Bio/Matrix/PSM/PsmHeaderI.pm

   1 #---------------------------------------------------------
   2
   3 =head1 NAME
   4
   5 Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file
   6
   7 =head1 SYNOPSIS
   8
   9  use Bio::Matrix::PSM::IO;
  10  #Obtain an Bio::Matrix::PSM::IO object:
  11  my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast');
  12
  13  #Get some general data about the file you are parsing:
  14  my $release=$psmIO->release;
  15  my $version=$psmIO->version;
  16
  17  print "This analysis was performed using MAST version $version, release $release\n";
  18
  19  #Now let's see what are the consensus sequences of the motifs fed as an input:
  20  my %seq=$psmIO->seq;
  21
  22  #let's cycle through all consensus sequences now:
  23
  24  foreach my $id ($psmIO->hid) {
  25    print "Motif $id is \t",$seq{$id},"\n";
  26  }
  27
  28   #Finally look at the stuff we do not parse:
  29   my @inputfile=grep(/datafile/i,$psmIO->unstructured);
  30
  31 =head1 DESCRIPTION
  32
  33 Generally you should not use this object directly, you can access the
  34 information through a PSM driver (See Bio::Matrix::PSM::IO). It is
  35 handling the header data from a PSM file which may be very
  36 different. This means that some of the methods will return undef
  37 naturally, because this information is not present in the file which
  38 is parsed. Some important data might be left over in the unstructured
  39 part, and you might have to parse it yourself. I will try to
  40 'structure' this header more in the near future.
  41
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this
  48 and other Bioperl modules. Send your comments and suggestions preferably
  49  to one of the Bioperl mailing lists.
  50 Your participation is much appreciated.
  51
  52   bioperl-l@bioperl.org                  - General discussion
  53   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  54
  55 =head2 Support
  56
  57 Please direct usage questions or support issues to the mailing list:
  58
  59 I<bioperl-l@bioperl.org>
  60
  61 rather than to the module maintainer directly. Many experienced and
  62 reponsive experts will be able look at the problem and quickly
  63 address it. Please include a thorough description of the problem
  64 with code and data examples if at all possible.
  65
  66 =head2 Reporting Bugs
  67
  68 Report bugs to the Bioperl bug tracking system to help us keep track
  69 the bugs and their resolution.  Bug reports can be submitted via the
  70 web:
  71
  72   https://github.com/bioperl/bioperl-live/issues
  73
  74 =head1 AUTHOR - Stefan Kirov
  75
  76 Email skirov@utk.edu
  77
  78 =head1 APPENDIX
  79
  80 =cut
  81
  82
  83 # Let the code begin...
  84 package Bio::Matrix::PSM::PsmHeaderI;
  85 use Bio::Matrix::PSM::InstanceSite;
  86 use Bio::Matrix::PSM::Psm;
  87 use Bio::Matrix::PSM::IO;
  88 use strict;
  89 use base qw(Bio::Matrix::PSM::PsmI);
  90
  91 #Accessor methods, based on the driver
  92 @Bio::Matrix::PSM::PsmHeader::MASTHEADER=qw(html version release
  93                                             seq hid length instances
  94                                             unstructured);
  95 @Bio::Matrix::PSM::PsmHeader::MEMEHEADER=qw(html version release hid
  96                                             weight length unstructured);
  97 @Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER=qw(unstructured version release);
  98 @Bio::Matrix::PSM::PsmHeader::ALLHEADER=qw(header release type version html
  99                                            release weight length hid
 100                                            seq instances unstructured);
 101
 102 =head2 new
 103
 104  Title   : new
 105  Usage   : my $header= Bio::Matrix::PSM::PsmHeader->new
 106             ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
 107               -instances=>\%instances, -header=>\@header, -type=>'mast');
 108  Function: Creates a new Bio::Matrix::PSM::PsmHeader object
 109  Throws  :
 110  Example :
 111  Returns :  Bio::Matrix::PSM::PsmHeaderI object
 112  Args    :  hash
 113
 114
 115 =cut
 116
 117 =head2 seq
 118
 119  Title   : seq
 120  Usage   : my %seq= $header->seq();
 121  Function: Returns the sequence data as a hash, indexed by a
 122            sequence ID (motif id or accession number)
 123            In case the input data is a motif it would return the
 124            consenus seq for each of them (mast).
