Bio/SearchIO.pm

   1 #
   2 # BioPerl module for Bio::SearchIO
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason-at-bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SearchIO - Driver for parsing Sequence Database Searches
  17 (BLAST, FASTA, ...)
  18
  19 =head1 SYNOPSIS
  20
  21    use Bio::SearchIO;
  22    # format can be 'fasta', 'blast', 'exonerate', ...
  23    my $searchio = Bio::SearchIO->new( -format => 'blastxml',
  24                                      -file   => 'blastout.xml' );
  25    while ( my $result = $searchio->next_result() ) {
  26        while( my $hit = $result->next_hit ) {
  27         # process the Bio::Search::Hit::HitI object
  28            while( my $hsp = $hit->next_hsp ) {
  29             # process the Bio::Search::HSP::HSPI object
  30            }
  31        }
  32    }
  33
  34
  35 =head1 DESCRIPTION
  36
  37 This is a driver for instantiating a parser for report files from
  38 sequence database searches. This object serves as a wrapper for the
  39 format parsers in Bio::SearchIO::* - you should not need to ever
  40 use those format parsers directly. (For people used to the SeqIO
  41 system it, we are deliberately using the same pattern).
  42
  43 Once you get a SearchIO object, calling next_result() gives you back
  44 a L<Bio::Search::Result::ResultI> compliant object, which is an object that
  45 represents one Blast/Fasta/HMMER whatever report.
  46
  47 A list of module names and formats is below:
  48
  49   blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)
  50   fasta      FASTA -m9 and -m0
  51   blasttable BLAST -m9 or -m8 output (both NCBI and WUBLAST tabular)
  52   megablast  MEGABLAST
  53   psl        UCSC PSL format
  54   waba       WABA output
  55   axt        AXT format
  56   sim4       Sim4
  57   hmmer      HMMER2 hmmpfam and hmmsearch or HMMER3 hmmscan and hmmsearch
  58   exonerate  Exonerate CIGAR and VULGAR format
  59   blastxml   NCBI BLAST XML
  60   wise       Genewise -genesf format
  61
  62 Also see the SearchIO HOWTO:
  63 http://bioperl.open-bio.org/wiki/HOWTO:SearchIO
  64
  65 =head1 FEEDBACK
  66
  67 =head2 Mailing Lists
  68
  69 User feedback is an integral part of the evolution of this and other
  70 Bioperl modules. Send your comments and suggestions preferably to
  71 the Bioperl mailing list.  Your participation is much appreciated.
  72
  73   bioperl-l@bioperl.org                  - General discussion
  74   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  75
  76 =head2 Support
  77
  78 Please direct usage questions or support issues to the mailing list:
  79
  80 I<bioperl-l@bioperl.org>
  81
  82 rather than to the module maintainer directly. Many experienced and
  83 reponsive experts will be able look at the problem and quickly
  84 address it. Please include a thorough description of the problem
  85 with code and data examples if at all possible.
  86
  87 =head2 Reporting Bugs
  88
  89 Report bugs to the Bioperl bug tracking system to help us keep track
  90 of the bugs and their resolution. Bug reports can be submitted via the
  91 web:
  92
  93   https://github.com/bioperl/bioperl-live/issues
  94
  95 =head1 AUTHOR - Jason Stajich & Steve Chervitz
  96
  97 Email jason-at-bioperl.org
  98 Email sac-at-bioperl.org
  99
 100 =head1 APPENDIX
 101
 102 The rest of the documentation details each of the object methods.
 103 Internal methods are usually preceded with a _
 104
 105 =cut
 106
 107
 108 # Let the code begin...
 109
 110
 111 package Bio::SearchIO;
 112 use strict;
 113 use warnings;
 114
 115 # Object preamble - inherits from Bio::Root::IO
 116
 117 use Bio::SearchIO::SearchResultEventBuilder;
 118
 119 # Special exception class for exceptions during parsing.
 120 # End users should not ever see these.
 121 # For an example of usage, see blast.pm.
