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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