Bio::SeqIO::bsml(3)

NAME
Bio::SeqIO::bsml - BSML sequence input/output stream

SYNOPSIS
 It is probably best not to use this object directly, but rather go
 through the SeqIO handler system. To read a BSML file:

    $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml');

    while ( my $bioSeqObj = $stream->next_seq() ) {
        # do something with $bioSeqObj
    }

 To write a Seq object to the current file handle in BSML XML format:

    $stream->write_seq( -seq => $seqObj);

 If instead you would like a XML::DOM object containing the BSML, use:

    my $newXmlObject = $stream->to_bsml( -seq => $seqObj);

DEPENDENCIES
 In addition to parts of the Bio:: hierarchy, this module uses:

 XML::DOM

DESCRIPTION
 This object can transform Bio::Seq objects to and from BSML (XML)
 flatfiles.

  NOTE:
 2/1/02 - I have changed the API to more closely match argument
 passing used by other BioPerl methods ( -tag => value ). Internal
 methods are using the same API, but you should not be calling those
 anyway...

FEEDBACK

  Mailing Lists
 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to one
 of the Bioperl mailing lists.  Your participation is much
 appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://www.bioperl.org/MailList.shtml  - About the mailing lists

  Reporting Bugs
 Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.
 Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

  Things Still to Do
 * The module now uses the new Collection.pm system. However,
   Annotations associated with a Feature object still seem to use the
   old system, so parsing with the old methods are included..

 * Generate Seq objects with no sequence data but an assigned
   length. This appears to be an issue with Bio::Seq. It is possible
   (and reasonable) to make a BSML document with features but no
   sequence data.

 * Support <Seq-data-import>. Do not know how commonly this is used.

 * Some features are awaiting implementation in later versions of
   BSML. These include:

       * Nested feature support

       * Complex feature (ie joins)

       * Unambiguity in strand (ie -1,0,1, not just  'complement' )

       * More friendly dblink structures

 * Location.pm (or RangeI::union?) appears to have a bug when 'expand'
   is used.

 * More intelligent hunting for sequence and feature titles? It is not
   terribly clear where the most appropriate field is located, better
   grepping (eg looking for a reasonable count for spaces and numbers)
   may allow for titles better than "AE008041".

AUTHOR - Charles Tilford
Bristol-Myers Squibb Bioinformatics

Email tilfordc@bms.com

I have developed the BSML specific code for this package, but have used code from other SeqIO packages for much of the nuts-and-bolts. In particular I have used code from the embl.pm module either directly or as a framework for many of the subroutines that are common to SeqIO modules.

METHODS

  next_seq
 Title   : next_seq
 Usage   : my $bioSeqObj = $stream->next_seq
 Function: Retrieves the next sequence from a SeqIO::bsml stream.
 Returns : A reference to a Bio::Seq::RichSeq object
 Args    :

  to_bsml
 Title   : to_bsml
 Usage   : my $domDoc = $obj->to_bsml(@args)
 Function: Generates an XML structure for one or more Bio::Seq objects.
           If $seqref is an array ref, the XML tree generated will include
           all the sequences in the array.
 Returns : A reference to the XML DOM::Document object generated / modified
 Args    : Argument array in form of -key => val. Recognized keys:

      -seq A Bio::Seq reference, or an array reference of many of them

   -xmldoc Specifies an existing XML DOM document to add the sequences
           to. If included, then only data (no page formatting) will
           be added. If not, a new XML::DOM::Document will be made,
           and will be populated with both <Sequence> data, as well as
           <Page> display elements.

   -nodisp Do not generate <Display> elements, or any children
           thereof, even if -xmldoc is not set.

 -skipfeat If set to 'all', all <Feature>s will be skipped.  If it is
           a hash reference, any <Feature> with a class matching a key
           in the hash will be skipped - for example, to skip 'source'
           and 'score' features, use:

               -skipfeat => { source => 'Y', score => 'Y' }

 -skiptags As above: if set to 'all', no tags are included, and if a
           hash reference, those specific tags will be ignored.

           Skipping some or all tags and features can result in
           noticable speed improvements.

   -nodata If true, then <Seq-data> will not be included.  This may be
           useful if you just want annotations and do not care about
           the raw ACTG information.

