Bio/SeqIO.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqIO
   4 #
   5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   6 #       and Lincoln Stein  <lstein@cshl.org>
   7 #
   8 # Copyright Ewan Birney
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #
  12 # _history
  13 # October 18, 1999  Largely rewritten by Lincoln Stein
  14
  15 # POD documentation - main docs before the code
  16
  17 =head1 NAME
  18
  19 Bio::SeqIO - Handler for SeqIO Formats
  20
  21 =head1 SYNOPSIS
  22
  23     use Bio::SeqIO;
  24
  25     $in  = Bio::SeqIO->new(-file => "inputfilename" ,
  26                            -format => 'Fasta');
  27     $out = Bio::SeqIO->new(-file => ">outputfilename" ,
  28                            -format => 'EMBL');
  29
  30     while ( my $seq = $in->next_seq() ) {
  31             $out->write_seq($seq);
  32     }
  33
  34   # Now, to actually get at the sequence object, use the standard Bio::Seq
  35   # methods (look at Bio::Seq if you don't know what they are)
  36
  37     use Bio::SeqIO;
  38
  39     $in  = Bio::SeqIO->new(-file => "inputfilename" ,
  40                            -format => 'genbank');
  41
  42     while ( my $seq = $in->next_seq() ) {
  43        print "Sequence ",$seq->id, " first 10 bases ",
  44              $seq->subseq(1,10), "\n";
  45     }
  46
  47
  48   # The SeqIO system does have a filehandle binding. Most people find this
  49   # a little confusing, but it does mean you can write the world's
  50   # smallest reformatter
  51
  52     use Bio::SeqIO;
  53
  54     $in  = Bio::SeqIO->newFh(-file => "inputfilename" ,
  55                              -format => 'Fasta');
  56     $out = Bio::SeqIO->newFh(-format => 'EMBL');
  57
  58     # World's shortest Fasta<->EMBL format converter:
  59     print $out $_ while <$in>;
  60
  61
  62 =head1 DESCRIPTION
  63
  64 Bio::SeqIO is a handler module for the formats in the SeqIO set (eg,
  65 Bio::SeqIO::fasta). It is the officially sanctioned way of getting at
  66 the format objects, which most people should use.
  67
  68 The Bio::SeqIO system can be thought of like biological file handles.
  69 They are attached to filehandles with smart formatting rules (eg,
  70 genbank format, or EMBL format, or binary trace file format) and
  71 can either read or write sequence objects (Bio::Seq objects, or
  72 more correctly, Bio::SeqI implementing objects, of which Bio::Seq is
  73 one such object). If you want to know what to do with a Bio::Seq
  74 object, read L<Bio::Seq>.
  75
  76 The idea is that you request a stream object for a particular format.
  77 All the stream objects have a notion of an internal file that is read
  78 from or written to. A particular SeqIO object instance is configured
  79 for either input or output. A specific example of a stream object is
  80 the Bio::SeqIO::fasta object.
  81
  82 Each stream object has functions
  83
  84    $stream->next_seq();
  85
  86 and
  87
  88    $stream->write_seq($seq);
  89
  90 As an added bonus, you can recover a filehandle that is tied to the
  91 SeqIO object, allowing you to use the standard E<lt>E<gt> and print
  92 operations to read and write sequence objects:
  93
  94     use Bio::SeqIO;
  95
  96     $stream = Bio::SeqIO->newFh(-format => 'Fasta',
  97                                 -fh     => \*ARGV);
  98     # read from standard input or the input filenames
  99
 100     while ( $seq = <$stream> ) {
 101           # do something with $seq
 102     }
 103
 104 and
 105
 106     print $stream $seq; # when stream is in output mode
 107
 108 This makes the simplest ever reformatter
 109
 110     #!/usr/bin/perl
 111
 112     $format1 = shift;
 113     $format2 = shift || die
 114        "Usage: reformat format1 format2 < input > output";
 115
 116     use Bio::SeqIO;
 117
 118     $in  = Bio::SeqIO->newFh(-format => $format1, -fh => \*ARGV );
 119     $out = Bio::SeqIO->newFh(-format => $format2 );
 120     # Note: you might want to quote -format to keep older
 121     # perl's from complaining.