 122 @Bio::SearchIO::InternalParserError::ISA = qw(Bio::Root::Exception);
 123
 124 use Symbol;
 125
 126 use base qw(Bio::Root::IO Bio::Event::EventGeneratorI Bio::AnalysisParserI);
 127
 128 =head2 new
 129
 130  Title   : new
 131  Usage   : my $obj = Bio::SearchIO->new();
 132  Function: Builds a new Bio::SearchIO object
 133  Returns : Bio::SearchIO initialized with the correct format
 134  Args    : -file           => $filename
 135            -format         => format
 136            -fh             => filehandle to attach to
 137            -result_factory => object implementing Bio::Factory::ObjectFactoryI
 138            -hit_factory    => object implementing Bio::Factory::ObjectFactoryI
 139            -hsp_factory    => object implementing Bio::Factory::ObjectFactoryI
 140            -writer         => object implementing Bio::SearchIO::SearchWriterI
 141            -output_format  => output format, which will dynamically load writer
 142            -inclusion_threshold => e-value threshold for inclusion in the
 143                                    PSI-BLAST score matrix model
 144            -signif         => float or scientific notation number to be used
 145                               as a P- or Expect value cutoff
 146            -check_all_hits => boolean. Check all hits for significance against
 147                               significance criteria.  Default = false.
 148                               If false, stops processing hits after the first
 149                               non-significant hit or the first hit that fails
 150                               the hit_filter call. This speeds parsing,
 151                               taking advantage of the fact that the hits are
 152                               processed in the order they appear in the report.
 153            -min_query_len  => integer to be used as a minimum for query sequence
 154                               length. Reports with query sequences below this
 155                               length will not be processed.
 156                               default = no minimum length.
 157            -best           => boolean. Only process the best hit of each report;
 158                               default = false.
 159
 160 See L<Bio::Factory::ObjectFactoryI>, L<Bio::SearchIO::SearchWriterI>
 161
 162 Any factory objects in the arguments are passed along to the
 163 SearchResultEventBuilder object which holds these factories and sets
 164 default ones if none are supplied as arguments.
 165
 166 =cut
 167
 168 # TODO: The below don't seem to be implemented (e.g. in Bio::SearchIO::blast)
 169 #
 170 # -score          => integer or scientific notation number to be used
 171 #                    as a blast score value cutoff
 172 # -bits           => integer or scientific notation number to be used
 173 #                    as a bit score value cutoff
 174 # -overlap        => integer. The amount of overlap to permit between
 175 #                    adjacent HSPs when tiling HSPs. A reasonable value is 2.
 176 #                    default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP.
 177
 178 sub new {
 179   my($caller,@args) = @_;
 180   my $class = ref($caller) || $caller;
 181
 182   # or do we want to call SUPER on an object if $caller is an
 183   # object?
 184   if( $class =~ /Bio::SearchIO::(\S+)/ ) {
 185     my ($self) = $class->SUPER::new(@args);
 186     $self->_initialize(@args);
 187     return $self;
 188   } else {
 189     my %param = @args;
 190     @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 191     my $format = $param{'-format'} ||
 192       $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'blast';
 193
 194     my $output_format = $param{'-output_format'};
 195     my $writer = undef;
 196
 197     if( defined $output_format ) {
 198         if( defined $param{'-writer'} ) {
 199             my $dummy = Bio::Root::Root->new();
 200             $dummy->throw("Both writer and output format specified - not good");
 201         }
 202
 203         if( $output_format =~ /^blast$/i ) {
 204             $output_format = 'TextResultWriter';
 205         }
 206         my $output_module = "Bio::SearchIO::Writer::".$output_format;
 207         $class->_load_module($output_module);
 208         $writer = $output_module->new(@args);
 209         push(@args,"-writer",$writer);
 210     }
 211
 212
 213     # normalize capitalization to lower case
 214     $format = "\L$format";
 215
 216     return unless( $class->_load_format_module($format) );
 217     return "Bio::SearchIO::${format}"->new(@args);
 218   }
 219 }
 220
 221 sub _initialize {
 222     my($self, @args) = @_;
 223     $self->{'_handler'} = undef;
 224     # not really necessary unless we put more in RootI
 225     #$self->SUPER::_initialize(@args);
 226
 227     # initialize the IO part
