lib/Bio/Tools/OddCodes.pm

   1 #$Id$
   2 #-----------------------------------------------------------------------------
   3 # PACKAGE    : OddCodes.pm
   4 # PURPOSE    : To write amino acid sequences in alternative alphabets
   5 # AUTHOR     : Derek Gatherer (D.Gatherer@organon.nhe.akzonobel.nl)
   6 # SOURCE     :
   7 # CREATED    : 8th July 2000
   8 # MODIFIED   :
   9 # DISCLAIMER : I am employed in the pharmaceutical industry but my
  10 #            : employers do not endorse or sponsor this module
  11 #            : in any way whatsoever.  The above email address is
  12 #            : given purely for the purpose of easy communication
  13 #            : with the author, and does not imply any connection
  14 #            : between my employers and anything written below.
  15 # LICENCE    : You may distribute this module under the same terms
  16 #            : as the rest of BioPerl.
  17 #----------------------------------------------------------------------------
  18
  19 =head1 NAME
  20
  21 Bio::Tools::OddCodes - Object holding alternative alphabet coding for
  22 one protein sequence
  23
  24 =head1 SYNOPSIS
  25
  26   # Take a sequence object from eg, an inputstream, and creates an
  27   # object for the purposes of rewriting that sequence in another
  28   # alphabet.  These are abbreviated amino acid sequence alphabets,
  29   # designed to simplify the statistical aspects of analysing protein
  30   # sequences, by reducing the combinatorial explosion of the
  31   # 20-letter alphabet.  These abbreviated alphabets range in size
  32   # from 2 to 8.
  33
  34   # Creating the OddCodes object, eg:
  35
  36         my $inputstream = Bio::SeqIO->new( '-file' => "seqfile",
  37                                            '-format' => 'Fasta');
  38         my $seqobj = $inputstream->next_seq();
  39         my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj);
  40
  41   # or:
  42
  43         my $seqobj = Bio::PrimarySeq->new
  44               (-seq=>'[cut and paste a sequence here]',
  45                -alphabet => 'protein',
  46                -id => 'test');
  47         my $oddcode_obj  =  Bio::Tools::OddCodes->new(-seq => $seqobj);
  48
  49   # do the alternative coding, returning the answer as a reference to
  50   # a string
  51
  52         my $output = $oddcode_obj->structural();
  53         my $output = $oddcode_obj->chemical();
  54         my $output = $oddcode_obj->functional();
  55         my $output = $oddcode_obj->charge();
  56         my $output = $oddcode_obj->hydrophobic();
  57         my $output = $oddcode_obj->Dayhoff();
  58         my $output = $oddcode_obj->Sneath();
  59         my $output = $oddcode_obj->Stanfel();
  60
  61
  62   # display sequence in new form, eg:
  63
  64         my $new_coding = $$output;
  65         print "\n$new_coding";
  66
  67 =head1 DESCRIPTION
  68
  69 Bio::Tools::Oddcodes is a welterweight object for rewriting a protein
  70 sequence in an alternative alphabet.  Eight of these are provided, ranging
  71 from the the 2-letter hydrophobic alphabet, to the 8-letter chemical
  72 alphabet.  These are useful for the statistical analysis of protein
  73 sequences since they can partially avoid the combinatorial explosion
  74 produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers
  75 etc.)
  76
  77 The objects will print out a warning if the input sequence is not a
  78 protein. If you know what you are doing, you can silence the warning
  79 by setting verbose() to a negative value.
  80
  81 See SYNOPSIS above for object creation code.
  82
  83 =head1 REFERENCES
  84
  85 Stanfel LE (1996) A new approach to clustering the amino acids.  J. theor.
  86 Biol. 183, 195-205.
  87
  88 Karlin S, Ost F and Blaisdell BE (1989)  Patterns in DNA and amino acid
  89 sequences and their statistical significance.  Chapter 6 of: Mathematical
  90 Methods for DNA Sequences.  Waterman MS (ed.)  CRC Press, Boca Raton , FL.
  91
  92 =head1 FEEDBACK
  93
  94 =head2 Mailing Lists
  95
  96 User feedback is an integral part of the evolution of this and other
  97 Bioperl modules. Send your comments and suggestions preferably to one
  98 of the Bioperl mailing lists.  Your participation is much appreciated.
