[Biojava-l] Filtering mRNA from GenBank format files

[Schreiber, Mark]

Hi -

If you want to filter while reading sequence in you could write
something that overides SeqIOFilter and implements ParseErrorSource and
only passes on events from GenBank sequences of interest. This is a bit
more complicated and requires a more detailed understanding of the SeqIO
API but is ultimately more efficient if you are doing this on a large
scale.

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
> Sent: Saturday, 8 March 2003 1:12 a.m.
> To: Takeshi Sasayama
> Cc: biojava-l at biojava.org
> Subject: Re: [Biojava-l] Filtering mRNA from GenBank format files
> 
> 
> 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
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> -- 
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> http://www.biojava.co.uk
> 
> _______________________________________________
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> 
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