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# $Id: swissdriver.pm 15212 2008-12-19 05:47:58Z cjfields $
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# BioPerl module for Bio::SeqIO::swissdriver
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# Cared for by Bioperl project bioperl-l(at)bioperl.org
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# Copyright Chris Fields and contributors see AUTHORS section
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser
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#It is probably best not to use this object directly, but
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#rather go through the SeqIO handler:
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$stream = Bio::SeqIO->new(-file => $filename,
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-format => 'swissdriver');
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while ( my $seq = $stream->next_seq() ) {
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# do something with $seq
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This object can transform Bio::Seq objects to and from UniProt flat file
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databases. The key difference between this parser and the tried-and-true
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Bio::SeqIO::swiss parser is this version separates the parsing and data
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manipulation into a 'driver' method (next_seq) and separate object handlers
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which deal with the data passed to it.
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The main purpose of the driver routine, in this case next_seq(), is to carve out
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the data into meaningful chunks which are passed along to relevant handlers (see
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Each chunk of data in the has a NAME tag attached to it, similar to that for XML
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parsing. This designates the type of data passed (annotation type or seqfeature)
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and the handler to be called for processing the data.
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution. Bug reports can be submitted via the web:
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http://bugzilla.open-bio.org/
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=head1 AUTHOR - Bioperl Project
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bioperl-l at bioperl.org
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The rest of the documentation details each of the object
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methods. Internal methods are usually preceded with a _
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# POD is at the end of the module
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# Let the code begin...
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# Let the code begin...
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package Bio::SeqIO::swissdriver;
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use vars qw(%FTQUAL_NO_QUOTE);
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use Bio::SeqIO::Handler::GenericRichSeqHandler;
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use base qw(Bio::SeqIO);
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# signals to process what's in the hash prior to next round, maps ann => names
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OC => 'CLASSIFICATION',
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OH => 'HOST', # not currently handled, bundled with organism data for now
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AS => 'ASSEMBLYINFO', # Third party annotation
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# add specialized delimiters here for easier postprocessing
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my($self,@args) = @_;
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$self->SUPER::_initialize(@args);
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my $handler = $self->_rearrange([qw(HANDLER)],@args);
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# hash for functions for decoding keys.
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$handler ? $self->seqhandler($handler) :
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$self->seqhandler(Bio::SeqIO::Handler::GenericRichSeqHandler->new(
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-verbose => $self->verbose,
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-builder => $self->sequence_builder
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if( ! defined $self->sequence_factory ) {
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$self->sequence_factory(Bio::Seq::SeqFactory->new
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(-verbose => $self->verbose(),
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-type => 'Bio::Seq::RichSeq'));
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Usage : $seq = $stream->next_seq()
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Function: returns the next sequence in the stream
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Returns : Bio::Seq object
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my $hobj = $self->seqhandler;
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# these contain values that need to carry over each round
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my ($featkey, $qual, $annkey, $seqdata, $location);
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while(defined(my $line = $self->_readline)) {
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my ($ann, $data) = split(m{\s+}, $line, 2);
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if ($data =~ m{^(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)(?:\s+?(\S.*))?}ox) {
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# has location data and desc
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$hobj->data_handler($seqdata);
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($seqdata->{FEATURE_KEY}, my $loc1, my $loc2, $data) = ($1, $2, $3, $4);
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$qual = 'description';
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$seqdata->{$qual} = $data;
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$seqdata->{NAME} = $ann;
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$seqdata->{LOCATION} = "$loc1..$loc2" if defined $loc1;
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} elsif ($data =~ m{^\s+/([^=]+)(?:=(.+))?}ox) {
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($qual, $data) = ($1, $2 || '');
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$ct = ($seqdata->{$qual}) ?
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((ref($seqdata->{$qual})) ? scalar(@{ $seqdata->{$qual} }) : 1)
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$seqdata->{$qual} .= ($seqdata->{$qual}) ?
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if (!ref($seqdata->{$qual})) {
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$seqdata->{$qual} = [$seqdata->{$qual}];
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($seqdata->{$qual}->[$ct]) ?
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($seqdata->{$qual}->[$ct] .= ' '.$data) :
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($seqdata->{$qual}->[$ct] .= $data);
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if ($ann ne $lastann) {
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if (!$SEC{$ann} && $seqdata) {
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$hobj->data_handler($seqdata);
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# can't use undef here; it can lead to subtle mem leaks
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$annkey = (!$SEC{$ann}) ? 'DATA' : # primary data
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$seqdata->{'NAME'} = $ann if !$SEC{$ann};
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last PARSER if $ann eq '//';
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next PARSER if $ann eq 'SQ';
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my $delim = $DELIM{$ann} || ' ';
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$seqdata->{$annkey} .= ($seqdata->{$annkey}) ?
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$delim.$data : $data;
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# this should only be sequence (fingers crossed!)
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while (defined ($line = $self->_readline)) {
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if (index($line, '//') == 0) {
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$data =~ tr{0-9 \n}{}d;
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$seqdata->{DATA} = $data;
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#$self->debug(Dumper($seqdata));
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$hobj->data_handler($seqdata);
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# some files have no // for the last file; this catches the last bit o' data
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$hobj->data_handler($seqdata) if $seqdata;
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return $hobj->build_sequence;
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Usage : $stream->write_seq($seq)
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Function: writes the $seq object (must be seq) to the stream
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Returns : 1 for success and 0 for error
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Args : array of 1 to n Bio::SeqI objects
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shift->throw("Use Bio::SeqIO::swiss write_seq() for output");
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# maybe make a Writer class as well????
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Usage : $stream->seqhandler($handler)
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Function: Get/Set teh Bio::Seq::HandlerBaseI object
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Returns : Bio::Seq::HandlerBaseI
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Args : Bio::Seq::HandlerBaseI
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my ($self, $handler) = @_;
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$self->throw("Not a Bio::HandlerBaseI") unless
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ref($handler) && $handler->isa("Bio::HandlerBaseI");
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$self->{'_seqhandler'} = $handler;
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return $self->{'_seqhandler'};
added
removed
Bio/SeqIO/swissdriver.pm
