[Biojava-l] Filtering mRNA from GenBank format files

[Matthew Pocock]

Hi Takeshi,

The genbank (and I presume embl) parser sets a property "TYPE" in the
sequence's annotation. So, doing something like this would work:

(untested code)

public static void main(String[] args)
throws Exception {
  for(int i = 0; i < args.length; i++) {
    SequenceIterator si = SeqIOTools.readGenbank(
      new BufferedReader(
        new FileReader(
          new File(args[i]) )));
    while(si.hasNext()) {
      Sequence seq = si.next();
      Annotation ann = seq.getAnnotation();
      if(ann.hasProperty("TYPE")) {
        Object type = ann.getProperty("TYPE");
        if("DNA".equals(type)) {
          // do something with DNA entries
        } else if("mRNA".equals(type)) {
          // do something with RNA entries
        } ...
      }
  }
}

Takeshi Sasayama wrote:
> Hi,
> 
> I'm a newbee in Biojava and I have a question.
> I would like to make a filter which reads from multiple GenBank format files
> (gbpri1.seq, gbpri2.seq, ..., gbpri24.seq) and writes only entries which
> have molecule type of "mRNA"(I mean molecule type is "DNA", "mRNA" etc.
> which is written just after sequence length in LOCUS line.) to a file.
> 
> Could anyone show me overview of this flow? I saw "Biojava in Anger" web
> page but I don't know how to do that using Biojava.
> Also any suggestions, information are welcome.
> Thanks
> 
> Takeshi Sasayama
> 
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