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Extracting Genbank Features With Biojava3 Or Java Library

Does anyone have experience extracting feature information from a genbank file in biojava3 or any other java api?

biojava genbank feature
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updated by Pavel Senin Pavel Senin • written by Raygozak Raygozak

Currently there doesn't seem to be a way of parsing genbank files with biojava3. The only mention of genbank in the whole project seems to be in the DataSource class and some tests that use it (looking at the git project). There is nothing that seems related in the API either. There is a thread in one of their mailing lists where until December 2012 it didn't seem to be an implementation available Lets hope this changes.

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written by Pablacious Pablacious

1 answer

I am not sure how it works in BioJava 3.X, but I used to read genbank in with SeqIOTools in 1.8X http://www.biojava.org/docs/api1.8.2/org/biojava/bio/seq/io/SeqIOTools.html

Here are some examples: http://www.biojava.org/docs/api1.8.2/org/biojava/bio/seq/Sequence.html

 System.out.println("Length: " + myGenbank.length());
 System.out.println("Features: " + myGenbank.countFeatures());
 for(Iterator fi = myGenbank.features(); fi.hasNext(); ) {
   Feature f = (Feature) fi.next();
   System.out.println(f.getType() + "\t" + f.getLocation());
 }
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written by Pavel Senin Pavel Senin

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