 228     $self->_initialize_io(@args);
 229     $self->attach_EventHandler(Bio::SearchIO::SearchResultEventBuilder->new(@args));
 230     $self->{'_reporttype'} = '';
 231     $self->{_notfirsttime} = 0;
 232     my ($min_qlen, $check_all, $overlap, $best, $it, $writer ) =
 233         $self->_rearrange([qw(
 234               MIN_LENGTH
 235               CHECK_ALL_HITS
 236               OVERLAP
 237               BEST
 238               INCLUSION_THRESHOLD
 239               WRITER)], @args);    # note: $overlap isn't used for some reason
 240
 241     $writer            && $self->writer( $writer );
 242     defined $it        && $self->inclusion_threshold($it);
 243     defined $min_qlen  && $self->min_query_length($min_qlen);
 244     defined $best      && $self->best_hit_only($best);
 245     defined $check_all && $self->check_all_hits($check_all);
 246 }
 247
 248 =head2 newFh
 249
 250  Title   : newFh
 251  Usage   : $fh = Bio::SearchIO->newFh(-file=>$filename,
 252                                       -format=>'Format')
 253  Function: does a new() followed by an fh()
 254  Example : $fh = Bio::SearchIO->newFh(-file=>$filename,
 255                                       -format=>'Format')
 256            $result = <$fh>;   # read a ResultI object
 257            print $fh $result; # write a ResultI object
 258  Returns : filehandle tied to the Bio::SearchIO::Fh class
 259  Args    :
 260
 261 =cut
 262
 263 sub newFh {
 264   my $class = shift;
 265   return unless my $self = $class->new(@_);
 266   return $self->fh;
 267 }
 268
 269 =head2 fh
 270
 271  Title   : fh
 272  Usage   : $obj->fh
 273  Function:
 274  Example : $fh = $obj->fh;      # make a tied filehandle
 275            $result = <$fh>;     # read a ResultI object
 276            print $fh $result;   # write a ResultI object
 277  Returns : filehandle tied to the Bio::SearchIO::Fh class
 278  Args    :
 279
 280 =cut
 281
 282
 283 sub fh {
 284   my $self = shift;
 285   my $class = ref($self) || $self;
 286   my $s = Symbol::gensym;
 287   tie $$s,$class,$self;
 288   return $s;
 289 }
 290
 291
 292 =head2 format
 293
 294  Title   : format
 295  Usage   : $format = $obj->format()
 296  Function: Get the search format
 297  Returns : search format
 298  Args    : none
 299
 300 =cut
 301
 302 # format() method inherited from Bio::Root::IO
 303
 304
 305 =head2 attach_EventHandler
 306
 307  Title   : attach_EventHandler
 308  Usage   : $parser->attatch_EventHandler($handler)
 309  Function: Adds an event handler to listen for events
 310  Returns : none
 311  Args    : Bio::SearchIO::EventHandlerI
 312
 313 See L<Bio::SearchIO::EventHandlerI>
 314
 315 =cut
 316
 317 sub attach_EventHandler{
 318     my ($self,$handler) = @_;
 319     return if( ! $handler );
 320     if( ! $handler->isa('Bio::SearchIO::EventHandlerI') ) {
 321         $self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::SearchIO::EventHandlerI');
 322     }
 323     $self->{'_handler'} = $handler;
 324     return;
 325 }
 326
 327 =head2 _eventHandler
 328
 329  Title   : _eventHandler
 330  Usage   : private
 331  Function: Get the EventHandler
 332  Returns : Bio::SearchIO::EventHandlerI
 333  Args    : none
 334
 335 See L<Bio::SearchIO::EventHandlerI>
 336
 337 =cut
 338
 339 sub _eventHandler{
 340    my ($self) = @_;
 341    return $self->{'_handler'};
 342 }
 343
 344 =head2 next_result
 345
 346  Title   : next_result
 347  Usage   : $result = stream->next_result
 348  Function: Reads the next ResultI object from the stream and returns it.
 349
 350            Certain driver modules may encounter entries in the stream that
 351            are either misformatted or that use syntax not yet understood
 352            by the driver. If such an incident is recoverable, e.g., by
 353            dismissing a feature of a feature table or some other non-mandatory
 354            part of an entry, the driver will issue a warning. In the case
 355            of a non-recoverable situation an exception will be thrown.
 356            Do not assume that you can resume parsing the same stream after
 357            catching the exception. Note that you can always turn recoverable
 358            errors into exceptions by calling $stream->verbose(2) (see
 359            Bio::Root::RootI POD page).
 360  Returns : A Bio::Search::Result::ResultI object
 361  Args    : n/a
 362
 363 See L<Bio::Root::RootI>
 364
 365 =cut
 366
 367 sub next_result {
 368    my ($self) = @_;
 369    $self->throw_not_implemented;
 370 }
 371
 372 =head2 write_result
 373
 374  Title   : write_result
 375  Usage   : $stream->write_result($result_result, @other_args)
 376  Function: Writes data from the $result_result object into the stream.
 377          : Delegates to the to_string() method of the associated
 378          : WriterI object.