   -return Default is 'xml', which will return a reference to the BSML
           XML object. If set to 'seq' will return an array ref of the
           <Sequence> objects added (rather than the whole XML object)

    -close Early BSML browsers will crash if an element *could* have
           children but does not, and is closed as an empty element
           e.g. <Styles/>. If -close is true, then such tags are given
           a comment child to explicitly close them e.g.  <Styles><!--
           --></Styles>. This is default true, set to "0" if you do
           not want this behavior.

 Examples : my $domObj = $stream->to_bsml( -seq => \@fourCoolSequenceObjects,
                                           -skipfeat => { source => 1 },
                                           );

            # Or add sequences to an existing BSML document:
            $stream->to_bsml( -seq => \@fourCoolSequenceObjects,
                              -skipfeat => { source => 1 },
                              -xmldoc => $myBsmlDocumentInProgress,  );

  write_seq
 Title   : write_seq
 Usage   : $obj->write_seq(@args)
 Function: Prints out an XML structure for one or more Bio::Seq objects.
           If $seqref is an array ref, the XML tree generated will include
           all the sequences in the array. This method is fairly simple,
           most of the processing is performed within to_bsml.
 Returns : A reference to the XML object generated / modified
 Args    : Argument array. Recognized keys:

      -seq A Bio::Seq reference, or an array reference of many of them

           Alternatively, the method may be called simply as...

           $obj->write_seq( $bioseq )

           ... if only a single argument is passed, it is assumed that
           it is the sequence object (can also be an array ref of
           many Seq objects )

-printmime If true prints "Content-type: $mimetype\n\n" at top of
           document, where $mimetype is the value designated by this
           key. For generic XML use text/xml, for BSML use text/x-bsml

   -return This option will be supressed, since the nature of this
           method is to print out the XML document. If you wish to
           retrieve the <Sequence> objects generated, use the to_bsml
           method directly.

INTERNAL METHODS #-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-
 The following methods are used for internal processing, and should probably
 not be accessed by the user.

  _parse_location
 Title   : _parse_location
 Usage   : $obj->_parse_location($xmlDocument, $parentElem, $SeqFeatureObj)
 Function: Adds <Interval-loc> and <Site-loc> children to <$parentElem> based
           on locations / sublocations found in $SeqFeatureObj. If
           sublocations exist, the original location will be ignored.
 Returns : An array ref containing the elements added to the parent.
           These will have already been added to <$parentElem>
 Args    : 0 The DOM::Document being modified
           1 The DOM::Element parent that you want to add to
           2 Reference to the Bio::SeqFeature being analyzed

  _parse_bsml_feature
 Title   : _parse_bsml_feature
 Usage   : $obj->_parse_bsml_feature($xmlFeature )
 Function: Will examine the <Feature> element provided by $xmlFeature and
           return a generic seq feature.
 Returns : Bio::SeqFeature::Generic
 Args    : 0 XML::DOM::Element <Feature> being analyzed.

  _parse_bsml_location
 Title   : _parse_bsml_location
 Usage   : $obj->_parse_bsml_feature( $intOrSiteLoc, $gsfObject )
 Function: Will examine the <Interval-loc> or <Site-loc> element provided
 Returns : Bio::SeqFeature::Generic
 Args    : 0 XML::DOM::Element <Interval/Site-loc> being analyzed.
           1 Optional SeqFeature::Generic to use

  _parse_reference
 Title   : _parse_reference
 Usage   : $obj->_parse_reference(@args )
 Function: Makes a new <Reference> object from a ::Reference, which is
           then stored in an array provide by -refs. It will be
           appended to the XML tree later.
 Returns :
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

   -refobj The Annotation::Reference Object

     -refs An array reference to hold the new <Reference> DOM object

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any <Reference> refs
           attribute.

  _parse_annotation
 Title   : _parse_annotation
 Usage   : $obj->_parse_annotation(@args )
 Function: Will examine any Annotations found in -obj. Data found in
           ::Comment and ::DBLink structures, as well as Annotation
           description fields are stored in -desc for later
           generation of <Attribute>s. <Reference> objects are generated
           from ::References, and are stored in -refs - these will
           be appended to the XML tree later.
 Returns :
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

      -obj Reference to the Bio object being analyzed

    -descr An array reference for holding description text items

     -refs An array reference to hold <Reference> DOM objects

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any <Reference> refs
           attribute.