  99
 100   bioperl-l@bioperl.org                  - General discussion
 101   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 102
 103 =head2 Support
 104
 105 Please direct usage questions or support issues to the mailing list:
 106
 107 I<bioperl-l@bioperl.org>
 108
 109 rather than to the module maintainer directly. Many experienced and
 110 reponsive experts will be able look at the problem and quickly
 111 address it. Please include a thorough description of the problem
 112 with code and data examples if at all possible.
 113
 114 =head2 Reporting Bugs
 115
 116 Report bugs to the Bioperl bug tracking system to help us keep track
 117 the bugs and their resolution.  Bug reports can be submitted via the
 118 web:
 119
 120   https://github.com/bioperl/bioperl-live/issues
 121
 122 =head1 AUTHOR
 123
 124 Derek Gatherer
 125
 126 =head1 APPENDIX
 127
 128 The rest of the documentation details each of the object methods.
 129 Internal methods are usually preceded with a _
 130
 131 =cut
 132
 133 package Bio::Tools::OddCodes;
 134 use strict;
 135
 136
 137 use base qw(Bio::Root::Root);
 138
 139 sub new
 140 {
 141     my($class,@args) = @_;
 142
 143     my $self = $class->SUPER::new(@args);
 144
 145     my ($seqobj) = $self->_rearrange([qw(SEQ)],@args);
 146     if((! defined($seqobj)) && @args && ref($args[0])) {
 147         # parameter not passed as named parameter?
 148         $seqobj = $args[0];
 149     }
 150     unless  ($seqobj->isa("Bio::PrimarySeqI"))
 151     {
 152         $self->throw("Bio::Tools::OddCodes only works on PrimarySeqI objects");
 153     }
 154
 155     $self->{'_seqref'} = $seqobj;
 156
 157     return $self;
 158 }
 159
 160 =head2 structural
 161
 162  Title   : structural
 163  Usage   : $output = $oddcode_obj->structural();
 164  Function: turns amino acid sequence into 3-letter structural alphabet
 165          : A (ambivalent), E (external), I (internal)
 166  Example : a sequence ACDEFGH will become AAEEIAE
 167  Returns : Reference to the new sequence string
 168  Args    : none
 169
 170 =cut
 171
 172 sub structural()
 173 {
 174         my $self = $_[0];
 175         my $seqstring = &_pullseq($self);       # see _pullseq() below
 176
 177 # now the real business
 178
 179         $seqstring =~ tr/[ACGPSTWY]/1/;
 180         $seqstring =~ tr/[RNDQEHK]/2/;
 181         $seqstring =~ tr/[ILMFV]/3/;
 182         $seqstring =~ tr/1/A/;
 183         $seqstring =~ tr/2/E/;
 184         $seqstring =~ tr/3/I/;
 185
 186         return \$seqstring;
 187
 188 # and that's that one
 189 }
 190
 191 =head2 functional
 192
 193  Title   : functional
 194  Usage   : $output = $oddcode_obj->functional();
 195  Function: turns amino acid sequence into 4-letter functional alphabet
 196          : A (acidic), C (basic), H (hydrophobic), P (polar)
 197  Example : a sequence ACDEFGH will become HPAAHHC
 198  Returns : Reference to the new sequence string
 199  Args    : none
 200
 201 =cut
 202
 203 sub functional()
 204 {
 205         my $self = $_[0];
 206         my $seqstring = &_pullseq($self);
 207
 208 # now the real business
 209
 210         $seqstring =~ tr/[DE]/1/;
 211         $seqstring =~ tr/[HKR]/2/;
 212         $seqstring =~ tr/[AFILMPVW]/3/;
 213         $seqstring =~ tr/[CGNQSTY]/4/;
 214         $seqstring =~ tr/1/A/;
 215         $seqstring =~ tr/2/C/;
 216         $seqstring =~ tr/3/H/;
 217         $seqstring =~ tr/4/P/;
 218
 219         return \$seqstring;
 220
 221 # and that's that one
 222 }
 223
