Bio::SeqIO::bsml - BSML sequence input/output stream 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); In addition to parts of the Bio:: hierarchy, this module uses: XML::DOM 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...

Mailing Lists
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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". 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.

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. 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 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 (??)