[Biojava-l] RichSequence annotations...

[Jolyon Holdstock]

Hi,

 

I use the following code to extract all the genes from a sequence file; 

I load the sequence then filter out only CDS features; iterating through
these lets me get the gene annotation for the feature

 

//======================================================================
=========

Sequence seq;

String fileName = new
File("C:/Scripts/Java/BioJava/BioJavaX/biojava-live/demos/seq/AL121903.e
mbl");

try {

  seq = SeqIOTools.readEmbl(new BufferedReader(new
FileReader(fileName))).nextSequence();

}

catch (IOException IOE) {

  System.out.println("IOException " + IOE);

}

catch (BioException BIOE) {

  System.out.println("BioException " + BIOE);

}

    

//Create a feature filter for CDS features only

FeatureFilter ff = new FeatureFilter.ByType("CDS");

 

//Get the filtered Features

FeatureHolder fh = seq.filter(ff);

 

//Iterate over the Features in fh

for (Iterator i = fh.features(); i.hasNext(); ) {

  Feature f = (Feature)i.next();

  Annotation annotation = f.getAnnotation();

  Object key = "gene";

  hash.put(annotation.getProperty(key), f);

}

//======================================================================
=========

 

I am now using the new BioJavaX classes which I cannot get to work. Does
anyone has any pointers for this?

I use the sequence data so have to use a RichSequence rather than a
BioEntry

 

//======================================================================
=========

RichSequence richSeq;

String fileName =
"C:/Scripts/Java/BioJava/BioJavaX/biojava-live/demos/seq/AL121903.embl";

  try {

    richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new
FileReader(fileName)), null).nextRichSequence();

  }

  catch (IOException IOE) {

    System.out.println("IOException " + IOE);

  }

  catch (BioException BIOE) {

    System.out.println("BioException " + BIOE);

}

 

//Create a feature filter for CDS features only

FeatureFilter ff = new FeatureFilter.ByType("CDS");

 

//Get the filtered Features

FeatureHolder fh = richSeq.filter(ff);

 

//Iterate through the features

for (Iterator i = fh.features(); i.hasNext(); ) {

  RichFeature rf = (RichFeature) i.next();

  System.out.println("RichFeature: " + rf.toString());

  RichAnnotation ra = (RichAnnotation) rf.getAnnotation();

  System.out.println("RichAnnotation: " + ra.toString());

}

//======================================================================
=========

 

The output  shows that CDS features have been filtered successfully and
that the gene name is in the annotation

 

RichFeature: (#1)
lcl:HSDJ155G6/AL121903.13:CDS,EMBL(biojavax:join:[<5642..5793,10804..109
76,12496..12656,14136..14266])

RichAnnotation: [(#2) biojavax:clone_lib: RPCI-1"

14403..14532,16852..16987,17821..17959,18068..18122,

19456..19570,23623..23753,25885..26053,29102..29240,

32621..32738,33595..33771],[(#3) biojavax:codon_start: 1],[(#4)
biojavax:evidence: NOT_EXPERIMENTAL],[(#5) biojavax:note: match:
proteins: Tr:Q9Y6D5 Tr:O46382 Tr:Q9Y6D6],[(#6) biojavax:gene:
dJ155G6.1],[(#7) biojavax:product: dJ155G6.1 (brefeldin A-inhibited
guanine

nucleotide-exchange protein 2)],[(#8) biojavax:protein_id: CAB86643.1]

 

 

If I add the following then I can see what keys are in the annotation

//======================================================================
=========

Set keySet = ra.keys();

for (Iterator it = keySet.iterator(); it.hasNext(); ) {

  String key = it.next().toString();

  System.out.println("Key: " + key);

}

//======================================================================
=========

 

The output shows that there is a gene

 

Key: biojavax:clone_lib

Key: biojavax:codon_start

Key: biojavax:evidence

Key: biojavax:gene

Key: biojavax:note

Key: biojavax:product

Key: biojavax:protein_id

 

My understanding is that I need to use a ComparableTerm to access the
value but when I create it I get a NoSuchElementException error

 

ComparableTerm gene =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

System.out.println("Gene: " + ra.getProperty(gene));

 

java.util.NoSuchElementException: No such property: biojavax:gene, rank
0

 

cheers,

 

Jolyon

 

 

 

 

Jolyon Holdstock Ph.D.

Senior Computational Biologist,

Oxford Gene Technology (Ops) Ltd.

Begbroke Business and Science Park

Sandy Lane, Yarnton

Oxford, OX5 1PF

 

Tel: 01865 309699

Fax: 01865 842116

 

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