 224 =head2 hydrophobic
 225
 226  Title   : hydrophobic
 227  Usage   : $output = $oddcode_obj->hydrophobic();
 228  Function: turns amino acid sequence into 2-letter hydrophobicity alphabet
 229          : O (hydrophobic), I (hydrophilic)
 230  Example : a sequence ACDEFGH will become OIIIOII
 231  Returns : Reference to the new sequence string
 232  Args    : none
 233
 234 =cut
 235
 236 sub hydrophobic()
 237 {
 238         my $self = $_[0];
 239         my $seqstring = &_pullseq($self);
 240
 241 # now the real business
 242
 243         $seqstring =~ tr/[AFILMPVW]/1/;
 244         $seqstring =~ tr/[CDEGHKNQRSTY]/2/;
 245         $seqstring =~ tr/1/I/;
 246         $seqstring =~ tr/2/O/;
 247
 248         return \$seqstring;
 249
 250 # and that's that one
 251 }
 252
 253 =head2 Dayhoff
 254
 255  Title   : Dayhoff
 256  Usage   : $output = $oddcode_obj->Dayhoff();
 257  Function: turns amino acid sequence into 6-letter Dayhoff alphabet
 258  Example : a sequence ACDEFGH will become CADDGCE
 259          : A (=C),   C (=AGPST), D (=DENQ),
 260          : E (=HKR), F (=ILMV),  G (=FWY)
 261  Returns : Reference to the new sequence string
 262  Args    : none
 263
 264 =cut
 265
 266 sub Dayhoff()
 267 {
 268         my $self = $_[0];
 269         my $seqstring = &_pullseq($self);
 270
 271 # now the real business
 272
 273         $seqstring =~ tr/[C]/1/;
 274         $seqstring =~ tr/[AGPST]/2/;
 275         $seqstring =~ tr/[DENQ]/3/;
 276         $seqstring =~ tr/[HKR]/4/;
 277         $seqstring =~ tr/[ILMV]/5/;
 278         $seqstring =~ tr/[FWY]/6/;
 279         $seqstring =~ tr/1/A/;
 280         $seqstring =~ tr/2/C/;
 281         $seqstring =~ tr/3/D/;
 282         $seqstring =~ tr/4/E/;
 283         $seqstring =~ tr/5/F/;
 284         $seqstring =~ tr/6/G/;
 285
 286         return \$seqstring;
 287
 288 # and that's that one
 289 }
 290
 291 =head2 Sneath
 292
 293  Title   : Sneath
 294  Usage   : $output = $oddcode_obj->Sneath();
 295  Function: turns amino acid sequence into 7-letter Sneath alphabet
 296  Example : a sequence ACDEFGH will become CEFFHCF
 297          : A (=ILV), C (=AGP), D (=MNQ), E (=CST),
 298          : F (=DE),  G (=KR),  H (=FHWY)
 299  Returns : Reference to the new sequence string
 300  Args    : none
 301
 302 =cut
 303
 304 sub Sneath()
 305 {
 306         my $self = $_[0];
 307         my $seqstring = &_pullseq($self);
 308
 309 # now the real business
 310
 311         $seqstring =~ tr/[ILV]/1/;
 312         $seqstring =~ tr/[AGP]/2/;
 313         $seqstring =~ tr/[MNQ]/3/;
 314         $seqstring =~ tr/[CST]/4/;
 315         $seqstring =~ tr/[DE]/5/;
 316         $seqstring =~ tr/[KR]/6/;
 317         $seqstring =~ tr/[FHWY]/7/;
 318         $seqstring =~ tr/1/A/;
 319         $seqstring =~ tr/2/C/;
 320         $seqstring =~ tr/3/D/;
 321         $seqstring =~ tr/4/E/;
 322         $seqstring =~ tr/5/F/;
 323         $seqstring =~ tr/6/G/;
 324         $seqstring =~ tr/7/H/;
 325
 326         return \$seqstring;
 327
 328 # and that's that one
 329 }
 330
 331 =head2 Stanfel
 332
 333  Title   : Stanfel
 334  Usage   : $output = $oddcode_obj->Stanfel();
 335  Function: turns amino acid sequence into 4-letter Stanfel alphabet
 336  Example : a sequence ACDEFGH will become AACCDAE
 337          : A (=ACGILMPSTV), C (=DENQ), D (=FWY), E (=HKR)
 338  Returns : Reference to the new sequence string
 339  Args    : none
 340
 341 =cut
 342
 343 sub Stanfel()
 344 {
 345         my $self = $_[0];