 379  Returns : 1 for success and 0 for error
 380  Args    : Bio::Search:Result::ResultI object,
 381          : plus any other arguments for the Writer
 382  Throws  : Bio::Root::Exception if a Writer has not been set.
 383
 384 See L<Bio::Root::Exception>
 385
 386 =cut
 387
 388 sub write_result {
 389    my ($self, $result, @args) = @_;
 390
 391    if( not ref($self->{'_result_writer'}) ) {
 392        $self->throw("ResultWriter not defined.");
 393    }
 394    @args = $self->{'_notfirsttime'} unless( @args );
 395
 396    my $str = $self->writer->to_string( $result, @args);
 397    $self->{'_notfirsttime'} = 1;
 398    $self->_print( "$str" ) if defined $str;
 399
 400    $self->flush if $self->_flush_on_write && defined $self->_fh;
 401    return 1;
 402 }
 403
 404 =head2 write_report
 405
 406  Title   : write_report
 407  Usage   : $stream->write_report(SearchIO stream, @other_args)
 408  Function: Writes data directly from the SearchIO stream object into the
 409          : writer.  This is mainly useful if one has multiple ResultI objects
 410          : in a SearchIO stream and you don't want to reiterate header/footer
 411          : between each call.
 412  Returns : 1 for success and 0 for error
 413  Args    : Bio::SearchIO stream object,
 414          : plus any other arguments for the Writer
 415  Throws  : Bio::Root::Exception if a Writer has not been set.
 416
 417 See L<Bio::Root::Exception>
 418
 419 =cut
 420
 421 sub write_report {
 422    my ($self, $result, @args) = @_;
 423
 424    if( not ref($self->{'_result_writer'}) ) {
 425        $self->throw("ResultWriter not defined.");
 426    }
 427    @args = $self->{'_notfirsttime'} unless( @args );
 428
 429    my $str = $self->writer->to_string( $result, @args);
 430    $self->{'_notfirsttime'} = 1;
 431    $self->_print( "$str" ) if defined $str;
 432
 433    $self->flush if $self->_flush_on_write && defined $self->_fh;
 434    return 1;
 435 }
 436
 437 =head2 writer
 438
 439  Title   : writer
 440  Usage   : $writer = $stream->writer;
 441  Function: Sets/Gets a SearchWriterI object to be used for this searchIO.
 442  Returns : 1 for success and 0 for error
 443  Args    : Bio::SearchIO::SearchWriterI object (when setting)
 444  Throws  : Bio::Root::Exception if a non-Bio::SearchIO::SearchWriterI object
 445            is passed in.
 446
 447 =cut
 448
 449 sub writer {
 450     my ($self, $writer) = @_;
 451     if( ref($writer) and $writer->isa( 'Bio::SearchIO::SearchWriterI' )) {
 452         $self->{'_result_writer'} = $writer;
 453     }
 454     elsif( defined $writer ) {
 455         $self->throw("Can't set ResultWriter. Not a Bio::SearchIO::SearchWriterI: $writer");
 456     }
 457     return $self->{'_result_writer'};
 458 }
 459
 460 =head2 result_count
 461
 462  Title   : result_count
 463  Usage   : $num = $stream->result_count;
 464  Function: Gets the number of Blast results that have been successfully parsed
 465            at the point of the method call.  This is not the total # of results
 466            in the file.
 467  Returns : integer
 468  Args    : none
 469  Throws  : none
 470
 471 =cut
 472
 473 sub result_count {
 474     my $self = shift;
 475     $self->throw_not_implemented;
 476 }
 477
 478 =head2 inclusion_threshold
 479
 480  Title   : inclusion_threshold
 481  Usage   : my $incl_thresh = $isreb->inclusion_threshold;
 482          : $isreb->inclusion_threshold(1e-5);
 483  Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
 484            score matrix model (blastpgp) that was used for generating the reports
 485            being parsed.
 486  Returns : number (real)
 487            Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
 488  Args    : number (real)  (e.g., 0.0001 or 1e-4 )
 489
 490 =cut
 491
 492 # Delegates to the event handler.