 122
 123     print $out $_ while <$in>;
 124
 125
 126 =head1 CONSTRUCTORS
 127
 128 =head2 Bio::SeqIO-E<gt>new()
 129
 130    $seqIO = Bio::SeqIO->new(-file => 'filename',   -format=>$format);
 131    $seqIO = Bio::SeqIO->new(-fh   => \*FILEHANDLE, -format=>$format);
 132    $seqIO = Bio::SeqIO->new(-format => $format);
 133
 134 The new() class method constructs a new Bio::SeqIO object.  The
 135 returned object can be used to retrieve or print Seq objects. new()
 136 accepts the following parameters:
 137
 138 =over 5
 139
 140 =item -file
 141
 142 A file path to be opened for reading or writing.  The usual Perl
 143 conventions apply:
 144
 145    'file'       # open file for reading
 146    '>file'      # open file for writing
 147    '>>file'     # open file for appending
 148    '+<file'     # open file read/write
 149    'command |'  # open a pipe from the command
 150    '| command'  # open a pipe to the command
 151
 152 =item -fh
 153
 154 You may provide new() with a previously-opened filehandle.  For
 155 example, to read from STDIN:
 156
 157    $seqIO = Bio::SeqIO->new(-fh => \*STDIN);
 158
 159 Note that you must pass filehandles as references to globs.
 160
 161 If neither a filehandle nor a filename is specified, then the module
 162 will read from the @ARGV array or STDIN, using the familiar E<lt>E<gt>
 163 semantics.
 164
 165 A string filehandle is handy if you want to modify the output in the
 166 memory, before printing it out. The following program reads in EMBL
 167 formatted entries from a file and prints them out in fasta format with
 168 some HTML tags:
 169
 170   use Bio::SeqIO;
 171   use IO::String;
 172   my $in  = Bio::SeqIO->new(-file => "emblfile",
 173                             -format => 'EMBL');
 174   while ( my $seq = $in->next_seq() ) {
 175       # the output handle is reset for every file
 176       my $stringio = IO::String->new($string);
 177       my $out = Bio::SeqIO->new(-fh => $stringio,
 178                                 -format => 'fasta');
 179       # output goes into $string
 180       $out->write_seq($seq);
 181       # modify $string
 182       $string =~ s|(>)(\w+)|$1<font color="Red">$2</font>|g;
 183       # print into STDOUT
 184       print $string;
 185   }
 186
 187 =item -format
 188
 189 Specify the format of the file.  Supported formats include fasta,
 190 genbank, embl, swiss (SwissProt), Entrez Gene and tracefile formats
 191 such as abi (ABI) and scf. There are many more, for a complete listing
 192 see the SeqIO HOWTO (L<http://bioperl.open-bio.org/wiki/HOWTO:SeqIO>).
 193
 194 If no format is specified and a filename is given then the module will
 195 attempt to deduce the format from the filename suffix. If there is no
 196 suffix that Bioperl understands then it will attempt to guess the
 197 format based on file content. If this is unsuccessful then Fasta
 198 format is assumed.
 199
 200 The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta' are
 201 all valid.
 202
 203 Currently, the tracefile formats (except for SCF) require installation
 204 of the external Staden "io_lib" package, as well as the
 205 Bio::SeqIO::staden::read package available from the bioperl-ext
 206 repository.
 207
 208 =item -alphabet
 209
 210 Sets the alphabet ('dna', 'rna', or 'protein'). When the alphabet is
 211 set then Bioperl will not attempt to guess what the alphabet is. This
 212 may be important because Bioperl does not always guess correctly.
