by Cambridge Antibody Technology

This section of the BioJava tutorial covers making use of the output from software used for sequence similarity/homology based searches of biological databases. The material is presented in a Cook Book fashion giving practical examples that should be enough to get you going. If you want to make use of the output from the following programs by using BioJava, this is a useful tutorial to work through:

• NCBI Blast (blastn, blastx, blastp, tblastn, tblastx)
• WU-Blast (blastn, blastx, blastp, tblastn, tblastx)
• or HMMER

NB Please check the JavaDocs of BlastLikeSAXParser to see the extent of support for output from the various applications.

The section of BioJava you will be making use of in the tutorial is the SAX2-compliant event-based parsing framework. After following this tutorial, you will you be able to not only to deal with output from the above pieces for bioinformatics software, but also get started with working with other types of data, such as three-dimensional macromolecular structures which are also supported by the framework.

What you need to know about the parsing framework

The framework has been designed in such a way that you don’t need to understand the details of how it works in order to use it. This is achieved by providing facade classes that are simple to use. For parsing Blast-like output, the facade class you need to use is org.biojava.bio.program.sax.BlastLikeSAXParser. You pass streams of data to this class, and the framework will do the rest. As the name suggests, this class is actually a SAX parser, and implements the org.xml.sax.XMLReader interface. You are thus able to treat the output data as thought it is in an XML format.

The framework performs the magic of emitting SAX2 events from non-XML format data. Thus you don’t have to do any parsing yourself. Rather you will simply be writing XML Content Handlers. The recipes for XML Content Handlers presented here will point you in the direction of populating your own (or BioJava) objects with bioinformatics data.

It is also worth noting, that the SAX events that the framework emits are consistent with a scenario where all the pieces of bioinformatics software above, actually produced identically formatted data.

Benefits of using the framework

• Allows you to focus on the objects you want to create, and forget about writing complex parsing code
• Allows you to make use of the output from more pieces of software. Because of the “concept-based” approach to the representation of data, many of the Content Handler classes you write can be re-used with the output of several different programs.

Recipes

The recipes are simple examples designed to get you up and running populating objects in the way you want. For each example recipe, two classes are provided:

• An XML Content Handler (this is the class that does the work of populating objects with data)
• A sample application class that takes blast-like program output and and sets up for parsing using the Content Handler class.

NB You will find the complete source code for all the classes described here the demos section of biojava, in the eventbasedparsing package.

After Example 1, the only classes that are described are the XML Content Hander classes, because the application classes are essentially identical for all examples.

To help you get going, in addition to the source code for the examples, there are also several example examples of raw ouput from NCBI-blast, WU-blast, and HMMER the “files” directory of the demos section of biojava.

Example 1

For all the hits from a search as detailed in the summary section of the output, prepare a list of Hit Ids. This is an example of a re-useable Content Handler. The same piece of code works equally well with the output from multiple flavours of NCBI Blast, WU-Blast, and HMMER.

Step A - Create an application that sets up the parser and does the parsing

The full source is in eventbasedparsing.TutorialEx1. Because there is no difference between what you do here, and what you would do to parse XML files there isn’t much to do. First create a SAX Parser that deals with Blast-like output.

XMLReader oParser = (XMLReader) new BlastLikeSAXParser(); 

Next choose the Content Handler. In this case, we will be using the class TutorialEx1Handler, which takes a reference to an ArrayList in the constructor. When the SAX Parser parses the file, the Content Handler will populate the ArrayList with Hit Ids from the summary section of the output.

ContentHandler oHandler =
   (ContentHandler) new TutorialEx1Handler(oDatabaseIdList);  

The final step in the set-up is to connect the Content Handler to the SAX Parser.

oParser.setContentHandler(oHandler); 

For the purposes of the tutorial applications, we will simply be reading output from files on disk. Create a FileInputStream, and parse it by calling the parse method on the SAX Parser.

oInputFileStream = new FileInputStream(oInput);
oParser.parse(new InputSource(oInputFileStream));

Finally, having populated the ArrayList with HitIds, we simply print them out.

System.out.println("Results of parsing");
System.out.println("==================");
for (int i = 0; i < oDatabaseIdList.size();i++) {
      System.out.println(oDatabaseIdList.get(i));
}

Step B - Create the logic for parsing

This is simply of matter of writing an XML Content Handler. The full source is in eventbasedparsing.TutorialEx1Handler. The logic here is trivial, we simply wish to identify Hit Ids that are contained within in the Summary sections of the output data, and add each Hit Id to the ArrayList.

if ( (oNameStack.peek().toString().equals("HitId")) &&
     (this.findInStack("Summary") != -1) ) {
   oDatabaseIdList.add(poAtts.getValue("id"));
}

Running the application

After compiling, if you run the application from the demos directory by typing the following:

java eventbasedparsing/TutorialEx1 files/ncbiblast/shortBlastn.out

You should see the following output:

Results of parsing
==================
U51677
L38477
X80457