[Biojava-l] Multiple questions
Richard HOLLAND
hollandr at gis.a-star.edu.sg
Wed Nov 30 00:48:50 EST 2005
Hi there,
Seeing as people think it'd be quite useful, I've added some format-guessing functionality to BioJavaX (although I haven't touched the old one).
Here's how you would use it:
// Load the classes that represent the selection of formats your program expects to receive
Class.forName("org.biojavax.bio.seq.io.EMBLFormat");
Class.forName("org.biojavax.bio.seq.io.GenbankFormat");
Class.forName("org.biojavax.bio.seq.io.FastaFormat");
// Obtain the default BioJavaX namespace.
Namespace ns = RichObjectFactory.getDefaultNamespace();
// Find the file
File file = new File("myfile.seq");
// Read the file (indicating that you want to load sequences into the default namespace).
// BioJavaX will guess the format based only on the selection of format classes that have
// previously been loaded either using Class.forName above or by instantiating them elsewhere.
RichSequenceIterator seqs = RichSequence.IOTools.readFile(file,ns);
// NB. If you do know the format in advance, you don't need to load the class first, and instead
// you should just use one of the predefined methods in RichSequence.IOTools, eg.:
// BufferedReader br = new BufferedReader(new FileReader(file))
// RichSequenceIterator seqs = RichSequence.IOTools.readFastaDNA(br, ns);
// Iterate over the sequences
while (seqs.hasNext()) {
RichSequence rs = seqs.nextRichSequence();
// ... Do something with it here ...
}
cheers,
Richard
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of Ola Spjuth
> Sent: Tuesday, November 29, 2005 9:55 PM
> To: Kalle Näslund
> Cc: biojava-l at biojava.org
> Subject: Re: [Biojava-l] Multiple questions
>
>
> Thanks for all the comments, it should get me started.
> I do not intend to write a file-format guesser (out of my scope) but I
> would like to make an RFE for it here and now. I think many
> people would
> benefit from it.
>
> Cheers,
>
> .../Ola
>
>
> On Tue, 2005-11-29 at 14:34, Kalle Näslund wrote:
> > Ola Spjuth wrote:
> >
> > >Hi,
> > >
> > >I am investigating the usefulness of BioJava as a backend
> for sequence
> > >management in Bioclipse (www.bioclipse.net). As a total newbie to
> > >Biojava, I have read the tutorial, BIA examples, glanced
> at the API,
> > >read my first FASTA-sequence and have come up with a few questions:
> > >
> > >1) Is it possible to search the Biojava-l archives without
> having to
> > >manually browse by month?
> > >
> > >2) Is there a wrapper for SequenceIO.fileToBiojava(..) that
> > >automatically detects file formats or is it necessary to
> distinguish
> > >sequence formats externally, i.e. with different
> file-extensions? If so,
> > >does anyone know of a complete list of file-extensions
> that could be
> > >mapped to a format?
> > >
> > >
> > There is a deprecated piece of code available, that quite
> many people
> > actualy use
> > in their code still. Even though it might not be the
> greatest thing to
> > try to auto
> > guess file format, its the desireable thing to do in many cases.
> > If i just look at people in my lab, they want to open the
> file, they
> > dont want to keep
> > track of what file format that particular sequence was in,
> and so on.
> >
> > So, even if file format guessing is bad, people are going
> to write it,
> > and imho its
> > better to have one centralised good, known to work file
> guesser, then
> > several
> > different implementations that differ in each persons own
> application.
> >
> > So, my suggestion is to start with using the deprecated
> version thats in
> > biojava, if
> > it gets removed you can easily just copy that small part of
> the code
> > into your own
> > application, or as an external little jarfile.
> >
> > >3) How robust are the I/O-classes for different formats? The
> > >test-library provided is rather short in my opinion and my
> first test
> > >broke since there was a space in the wrong position...
> > >
> > >4) What are the capabilities for multiple sequence
> alignment in Biojava?
> > >Is it limited to parse results into Biojava objects (as in
> BIA) or does
> > >it contain any stable MSA-implementations? Due to BioJavas
> size it is
> > >not easy to get an overview of the current capabilities
> and the standard
> > >of different parts.
> > >
> > >
> >
> > There is some support for multiple alignments in biojava.
> The Alignment
> > interface
> > and implementations happily handle multiple alignments. And you can
> > choose how
> > to interpret it, either as SymbolList over a crossproduct
> alphabet, or
> > as individual
> > sequences accessable by some label.
> >
> > There is a basic framework for handling multiple alignment
> formats in
> > the biojava
> > org.biojava.bio.seq.io package. It currently only implements two
> > formats, FASTA
> > and MSF. Most programs seem to be able to generate multiple
> alignment
> > output
> > into either FASTA or MSF format so you should be able to
> get the results
> > into
> > biojava.
> >
> > >5) As a novice, has anyone implemented BLAST or CLUSTALW
> in Java? Any
> > >public web-services running for this?
> > >
> > >
> > >
> > I have been told by greater deities that implementing BLAST
> in java is
> > hard, because
> > the blast algorithm makes heavy use of low level data structures,
> > pointers ? and similar
> > things that are very hard to implement and controll in java. So the
> > resulting implementation
> > would most likely run pretty darn slow, and not do what you want.
> >
> > Depending on what you want to do with BLAST, the biojava SSAHA
> > implementation
> > might be something you can use instead ( it works pretty ok
> on quite
> > conserved sequences,
> > but its not realy suited for more divergent sequences )
> >
> > When it comes to webservices i just know of a few things, i
> have not
> > used any of these
> > to an large extent, so i cant comment on how well they work
> for large
> > sequences, big
> > jobs and so on.
> >
> > http://www.ebi.ac.uk/Tools/webservices/services.html
> > http://xml.ddbj.nig.ac.jp/wsdl/index.jsp
> >
> > Sadly they all use their own data encoding and service
> invocation setup,
> > so its pretty darn
> > annoying to use.
> >
> >
> > >6) Is there some example-code on how to use DAS (as a client)?
> > >
> > >7) How can I submit an RFE?
> > >
> > >Sorry for so many questions in one post; I have a lot of
> catching up to
> > >do and was hoping for some guidance. Some answers have
> probably already
> > >been answered in earlier posts but I have not been able to
> search the
> > >archives.
> > >
> > >Cheers,
> > >
> > > .../Ola
> > >
> > >
> > >
> > >
> > >_______________________________________________
> > >Biojava-l mailing list - Biojava-l at biojava.org
> > >http://biojava.org/mailman/listinfo/biojava-l
> > >
> > >
> --
> Ola Spjuth <ola.spjuth at farmbio.uu.se>
>
>
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