  _parse_annotation_old
    Title   : _parse_annotation_old
 Usage   : $obj->_parse_annotation_old(@args)
 Function: As above, but for the old Annotation system.
           Apparently needed because Features are still using the old-style
           annotations?
 Returns :
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

      -obj Reference to the Bio object being analyzed

    -descr An array reference for holding description text items

     -refs An array reference to hold <Reference> DOM objects

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any <Reference> refs
           attribute.

  _add_page
 Title   : _add_page
 Usage   : $obj->_add_page($xmlDocument, $xmlSequenceObject)
 Function: Adds a simple <Page> and <View> structure for a <Sequence>
 Returns : a reference to the newly created <Page>
 Args    : 0 The DOM::Document being modified
           1 Reference to the <Sequence> object

  _addel
 Title   : _addel
 Usage   : $obj->_addel($parentElem, 'ChildName',
                        { anAttr => 'someValue', anotherAttr => 'aValue',})
 Function: Add an element with attribute values to a DOM tree
 Returns : a reference to the newly added element
 Args    : 0 The DOM::Element parent that you want to add to
           1 The name of the new child element
           2 Optional hash reference containing
             attribute name => attribute value assignments

  _show_dna
 Title   : _show_dna
 Usage   : $obj->_show_dna($newval)
 Function: (cut-and-pasted directly from embl.pm)
 Returns : value of _show_dna
 Args    : newvalue (optional)

  _initialize
 Title   : _initialize
 Usage   : $dom = $obj->_initialize(@args)
 Function: Coppied from embl.pm, and augmented with initialization of the
           XML DOM tree
 Returns :
 Args    : -file => the XML file to be parsed

  _parseparams
 Title   : _parseparams
 Usage   : my $paramHash = $obj->_parseparams(@args)
 Function: Borrowed from Bio::Parse.pm, who borrowed it from CGI.pm
           Lincoln Stein -> Richard Resnick -> here
 Returns : A hash reference of the parameter keys (uppercase) pointing to
           their values.
 Args    : An array of key, value pairs. Easiest to pass values as:
           -key1 => value1, -key2 => value2, etc
           Leading "-" are removed.

  _parse_xml
 Title   : _parse_xml
 Usage   : $dom = $obj->_parse_xml($filename)
 Function: uses XML::DOM to construct a DOM tree from the BSML document
 Returns : a reference to the parsed DOM tree
 Args    : 0 Path to the XML file needing to be parsed

TESTING SCRIPT
 The following script may be used to test the conversion process. You
 will need a file of the format you wish to test. The script will
 convert the file to BSML, store it in /tmp/bsmltemp, read that file
 into a new SeqIO stream, and write it back as the original
 format. Comparison of this second file to the original input file
 will allow you to track where data may be lost or corrupted. Note
 that you will need to specify $readfile and $readformat.

 use Bio::SeqIO;
 # Tests preservation of details during round-trip conversion:
 # $readformat -> BSML -> $readformat
 my $tempspot = "/tmp/bsmltemp";  # temp folder to hold generated files
 my $readfile = "rps4y.embl";     # The name of the file you want to test
 my $readformat = "embl";         # The format of the file being tested

 system "mkdir $tempspot" unless (-d $tempspot);
 # Make Seq object from the $readfile
 my $biostream = Bio::SeqIO->new( -file => "$readfile" );
 my $seq = $biostream->next_seq();

 # Write BSML from SeqObject
 my $bsmlout = Bio::SeqIO->new( -format => 'bsml',
                                   -file => ">$tempspot/out.bsml");
 warn "\nBSML written to $tempspot/out.bsml\n";
 $bsmlout->write_seq($seq);
 # Need to kill object for following code to work... Why is this so?
 $bsmlout = "";

 # Make Seq object from BSML
 my $bsmlin = Bio::SeqIO->new( -file => "$tempspot/out.bsml",
                                  -format => 'bsml');
 my $seq2 = $bsmlin->next_seq();

 # Write format back from Seq Object
 my $genout = Bio::SeqIO->new( -format => $readformat,
                                   -file => ">$tempspot/out.$readformat");
 $genout->write_seq($seq2);
 warn "$readformat  written to $tempspot/out.$readformat\n";

 # BEING LOST:
 # Join information (not possible in BSML 2.2)
 # Sequence type (??)