 346         my $seqstring = &_pullseq($self);
 347
 348 # now the real business
 349
 350         $seqstring =~ tr/[ACGILMPSTV]/1/;
 351         $seqstring =~ tr/[DENQ]/2/;
 352         $seqstring =~ tr/[FWY]/3/;
 353         $seqstring =~ tr/[HKR]/4/;
 354         $seqstring =~ tr/1/A/;
 355         $seqstring =~ tr/2/C/;
 356         $seqstring =~ tr/3/D/;
 357         $seqstring =~ tr/4/E/;
 358
 359         return \$seqstring;
 360
 361 # and that's that one
 362 }
 363
 364 =head2 chemical
 365
 366  Title   : chemical
 367  Usage   : $output = $oddcode_obj->chemical();
 368  Function: turns amino acid sequence into 8-letter chemical alphabet
 369          : A (acidic), L (aliphatic), M (amide), R (aromatic)
 370          : C (basic),  H (hydroxyl),  I (imino), S (sulphur)
 371  Example : a sequence ACDEFGH will become LSAARAC
 372  Returns : Reference to the new sequence string
 373  Args    : none
 374
 375 =cut
 376
 377 sub chemical()
 378 {
 379         my $self = $_[0];
 380         my $seqstring = &_pullseq($self);
 381
 382 # now the real business
 383
 384         $seqstring =~ tr/[DE]/1/;
 385         $seqstring =~ tr/[AGILV]/2/;
 386         $seqstring =~ tr/[NQ]/3/;
 387         $seqstring =~ tr/[FWY]/4/;
 388         $seqstring =~ tr/[RHK]/5/;
 389         $seqstring =~ tr/[ST]/6/;
 390         $seqstring =~ tr/P/7/;
 391         $seqstring =~ tr/[CM]/8/;
 392         $seqstring =~ tr/1/A/;
 393         $seqstring =~ tr/2/L/;
 394         $seqstring =~ tr/3/M/;
 395         $seqstring =~ tr/4/R/;
 396         $seqstring =~ tr/5/C/;
 397         $seqstring =~ tr/6/H/;
 398         $seqstring =~ tr/7/I/;
 399         $seqstring =~ tr/8/S/;
 400
 401         return \$seqstring;
 402
 403 # and that's that one
 404 }
 405
 406 =head2 charge
 407
 408  Title   : charge
 409  Usage   : $output = $oddcode_obj->charge();
 410  Function: turns amino acid sequence into 3-letter charge alphabet
 411  Example : a sequence ACDEFGH will become NNAANNC
 412          : A (negative; NOT anode), C (positive; NOT cathode), N (neutral)
 413  Returns : Reference to the new sequence string
 414  Args    : none
 415
 416 =cut
 417
 418 sub charge()
 419 {
 420         my $self = $_[0];
 421         my $seqstring = &_pullseq($self);
 422
 423 # now the real business
 424
 425         $seqstring =~ tr/[DE]/1/;
 426         $seqstring =~ tr/[HKR]/2/;
 427         $seqstring =~ tr/[ACFGILMNPQSTVWY]/3/;
 428         $seqstring =~ tr/1/A/;
 429         $seqstring =~ tr/2/C/;
 430         $seqstring =~ tr/3/N/;
 431
 432         return \$seqstring;
 433
 434 # and that's that one
 435 }
 436
 437 # _pullseq is called within each of the subroutines
 438 # it just checks a few things and returns the sequence
 439
 440 sub _pullseq
 441 {
 442         my $self = $_[0];
 443
 444         my $seqobj =  $self->{'_seqref'};
 445
 446         unless  ($seqobj->isa("Bio::PrimarySeqI"))
 447         {
 448                 $self->throw("die, OddCodes works only on PrimarySeqI objects\n");
 449         }
 450         $self->warn("\tAll OddCode alphabets need a protein sequence,\n".
 451                     "\tbut BioPerl thinks this is not: [". $seqobj->id. "]")
 452             unless $seqobj->alphabet eq 'protein' or $self->verbose < 0;;
 453
 454         my $seqstring = uc $seqobj->seq();
 455
 456         if(length($seqstring)<1)
 457         {
 458                 $self->throw("$seqstring: die, sequence has zero length\n");
 459         }
 460         return $seqstring;
 461 }
 462
 463 1;