 125  Throws  :
 126  Example :
 127  Returns :  hash
 128  Args    :
 129
 130
 131 =cut
 132
 133 sub seq {
 134      my $self = shift;
 135     $self->throw_not_implemented();
 136 }
 137
 138
 139 =head2 hid
 140
 141  Title   : hid
 142  Usage   : my @ids= $header->hid();
 143  Function: Returns array with the motif/instance ids
 144  Throws  :
 145  Example :
 146  Returns :  array
 147  Args    :
 148
 149
 150 =cut
 151
 152 sub hid {
 153      my $self = shift;
 154     $self->throw_not_implemented();
 155 }
 156
 157 =head2 length
 158
 159  Title   : length
 160  Usage   : my %length= $header->length();
 161  Function: Returns the length of the input sequence or motifs as a hash, indexed
 162            by a sequence ID (motif id or accession number)
 163  Throws  :
 164  Example :
 165  Returns :  hash
 166  Args    :
 167
 168
 169 =cut
 170
 171 sub length {
 172      my $self = shift;
 173     $self->throw_not_implemented();
 174 }
 175
 176 =head2 instances
 177
 178  Title   : instances
 179  Usage   : my %instances= $header->length();
 180  Function: Returns the instance, used  as a hash, indexed
 181            by a sequence ID (motif id or accession number)
 182  Throws  :
 183  Example :
 184  Returns :  hash of Bio::Matrix::PSM::InstanceSite objects
 185  Args    :
 186
 187
 188 =cut
 189
 190 sub instances {
 191      my $self = shift;
 192     $self->throw_not_implemented();
 193 }
 194
 195 =head2 weights
 196
 197  Title   : weights
 198  Usage   : my %weights= $header->weights();
 199  Function: Returns the weights of the input sequence as a hash, indexed
 200            by a sequence ID
 201  Throws  :
 202  Example :
 203  Returns :  hash
 204  Args    :
 205
 206
 207 =cut
 208
 209 sub weights {
 210      my $self = shift;
 211     $self->throw_not_implemented();
 212 }
 213
 214
 215 =head2 unstuctured
 216
 217  Title   : unstuctured
 218  Usage   : my @unstructured= $header->unstuctured();
 219  Function: Returns the unstructured data in the header as an array, one line per
 220            array element, all control symbols are removed with \W
 221  Throws  :
 222  Example :
 223  Returns :   array
 224  Args    :
 225
 226
 227 =cut
 228
 229 sub unstructured {
 230      my $self = shift;
 231     $self->throw_not_implemented();
 232 }
 233
 234 =head2 version
 235
 236  Title   : version
 237  Usage   : my $version= $header->version;
 238  Function: Returns the version of the file being parsed if such exists
 239  Throws  :
 240  Example :
 241  Returns :  string
 242  Args    :
 243
 244
 245 =cut
 246
 247 sub version {
 248      my $self = shift;
 249     $self->throw_not_implemented();
 250 }
 251
 252 =head2 revision
 253
 254  Title   : revision
 255  Usage   : my $revision= $header->revision;
 256  Function: Returns the revision of the file being parsed if such exists
 257  Throws  :
 258  Example :
 259  Returns :  string
 260  Args    :
 261
 262
 263 =cut
 264
 265 sub revision {
 266      my $self = shift;
 267     $self->throw_not_implemented();
 268 }
 269
 270 =head2 _check
 271
 272  Title   : _check
 273  Usage   : if ($self->_check('weights') { #do something} else {return 0;}
 274  Function: Checks if the method called is aplicable to the file format
 275  Throws  :
 276  Example :
 277  Returns :  boolean
 278  Args    :  string
 279
 280
 281 =cut
 282
 283 sub _check {
 284      my $self = shift;
 285     $self->throw_not_implemented();
 286 }
 287
 288 1;