 213
 214 =item -flush
 215
 216 By default, all files (or filehandles) opened for writing sequences
 217 will be flushed after each write_seq() (making the file immediately
 218 usable).  If you do not need this facility and would like to marginally
 219 improve the efficiency of writing multiple sequences to the same file
 220 (or filehandle), pass the -flush option '0' or any other value that
 221 evaluates as defined but false:
 222
 223   my $gb = Bio::SeqIO->new(-file   => "<gball.gbk",
 224                            -format => "gb");
 225   my $fa = Bio::SeqIO->new(-file   => ">gball.fa",
 226                            -format => "fasta",
 227                            -flush  => 0); # go as fast as we can!
 228   while($seq = $gb->next_seq) { $fa->write_seq($seq) }
 229
 230
 231 =back
 232
 233 =head2 Bio::SeqIO-E<gt>newFh()
 234
 235    $fh = Bio::SeqIO->newFh(-fh => \*FILEHANDLE, -format=>$format);
 236    $fh = Bio::SeqIO->newFh(-format => $format);
 237    # etc.
 238
 239 This constructor behaves like new(), but returns a tied filehandle
 240 rather than a Bio::SeqIO object.  You can read sequences from this
 241 object using the familiar E<lt>E<gt> operator, and write to it using
 242 print().  The usual array and $_ semantics work.  For example, you can
 243 read all sequence objects into an array like this:
 244
 245   @sequences = <$fh>;
 246
 247 Other operations, such as read(), sysread(), write(), close(), and
 248 printf() are not supported.
 249
 250 =head1 OBJECT METHODS
 251
 252 See below for more detailed summaries.  The main methods are:
 253
 254 =head2 $sequence = $seqIO-E<gt>next_seq()
 255
 256 Fetch the next sequence from the stream.
 257
 258 =head2 $seqIO-E<gt>write_seq($sequence [,$another_sequence,...])
 259
 260 Write the specified sequence(s) to the stream.
 261
 262 =head2 TIEHANDLE(), READLINE(), PRINT()
 263
 264 These provide the tie interface.  See L<perltie> for more details.
 265
 266 =head1 FEEDBACK
 267
 268 =head2 Mailing Lists
 269
 270 User feedback is an integral part of the evolution of this and other
 271 Bioperl modules. Send your comments and suggestions preferably to one
 272 of the Bioperl mailing lists.
 273
 274 Your participation is much appreciated.
 275
 276   bioperl-l@bioperl.org                  - General discussion
 277   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 278
 279 =head2 Reporting Bugs
 280
 281 Report bugs to the Bioperl bug tracking system to help us keep track
 282 the bugs and their resolution.  Bug reports can be submitted via the
 283 web:
 284
 285   http://bugzilla.open-bio.org/
 286
 287 =head1 AUTHOR - Ewan Birney, Lincoln Stein
 288
 289 Email birney@ebi.ac.uk
 290       lstein@cshl.org
 291
 292 =head1 APPENDIX
 293
 294 The rest of the documentation details each of the object
 295 methods. Internal methods are usually preceded with a _
 296
 297 =cut
 298
 299 #' Let the code begin...
 300
 301 package Bio::SeqIO;
 302
 303 use strict;
 304
 305 use Bio::Factory::FTLocationFactory;
 306 use Bio::Seq::SeqBuilder;
 307 use Bio::Tools::GuessSeqFormat;
 308 use Symbol;
 309
 310 use base qw(Bio::Root::Root Bio::Root::IO Bio::Factory::SequenceStreamI);
 311
 312 my %valid_alphabet_cache;
 313
 314 =head2 new
 315
 316  Title   : new
 317  Usage   : $stream = Bio::SeqIO->new(-file => $filename,
 318                                      -format => 'Format')
 319  Function: Returns a new sequence stream
 320  Returns : A Bio::SeqIO stream initialised with the appropriate format
 321  Args    : Named parameters:
 322              -file => $filename
 323              -fh => filehandle to attach to
 324              -format => format
 325
 326            Additional arguments may be used to set factories and
 327            builders involved in the sequence object creation. None of
 328            these must be provided, they all have reasonable defaults.