 493 sub inclusion_threshold {
 494     shift->_eventHandler->inclusion_threshold(@_);
 495 }
 496
 497 =head2 max_significance
 498
 499  Usage     : $obj->max_significance();
 500  Purpose   : Set/Get the P or Expect value used as significance screening cutoff.
 501              This is the value of the -signif parameter supplied to new().
 502              Hits with P or E-value above this are skipped.
 503  Returns   : Scientific notation number with this format: 1.0e-05.
 504  Argument  : Scientific notation number or float (when setting)
 505  Comments  : Screening of significant hits uses the data provided on the
 506            : description line. For NCBI BLAST1 and WU-BLAST, this data
 507            : is P-value. for NCBI BLAST2 it is an Expect value.
 508
 509 =cut
 510
 511 sub max_significance { shift->{'_handler_cache'}->max_significance(@_) }
 512
 513 =head2 signif
 514
 515 Synonym for L<max_significance()|max_significance>
 516
 517 =cut
 518
 519 sub signif { shift->max_significance(@_) }
 520
 521 =head2 min_score
 522
 523  Usage     : $obj->min_score();
 524  Purpose   : Set/Get the Blast score used as screening cutoff.
 525              This is the value of the -score parameter supplied to new().
 526              Hits with scores below this are skipped.
 527  Returns   : Integer or scientific notation number.
 528  Argument  : Integer or scientific notation number (when setting)
 529  Comments  : Screening of significant hits uses the data provided on the
 530            : description line.
 531
 532 =cut
 533
 534 sub min_score { shift->{'_handler_cache'}->min_score(@_) }
 535
 536 =head2 min_query_length
 537
 538  Usage     : $obj->min_query_length();
 539  Purpose   : Gets the query sequence length used as screening criteria.
 540              This is the value of the -min_query_len parameter supplied to new().
 541              Hits with sequence length below this are skipped.
 542  Returns   : Integer
 543  Argument  : n/a
 544
 545 =cut
 546
 547 sub min_query_length {
 548     my $self = shift;
 549     if (@_) {
 550         my $min_qlen = shift;
 551         if ( $min_qlen =~ /\D/ or $min_qlen <= 0 ) {
 552             $self->throw(
 553                 -class => 'Bio::Root::BadParameter',
 554                 -text  => "Invalid minimum query length value: $min_qlen\n"
 555                   . "Value must be an integer > 0. Value not set.",
 556                 -value => $min_qlen
 557             );
 558         }
 559         $self->{'_confirm_qlength'}  = 1;
 560         $self->{'_min_query_length'} = $min_qlen;
 561     }
 562
 563     return $self->{'_min_query_length'};
 564 }
 565
 566 =head2 best_hit_only
 567
 568  Title     : best_hit_only
 569  Usage     : print "only getting best hit.\n" if $obj->best_hit_only;
 570  Purpose   : Set/Get the indicator for whether or not to process only
 571            : the best BlastHit.
 572  Returns   : Boolean (1 | 0)
 573  Argument  : Boolean (1 | 0) (when setting)
 574
 575 =cut
 576
 577 sub best_hit_only {
 578     my $self = shift;
 579     if (@_) { $self->{'_best'} = shift; }
 580     $self->{'_best'};
 581 }
 582
 583 =head2 check_all_hits
 584
 585  Title     : check_all_hits
 586  Usage     : print "checking all hits.\n" if $obj->check_all_hits;
 587  Purpose   : Set/Get the indicator for whether or not to process all hits.
 588            : If false, the parser will stop processing hits after the
 589            : the first non-significance hit or the first hit that fails
 590            : any hit filter.
 591  Returns   : Boolean (1 | 0)
 592  Argument  : Boolean (1 | 0) (when setting)
 593
 594 =cut
 595
 596 sub check_all_hits {
 597     my $self = shift;
 598     if (@_) { $self->{'_check_all'} = shift; }
 599     $self->{'_check_all'};
 600 }
 601
 602 =head2 _load_format_module
 603
 604  Title   : _load_format_module
 605  Usage   : *INTERNAL SearchIO stuff*
 606  Function: Loads up (like use) a module at run time on demand
 607  Example :
 608  Returns :
 609  Args    :
 610
 611 =cut
 612
 613 sub _load_format_module {
 614   my ($self,$format) = @_;
 615   my $module = "Bio::SearchIO::" . $format;
 616   my $ok;
 617
 618   eval {
 619       $ok = $self->_load_module($module);
 620   };
 621   if ( $@ ) {
 622       print STDERR <<END;
