148             next;
 149         }
 150         if ($buf=~m/section ii:/i) {
 151             $self->_readline;
 152             $self->_readline;
 153             $self->_readline;
 154             last;
 155         }
 156         $buf=~s/[\t+\s+]/ /g;
 157         push @header,$buf unless (($buf=~/\*{10,}/)||($buf!~/\w/));
 158     }
 159     $self->throw('Could not read Section I, probably wrong format, make sure it is not HTML, giving up...') if !(%instances);
 160     $self->warn( "This file might be an unreadable version, proceed with caution!\n") if (!grep(/\s+MAST\s+version\s+3/,@header));
 161
 162     $self->{unstructured} = \@header;
 163     $self->_initialize;
 164     return $self;
 165 }
 166
 167
 168 # Get the file header and put store it as a hash, which later we'll use to create
 169 # the header for each Psm. See Bio::Matrix::PSM::PsmI for header function.
 170 sub _get_genes {
 171         my $self=shift;
 172         my %llid;
 173         my $ok=0;
 174         my $i=0;
 175         my %instances;
 176         while (my $line=$self->_readline) {
 177                 last if ($line=~/^[\s\t*]/); # Well, ids can be nearly anything...???
 178                 chomp($line);
 179                 $i++;
 180                 next if ($line eq '');
 181                 $line=~s/\s+/,/g;
 182                 my ($id,$key,$eval,$len)=split(/,/,$line);
 183                 unless ($len) {
 184                         warn "Malformed data found: $line\n";
 185                         next;
 186                 }
 187                 $instances{$id}=Bio::Matrix::PSM::InstanceSite->new(-id=>$id,
 188                                                                                                                                                           -desc=>$key,
 189                                                                                                                                                           -score=>$eval,
 190                                                                                                                                                           -width=>$len,
 191                                                                                                                                                           -seq=>'ACGT');
 192         }
 193         return %instances;
 194 }
 195
 196
 197 =head2 next_psm
 198
 199  Title   : next_psm
 200  Usage   : my $psm=$psmIO->next_psm();
 201  Function: Reads the next PSM from the input file, associated with this object
 202  Throws  : Throws if there ara format violations in the input file (checking is not
 203             very strict with all drivers).
 204  Example :
 205  Returns : Bio::Matrix::PSM::Psm object
 206  Args    : none
 207
 208 =cut
 209
 210
 211 sub next_psm {
 212     my $self=shift;
 213     return if ($self->{_end}==1);
 214     my (@lmotifsm,%index,$eval,$scheme,$sid);
 215     %index= %{$self->{length}};
 216     my (@instances,%instances);
 217     my $line=$self->_readline;
 218     $line=~s/[\t\n]//;
 219     if ($line =~ /\*{10,}/) { #Endo of Section II if we do only section II
 220         $self->{_end}=1;
 221         return ;
 222     }
 223     do {
 224         if ($line!~/^\s/) {
 225             ($sid,$eval,$scheme)=split(/\s+/,$line,3);
 226         }
 227         else
 228         { $scheme .=$line; }
 229         $line=$self->_readline;
 230         $line=~s/[\t\n]//;
 231     } until ($line!~/^\s/);
 232     my $pos=1;
 233     $scheme=~s/\s+//g;
 234     $scheme=~s/\n//g;
 235     my @motifs=split(/_/,$scheme);
 236     while (@motifs) {
 237         my $next=shift(@motifs);
 238         if (!($next=~/\D/)) {
 239             last if (!@motifs);
 240             $pos+=$next;
 241             next;
 242         }
 243         my $id=$next;
 244         my $score= $id=~m/\[/ ? 'strong' : 'weak' ;
 245         my $frame;
 246         my $strand = $id =~ m/\-\d/ ? -1 : 1 ;
 247         if ($self->{_mixquery}) {
 248                 $frame = 0 if $id =~ m/\d+a/ ;
 249                 $frame = 1 if $id =~ m/\d+b/ ;
 250                 $frame = 2 if $id =~ m/\d+c/ ;
 251         }
 252         $id=~s/\D+//g;
 253
 254         my @s;
 255         my $width=$index{$id};
 256     #We don't know the sequence, but we know the length
 257         my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq
 258         my $instance=Bio::Matrix::PSM::InstanceSite->new
 259             ( -id=>"$id\@$sid",
 260               -mid=>$id,
 261               -accession_number=>$sid,
 262               -desc=>"Motif $id occurrance in $sid",
 263               -score=>$score,
 264               -seq=>$seq,
 265                   -alphabet => 'dna',
 266               -start=>$pos,
 267               -strand=>$strand);
 268           $instance->frame($frame) if ($self->{_mixquery});
 269         push @instances,$instance;
 270         $pos+=$index{$id}*$self->{_factor};
 271     }
 272     my $psm= Bio::Matrix::PSM::Psm->new(-instances=> \@instances,
 273                                         -e_val    => $eval,
 274                                         -id       => $sid);
 275     $self->_pushback($line);
 276     return $psm;
 277 }
 278
 279
 280 =head2 write_psm
 281
 282  Title   : write_psm
 283  Usage   : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix)
 284             my $matrix=$psmin->next_matrix;
 285             #Create the stream
 286             my $psmio=new(-file=>">psms.mast",-format=>'mast');
 287             $psmio->write_psm($matrix);
 288             #Will warn if only PFM data is contained in $matrix, recalculate the PWM
 289             #based on normal distribution (A=>0.25, C=>0.25, etc)
 290  Function: writes pwm in mast format
 291  Throws  :
 292  Example :
 293  Args    : SiteMatrix object
 294  Returns :
 295
 296 =cut
 297
 298 sub write_psm {
 299     my ($self,$matrix)=@_;
 300 #    my $idline=">". $matrix->id . "\n";
 301     my $w=$matrix->width;
 302     my $header="ALPHABET= ACGT\nlog-odds matrix: alength= 4 w= $w\n";
 303     $self->_print($header);
 304     unless ($matrix->get_logs_array('A')) {
 305         warn "No log-odds data, available, using normal distribution to recalculate the PWM";
 306         $matrix->calc_weight({A=>0.25, C=>0.25, G=>0.25,T=>0.25});
 307     }
 308     while (my %h=$matrix->next_pos) {
 309         $self->_print (join("\t",$h{lA},$h{lC},$h{lG},$h{lT},"\n"));
 310     }
 311 }
 312
 313 1;