 329              -seqfactory   the Bio::Factory::SequenceFactoryI object
 330              -locfactory   the Bio::Factory::LocationFactoryI object
 331              -objbuilder   the Bio::Factory::ObjectBuilderI object
 332
 333 See L<Bio::SeqIO::Handler>
 334
 335 =cut
 336
 337 my $entry = 0;
 338
 339 sub new {
 340         my ($caller,@args) = @_;
 341         my $class = ref($caller) || $caller;
 342
 343         # or do we want to call SUPER on an object if $caller is an
 344         # object?
 345         if( $class =~ /Bio::SeqIO::(\S+)/ ) {
 346                 my ($self) = $class->SUPER::new(@args);
 347                 $self->_initialize(@args);
 348                 return $self;
 349         } else {
 350
 351                 my %param = @args;
 352                 @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 353
 354         if (!defined($param{-file}) && !defined($param{-fh})) {
 355           $class->throw("file argument provided, but with an undefined value") if exists($param{'-file'});
 356           $class->throw("fh argument provided, but with an undefined value") if (exists($param{'-fh'}));
 357         }
 358
 359         my $format = $param{'-format'} ||
 360             $class->_guess_format( $param{-file} || $ARGV[0] );
 361
 362         if( ! $format ) {
 363             if ($param{-file}) {
 364                 $format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file}||$ARGV[0] )->guess;
 365             } elsif ($param{-fh}) {
 366                 $format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh}||$ARGV[0] )->guess;
 367             }
 368         }
 369         $format = "\L$format";  # normalize capitalization to lower case
 370         $class->throw("Unknown format given or could not determine it [$format]")
 371             unless $format;
 372         return unless( $class->_load_format_module($format) );
 373         return "Bio::SeqIO::$format"->new(@args);
 374     }
 375 }
 376
 377 =head2 newFh
 378
 379  Title   : newFh
 380  Usage   : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
 381  Function: does a new() followed by an fh()
 382  Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
 383            $sequence = <$fh>;   # read a sequence object
 384            print $fh $sequence; # write a sequence object
 385  Returns : filehandle tied to the Bio::SeqIO::Fh class
 386  Args    :
 387
 388 See L<Bio::SeqIO::Fh>
 389
 390 =cut
 391
 392 sub newFh {
 393   my $class = shift;
 394   return unless my $self = $class->new(@_);
 395   return $self->fh;
 396 }
 397
 398 =head2 fh
 399
 400  Title   : fh
 401  Usage   : $obj->fh
 402  Function:
 403  Example : $fh = $obj->fh;      # make a tied filehandle
 404            $sequence = <$fh>;   # read a sequence object
 405            print $fh $sequence; # write a sequence object
 406  Returns : filehandle tied to Bio::SeqIO class
 407  Args    : none
 408
 409 =cut
 410
 411
 412 sub fh {
 413   my $self = shift;
 414   my $class = ref($self) || $self;
 415   my $s = Symbol::gensym;
 416   tie $$s,$class,$self;
 417   return $s;
 418 }
 419
 420 # _initialize is chained for all SeqIO classes
 421
 422 sub _initialize {
 423         my($self, @args) = @_;
 424
 425         # flush is initialized by the Root::IO init
 426
 427         my ($seqfact,$locfact,$objbuilder, $alphabet) =
 428           $self->_rearrange([qw(SEQFACTORY
 429                               LOCFACTORY
 430                               OBJBUILDER
 431                   ALPHABET)
 432                                                           ], @args);
 433
 434         $locfact = Bio::Factory::FTLocationFactory->new(-verbose => $self->verbose)
 435           if ! $locfact;
 436         $objbuilder = Bio::Seq::SeqBuilder->new(-verbose => $self->verbose)
 437           unless $objbuilder;
 438         $self->sequence_builder($objbuilder);
 439         $self->location_factory($locfact);
 440
 441         # note that this should come last because it propagates the sequence
 442         # factory to the sequence builder
 443         $seqfact && $self->sequence_factory($seqfact);
 444
 445     #bug 2160
 446     $alphabet && $self->alphabet($alphabet);
 447
 448
 449         # initialize the IO part
 450         $self->_initialize_io(@args);
