[Biojava-dev] Biojava.util package?

[David Felty]

Hey Andreas,

It it wouldn't be too difficult to make a method that can infer the
file type using the file extension. In fact, it looks like BioPerl's
SeqIO does something like this. On the other hand, BioPython's SeqIO
takes the route of "explicit is better than implicit," and requires
that you explicitly give the format. Perhaps BioJava could take both
routes, and have an overloaded parse method that infers the file type,
along with the regular explicit method.

As for non-fasta files, I implemented a couple of fasq parsers here:
http://pastebin.com/KLcpq8Qb
This would work similarly:

InputStream is = ...
ProteinSequence seq = SeqIO.parse(is, SeqIO.FASTQ_SANGER, SeqIO.PROTEIN);


It looks like the other sequence readers aren't as clear-cut, so they
may need a bit more wrapping before they can be adapted to this
method. A common problem is that sequence readers don't return a
specific type of sequence, like with
org.biojava3.core.sequence.loader.UniprotProxySequenceReader, which
just contains the sequence data in itself. We might want to create
methods that convert the UniprotProxySequenceReader into sequences
that make more sense, like DNASequence and ProteinSequence.

I'll look into this more later, I have to go to class.

Regards,
David

On Thu, Mar 29, 2012 at 10:39 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> Hi David,
>
> so far it still feels like a wrapper for what is already there. Try to
> take it to the next level. Why does the user still need to provide the
> type of file, can't this be auto-detected? What is the behaviour for
> non-fasta files, what can be supported and where are the limits, etc.
>
> Andreas
>
> On Thu, Mar 29, 2012 at 6:55 AM, David Felty <davfelty at gmail.com> wrote:
> > I've actually been working on something like this for my GSoC proposal,
> > here's what I came up with:
> >
> > public class SeqIO {
> >    public static final int FASTA = 0;
> >    public static final int FASTQ = 1;
> >    public static final Class<DNASequence> DNA = DNASequence.class;
> >    public static final Class<ProteinSequence> PROTEIN =
> > ProteinSequence.class;
> >
> >    public static <S extends Sequence> Iterable<S> parse(InputStream is,
> > int fileFormat, Class<S> seqType) throws Exception {
> >        switch (fileFormat) {
> >            case FASTA:
> >                if (seqType == DNA) {
> >                    return (Iterable<S>)
> > FastaReaderHelper.readFastaDNASequence(is);
> >                } else if (seqType == PROTEIN) {
> >                    // etc...
> >                }
> > break;
> >            case FASTQ:
> >                // etc...
> >        }
> >    }
> > }
> >
> > It would be used like so:
> >
> > InputStream is = ...
> > Iterable<DNASequence> seqs = SeqIO.parse(is, SeqIO.FASTA, SeqIO.DNA);
> > for (DNASequence s : seqs) {
> >   // do something
> > }
> >
> > Obviously it's not the prettiest and a lot could be changed, but that's my
> > initial design. I tried to base it off BioPython's SeqIO, but static typing
> > and the variety of Sequence types forced me to put in some nasty generics.
> > Any tips would be appreciated!
> >
> > David
> >
> > On Thu, Mar 29, 2012 at 4:27 AM, Hannes Brandstätter-Müller <
> > biojava at hannes.oib.com> wrote:
> >
> >> Yes, something like a simplifying and unifying wrapper would be what I
> >> am thinking of.
> >>
> >> Hannes
> >>
> >> On Thu, Mar 29, 2012 at 05:55, Andreas Prlic <andreas at sdsc.edu> wrote:
> >> > Hi Hannes,
> >> >
> >> > I guess this is pretty similar to:
> >> >
> >> > http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite
> >> >
> >> > we have also been using "proxy" objects to fetch sequence data on the fly
> >> >
> >> > http://biojava.org/wiki/BioJava:CookBook:Core:Sequences
> >> >
> >> > As such I think we should discuss this a bit more. If we can find a
> >> > common api that is simple and works with both local files as well as
> >> > remote proxy objects, that would be nice. There should be no need to
> >> > change much of the existing code, but perhaps there could be a
> >> > simplified wrapper for what is already there.
> >> >
> >> >  Andreas
> >> >
> >> > On Wed, Mar 28, 2012 at 12:04 PM, Hannes Brandstätter-Müller
> >> > <biojava at hannes.oib.com> wrote:
> >> >> Hi,
> >> >>
> >> >> I browsed around in the sister projects Biopython and Bioperl a bit,
> >> >> and noticed that many of the user interaction with the code goes
> >> >> through classes like SeqIO, SearchIO, AlignIO...
> >> >>
> >> >> So that got me thinking: how about we create similar "Interface"
> >> >> classes in Biojava?
> >> >>
> >> >> PROS:
> >> >>
> >> >>  - easy change for programmers who switch languages
> >> >>  - easy base interface that can be used in cookbook examples
> >> >>  - makes code more readable if designed properly
> >> >>  - easy access to features that are spread over the whole codebase but
> >> >> are connected anyway, like all file parsers
> >> >>
> >> >> CONS:
> >> >>
> >> >>  - another thing to maintain
> >> >>  - creates possible cross-dependencies (but if you don't want that,
> >> >> just use the existing classes directly)
> >> >>
> >> >>
> >> >> What are your thoughts?
> >> >>
> >> >> python from http://biopython.org/wiki/SeqIO:
> >> >>
> >> >> from Bio import SeqIO
> >> >> handle = open("example.fasta", "rU")
> >> >> for record in SeqIO.parse(handle, "fasta") :
> >> >>    print record.id
> >> >> handle.close()
> >> >>
> >> >> possible equivalent in biojava (support for streaming API, Iterators,
> >> etc?):
> >> >>
> >> >> import org.biojava3.util.SeqIO;
> >> >>
> >> >> File file = new File("example.fasta");
> >> >> SeqIO seqIO = new SeqIO(file, SeqIO.FASTA);
> >> >> while (seqIO.hasNext()) {
> >> >>    System.out.println(seqIO.next());
> >> >> }
> >> >> file.close();
> >> >>
> >> >> Hannes
> >> >> _______________________________________________
> >> >> biojava-dev mailing list
> >> >> biojava-dev at lists.open-bio.org
> >> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >> >
> >> >
> >> >
> >> > --
> >> > -----------------------------------------------------------------------
> >> > Dr. Andreas Prlic
> >> > Senior Scientist, RCSB PDB Protein Data Bank
> >> > University of California, San Diego
> >> > (+1) 858.246.0526
> >> > -----------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >>
> >
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