Question: Extracting Genbank Features With Biojava3 Or Java Library
2
gravatar for Raygozak
4.3 years ago by
Raygozak1.1k
State College, PA, Penn State
Raygozak1.1k wrote:

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

biojava feature genbank • 2.2k views
ADD COMMENTlink modified 4.3 years ago by Pavel Senin1.8k • written 4.3 years ago by Raygozak1.1k

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.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Pablacious610
0
gravatar for Pavel Senin
4.3 years ago by
Pavel Senin1.8k
Los Alamos, NM
Pavel Senin1.8k wrote:

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());
 }
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Pavel Senin1.8k
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