 451 }
 452
 453 =head2 next_seq
 454
 455  Title   : next_seq
 456  Usage   : $seq = stream->next_seq
 457  Function: Reads the next sequence object from the stream and returns it.
 458
 459            Certain driver modules may encounter entries in the stream
 460            that are either misformatted or that use syntax not yet
 461            understood by the driver. If such an incident is
 462            recoverable, e.g., by dismissing a feature of a feature
 463            table or some other non-mandatory part of an entry, the
 464            driver will issue a warning. In the case of a
 465            non-recoverable situation an exception will be thrown.  Do
 466            not assume that you can resume parsing the same stream
 467            after catching the exception. Note that you can always turn
 468            recoverable errors into exceptions by calling
 469            $stream->verbose(2).
 470
 471  Returns : a Bio::Seq sequence object
 472  Args    : none
 473
 474 See L<Bio::Root::RootI>, L<Bio::Factory::SeqStreamI>, L<Bio::Seq>
 475
 476 =cut
 477
 478 sub next_seq {
 479    my ($self, $seq) = @_;
 480    $self->throw("Sorry, you cannot read from a generic Bio::SeqIO object.");
 481 }
 482
 483 =head2 write_seq
 484
 485  Title   : write_seq
 486  Usage   : $stream->write_seq($seq)
 487  Function: writes the $seq object into the stream
 488  Returns : 1 for success and 0 for error
 489  Args    : Bio::Seq object
 490
 491 =cut
 492
 493 sub write_seq {
 494     my ($self, $seq) = @_;
 495     $self->throw("Sorry, you cannot write to a generic Bio::SeqIO object.");
 496 }
 497
 498
 499 =head2 alphabet
 500
 501  Title   : alphabet
 502  Usage   : $self->alphabet($newval)
 503  Function: Set/get the molecule type for the Seq objects to be created.
 504  Example : $seqio->alphabet('protein')
 505  Returns : value of alphabet: 'dna', 'rna', or 'protein'
 506  Args    : newvalue (optional)
 507  Throws  : Exception if the argument is not one of 'dna', 'rna', or 'protein'
 508
 509 =cut
 510
 511 sub alphabet {
 512    my ($self, $value) = @_;
 513
 514    if ( defined $value) {
 515                 $value = lc $value;
 516                 unless ($valid_alphabet_cache{$value}) {
 517                         # instead of hard-coding the allowed values once more, we check by
 518                         # creating a dummy sequence object
 519                         eval {
 520                                 require Bio::PrimarySeq;
 521                                 my $seq = Bio::PrimarySeq->new('-verbose' => $self->verbose,
 522                                                                                                                  '-alphabet' => $value);
 523                         };
 524                         if ($@) {
 525                                 $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values.");
 526                         }
 527                         $valid_alphabet_cache{$value} = 1;
 528                 }
 529                 $self->{'alphabet'} = $value;
 530    }
 531    return $self->{'alphabet'};
 532 }
 533
 534 =head2 _load_format_module
 535
 536  Title   : _load_format_module
 537  Usage   : *INTERNAL SeqIO stuff*
 538  Function: Loads up (like use) a module at run time on demand
 539  Example :
 540  Returns :
 541  Args    :
 542
 543 =cut
 544
 545 sub _load_format_module {
 546         my ($self, $format) = @_;
 547         my $module = "Bio::SeqIO::" . $format;
 548         my $ok;
 549
 550         eval {
 551                 $ok = $self->_load_module($module);
 552         };
 553         if ( $@ ) {
 554                 print STDERR <<END;