 623 $self: $format cannot be found
 624 Exception $@
 625 For more information about the SearchIO system please see the SearchIO docs.
 626 This includes ways of checking for formats at compile time, not run time
 627 END
 628   ;
 629   }
 630   return $ok;
 631 }
 632
 633 =head2 _get_seq_identifiers
 634
 635  Title   : _get_seq_identifiers
 636  Usage   : my ($gi, $acc,$ver) = &_get_seq_identifiers($id)
 637  Function: Private function to get the gi, accession, version data
 638            for an ID (if it is in NCBI format)
 639  Returns : 3-pule of gi, accession, version
 640  Args    : ID string to process (NCBI format)
 641
 642
 643 =cut
 644
 645 sub _get_seq_identifiers {
 646     my ($self, $id) = @_;
 647
 648     return unless defined $id;
 649     my ($gi, $acc, $version );
 650     if ( $id =~ /^gi\|(\d+)\|/ ) {
 651         $gi = $1;
 652     }
 653     if ( $id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|(.*)/ ) {
 654         ( $acc, $version ) = split /\./, $2;
 655     }
 656     elsif ( $id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/ ) {
 657         ( $acc, $version ) = split /\./, $3;
 658     }
 659     else {
 660
 661         #punt, not matching the db's at ftp://ftp.ncbi.nih.gov/blast/db/README
 662         #Database Name                     Identifier Syntax
 663         #============================      ========================
 664         #GenBank                           gb|accession|locus
 665         #EMBL Data Library                 emb|accession|locus
 666         #DDBJ, DNA Database of Japan       dbj|accession|locus
 667         #NBRF PIR                          pir||entry
 668         #Protein Research Foundation       prf||name
 669         #SWISS-PROT                        sp|accession|entry name
 670         #Brookhaven Protein Data Bank      pdb|entry|chain
 671         #Patents                           pat|country|number
 672         #GenInfo Backbone Id               bbs|number
 673         #General database identifier           gnl|database|identifier
 674         #NCBI Reference Sequence           ref|accession|locus
 675         #Local Sequence identifier         lcl|identifier
 676         $acc = $id;
 677     }
 678     return ($gi, $acc, $version );
 679 }
 680
 681 =head2 _guess_format
 682
 683  Title   : _guess_format
 684  Usage   : $obj->_guess_format($filename)
 685  Function:
 686  Example :
 687  Returns : guessed format of filename (lower case)
 688  Args    :
 689
 690 =cut
 691
 692 sub _guess_format {
 693    my $class = shift;
 694    return unless $_ = shift;
 695    return 'blast'   if (/\.(blast|t?bl\w)$/i );
 696    return 'fasta' if (/\.
 697                       (?: t? fas (?:ta)? |
 698                        m\d+ |
 699                        (?: t? (?: fa |  fx |  fy |  ff |  fs ) ) |
 700                        (?: (?:ss | os | ps) (?:earch)? ))
 701                       $/ix );
 702    return 'blastxml' if ( /\.(blast)?xml$/i);
 703    return 'exonerate' if ( /\.exon(erate)?/i );
 704 }
 705
 706 sub close {
 707     my $self = shift;
 708
 709     if( $self->writer ) {
 710         $self->_print($self->writer->end_report());
 711         $self->{'_result_writer'}= undef;
 712     }
 713     $self->SUPER::close(@_);
 714 }
 715
 716 sub DESTROY {
 717     my $self = shift;
 718     $self->close() if defined $self->_fh;
 719     $self->SUPER::DESTROY;
 720 }
 721
 722 sub TIEHANDLE {
 723   my $class = shift;
 724   return bless {processor => shift}, $class;
 725 }
 726
 727 sub READLINE {
 728   my $self = shift;
 729   return $self->{'processor'}->next_result() || undef unless wantarray;
 730   my (@list, $obj);
 731   push @list, $obj while $obj = $self->{'processor'}->next_result();
 732   return @list;
 733 }
 734
 735 sub PRINT {
 736   my $self = shift;
 737   $self->{'processor'}->write_result(@_);
 738 }
 739
 740
 741 1;
 742
 743 __END__