 555 $self: $format cannot be found
 556 Exception $@
 557 For more information about the SeqIO system please see the SeqIO docs.
 558 This includes ways of checking for formats at compile time, not run time
 559 END
 560                 ;
 561         }
 562         return $ok;
 563 }
 564
 565 =head2 _concatenate_lines
 566
 567  Title   : _concatenate_lines
 568  Usage   : $s = _concatenate_lines($line, $continuation_line)
 569  Function: Private. Concatenates two strings assuming that the second stems
 570            from a continuation line of the first. Adds a space between both
 571            unless the first ends with a dash.
 572
 573            Takes care of either arg being empty.
 574  Example :
 575  Returns : A string.
 576  Args    :
 577
 578 =cut
 579
 580 sub _concatenate_lines {
 581         my ($self, $s1, $s2) = @_;
 582
 583         $s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2);
 584         return ($s1 ? $s1 : "") . ($s2 ? $s2 : "");
 585 }
 586
 587 =head2 _filehandle
 588
 589  Title   : _filehandle
 590  Usage   : $obj->_filehandle($newval)
 591  Function: This method is deprecated. Call _fh() instead.
 592  Example :
 593  Returns : value of _filehandle
 594  Args    : newvalue (optional)
 595
 596 =cut
 597
 598 sub _filehandle {
 599     my ($self,@args) = @_;
 600     return $self->_fh(@args);
 601 }
 602
 603 =head2 _guess_format
 604
 605  Title   : _guess_format
 606  Usage   : $obj->_guess_format($filename)
 607  Function: guess format based on file suffix
 608  Example :
 609  Returns : guessed format of filename (lower case)
 610  Args    :
 611  Notes   : formats that _filehandle() will guess include fasta,
 612            genbank, scf, pir, embl, raw, gcg, ace, bsml, swissprot,
 613            fastq and phd/phred
 614
 615 =cut
 616
 617 sub _guess_format {
 618    my $class = shift;
 619    return unless $_ = shift;
 620    return 'abi'     if /\.ab[i1]$/i;
 621    return 'ace'     if /\.ace$/i;
 622    return 'alf'     if /\.alf$/i;
 623    return 'bsml'    if /\.(bsm|bsml)$/i;
 624    return 'ctf'     if /\.ctf$/i;
 625    return 'embl'    if /\.(embl|ebl|emb|dat)$/i;
 626         return 'entrezgene' if /\.asn$/i;
 627    return 'exp'     if /\.exp$/i;
 628    return 'fasta'   if /\.(fasta|fast|fas|seq|fa|fsa|nt|aa|fna|faa)$/i;
 629    return 'fastq'   if /\.fastq$/i;
 630    return 'gcg'     if /\.gcg$/i;
 631    return 'genbank' if /\.(gb|gbank|genbank|gbk|gbs)$/i;
 632    return 'phd'     if /\.(phd|phred)$/i;
 633    return 'pir'     if /\.pir$/i;
 634    return 'pln'     if /\.pln$/i;
 635    return 'raw'     if /\.(txt)$/i;
 636    return 'scf'     if /\.scf$/i;
 637    return 'swiss'   if /\.(swiss|sp)$/i;
 638
 639    # from Strider 1.4 Release Notes: The file name extensions used by
 640    # Strider 1.4 are ".xdna", ".xdgn", ".xrna" and ".xprt" for DNA,
 641    # DNA Degenerate, RNA and Protein Sequence Files, respectively
 642    return 'strider' if /\.(xdna|xdgn|xrna|xprt)$/i;
 643
 644    return 'ztr'     if /\.ztr$/i;
 645 }
 646
 647 sub DESTROY {
 648         my $self = shift;
 649         $self->close();
 650 }
 651
 652 sub TIEHANDLE {
 653         my ($class,$val) = @_;
 654         return bless {'seqio' => $val}, $class;
 655 }
 656
 657 sub READLINE {
 658         my $self = shift;
 659         return $self->{'seqio'}->next_seq() unless wantarray;
 660         my (@list, $obj);
 661         push @list, $obj while $obj = $self->{'seqio'}->next_seq();
 662         return @list;
 663 }
 664
 665 sub PRINT {
 666         my $self = shift;
 667         $self->{'seqio'}->write_seq(@_);
 668 }
 669
 670 =head2 sequence_factory
 671
 672  Title   : sequence_factory
 673  Usage   : $seqio->sequence_factory($seqfactory)
 674  Function: Get/Set the Bio::Factory::SequenceFactoryI
 675  Returns : Bio::Factory::SequenceFactoryI
 676  Args    : [optional] Bio::Factory::SequenceFactoryI
 677
 678 =cut
 679
 680 sub sequence_factory{
 681    my ($self,$obj) = @_;
 682    if( defined $obj ) {
 683                 if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) {
 684                         $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)."::sequence_factory()");
 685                 }
 686                 $self->{'_seqio_seqfactory'} = $obj;
 687                 my $builder = $self->sequence_builder();
 688                 if($builder && $builder->can('sequence_factory') &&
 689                         (! $builder->sequence_factory())) {
 690                         $builder->sequence_factory($obj);
 691                 }
 692    }
 693    $self->{'_seqio_seqfactory'};
 694 }
 695
 696 =head2 object_factory
 697
 698  Title   : object_factory
 699  Usage   : $obj->object_factory($newval)
 700  Function: This is an alias to sequence_factory with a more generic name.
 701  Example :
 702  Returns : value of object_factory (a scalar)
 703  Args    : on set, new value (a scalar or undef, optional)
 704
 705 =cut
 706
 707 sub object_factory{
 708         return shift->sequence_factory(@_);
 709 }
 710
 711 =head2 sequence_builder
 712
 713  Title   : sequence_builder
 714  Usage   : $seqio->sequence_builder($seqfactory)
 715  Function: Get/Set the Bio::Factory::ObjectBuilderI used to build sequence
 716            objects.
 717
 718            If you do not set the sequence object builder yourself, it
 719            will in fact be an instance of L<Bio::Seq::SeqBuilder>, and
 720            you may use all methods documented there to configure it.
 721
 722  Returns : a Bio::Factory::ObjectBuilderI compliant object
 723  Args    : [optional] a Bio::Factory::ObjectBuilderI compliant object
 724
 725 =cut
 726
 727 sub sequence_builder{
 728         my ($self,$obj) = @_;
 729         if( defined $obj ) {
 730                 if( ! ref($obj) || ! $obj->isa('Bio::Factory::ObjectBuilderI') ) {
 731                         $self->throw("Must provide a valid Bio::Factory::ObjectBuilderI object to ".ref($self)."::sequence_builder()");
 732                 }
 733                 $self->{'_object_builder'} = $obj;
 734         }
 735         $self->{'_object_builder'};
 736 }
 737
 738 =head2 location_factory
 739
 740  Title   : location_factory
 741  Usage   : $seqio->location_factory($locfactory)
 742  Function: Get/Set the Bio::Factory::LocationFactoryI object to be used for
 743            location string parsing
 744  Returns : a Bio::Factory::LocationFactoryI implementing object
 745  Args    : [optional] on set, a Bio::Factory::LocationFactoryI implementing
 746            object.
 747
 748 =cut
 749
 750 sub location_factory{
 751         my ($self,$obj) = @_;
 752         if( defined $obj ) {
 753                 if( ! ref($obj) || ! $obj->isa('Bio::Factory::LocationFactoryI') ) {
 754                         $self->throw("Must provide a valid Bio::Factory::LocationFactoryI" .
 755                                                          " object to ".ref($self)."->location_factory()");
 756                 }
 757                 $self->{'_seqio_locfactory'} = $obj;
 758         }
 759         $self->{'_seqio_locfactory'};
 760 }
 761
 762 1;
 763