Hi Dinesh,
That's an easy one to answer, although it's not the answer you probably
want. Unfortunately, the framework doesn't currently support PSIBlast
output.
Sorry,
Simon
--
Dr Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics
Cambridge Antibody Technology
Milstein Building
G
Olivier JEFFROY wrote:
Hello,
I have exactly the same problem using this method. Has anyone answered
you?
I can compile the code but when I ty to run it, I get this message:
org.xml.sax.SAXException: Could not recognise the format of this file as
one supported by the framework.
at
org.bi
Re: Parsing massive Blast output
In regard of recent mail to the list (and from up to a couple of years ago)
Up 'til now, when attempting to parse *very* large blast outputs
consisting of many (thousands of) separete reports concatenated
together, the Java Virtual Machine could sometimes run ou
Ewan Birney wrote:
On Mon, 10 Feb 2003, Simon Brocklehurst wrote:
Ewan Birney wrote:
True. Probably more of my reluctance is the relearning curve. But I often
my algorithms try to use all the memory of the machine, and if I start
running some extra overhead I wont be happy...
... but, yes
Ewan Birney wrote:
Ewan,
The issues in that memo are real. Are those *really* the reasons for
your reluctance to move to Java? Are you sure it's not more of a "not
wanting to start all over again" kind of learning issue?
I remember very well when I switched from C to Java in 1997, it was
pr
Alexander Churbanov wrote:
Hello Matthew or Thomas,
I just use SAX BLAST parser to parse a massive of
BLAST output. Unfortunately this package does a really
poor job in a batch mode. It runs out of memory
because of the recursive self-calls which adversely
affects the heap.
I know that
jon portuondo murguiondo wrote:
Hello! I am trying to convert pdb to XML. If you can help me I would be very pleased.
Hi Jon,
If you are still having difficulties, please feel free to e-mail me or
the biojava list with a description of what precisely you are trying to
do. I'll see if we ca
Pham wrote:
>
> Hello,
> I want to get the coordinates of amino acids (or atoms) of a protein in PDB.
> Which package in biojava should I use? Please help me.
You could try:
http://www.biojava.org/docs/api/org/biojava/bio/program/sax/PdbSAXParser.html
Simon
--
Dr Simon M. Brocklehurst, Ph.D.
Doug Rusch wrote:
>
> Actually I have made changes that fix both the no summary and "No hits found"
>>problems though I have not done extensive testing and I do not know if this would
>>work for wu-blast yet. Its more of a hack though than a nice solution. It would be
>>nice to use the regex i
Doug Rusch wrote:
>
> Hi all,
>
> I am relatively new to the biojava community and I had a question about the blast
>parser in biojava. While looking at the code and judging from its behavior, the blast
>parser has no way to deal with empty blast reports (where no hit was found). My
>questi
Ewan Birney wrote:
>
> anyway - build systems which work now is my motto ;)
>
To which I'd add:
o Build systems the work *well*
o Build systems that address an unmet need
o Build systems with low total cost of ownership
o Build systems by using productive development processes
Simon
--
Simon
Ewan Birney wrote:
> I remember all these discussions from those great CORBA days. Boy am I
> staying away from this for the moment... (too scared frankly!)
>
I don't blame ya...
I don't want to be negative (it's not useful), but I suspect not
everyone out there is too experienced at building
Susan Glass wrote:
>
> Hello there,
> Last year I wrote a class that parsed a BLAST search file and returned a List
>of SequenceDBSearchResults, using BlastLikeSAXParser and BlastLikeSearchBuilder. I
>modelled it on demo code that David Waring had written (thanks!). Once the results
>
Russell Smithies wrote:
>
> Has anyone extracted co-ordinates from protein database files and are there
> suitable parsers already in BioJava ?
>
Russell,
There's a parser for Protein Data Bank format files that parses
coordinates - have look at the PdbSAXParser in the
org.biojava.bio.program.
David Waring wrote:
>
> I have found on several occasions that I would like to extend a class, but
> variables and methods are private so it is impossible to make use of these
> in the subclass. Is there a policy about when things should be kept private,
> and when they should be protected? Is it
Patrick McConnell wrote:
>
> We (Duke Bioinformatics Shared Resource) are going to make a concerted
> effort to create a software package that allows the piping of web services.
> We are going to focus on bioinformatics web services, though the project
> should be generally applicable to all we
Vera Fleischer wrote:
> Hi,
>
> I'm interested in using the PdbtoXML converter and I'm wondering what
> the XML structure of the resulting files will look like. The class
> description mentions that the resulting XML "will validate against the
> biojava:MacromolecularStructure DTD." Is there an
Dave Waddell wrote:
Is
there any development being done in this area? Can I help?
Thanks,
Dave.
Exception
in thread "main" org.xml.sax.SAXException: Program ncbi-blastp Version
2.2.2 is not supported by the biojava blast-like parsing framework
Dave,
The code is "sort of" easy to unde
Matthew Pocock wrote:
> If editing is needed, then you realy need to maintain version
> information to allow rollbacks, resolution of clashes between different
> edits, keeping views current and the rest. My first stab would be on the
> unique key for features being an (ID,version) tuple where
Ewan Birney wrote:
> On Wed, 6 Mar 2002, Jason Stajich wrote:
>
> > #!/usr/bin/perl -w
> > use strict;
> >
> > use Bio::SearchIO;
> > use Bio::SearchIO::Writer::HTMLResultWriter;
> >
> > my $in = new Bio::SearchIO(-format => 'blastxml',
> >-file => shift @ARGV);
>
I don't think my last mail was completel clear (i.e. correct!) it needs to be:
file://
followed by the full path to the file i.e. you'll have 3 slashes... e.g.
file:///usr/local/people/matt/stuff/biojava/you/get/the/idea/...
S.
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced
Matthew Pocock wrote:
> Hi.
>
> I've tried to run the PDB parser example, but hit a snag.
>
> C:\stuff\biojava\biojava-live\demos>java eventbasedparsing.Pdb2XML
> files\pdb\hgh_ori.pdb
> WARNING: ignoring attempt to set illegal combination of parser features
>
> no protocol: files\pdb\hgh_ori.
Guoneng Zhong wrote:
> Hi all,
>
> Is there a tutorial on how to handle ClustalW outputs?
> Thanks,
>
Hi
We're definitely light on documentation for this - I will try to do a
tutorial
on this.Here's a little explanation... hope it helps.
o The parser simple deals with the *output* from C
Russell Smithies wrote:
> Has anyone had any luck running Blast locally from Java using Runtime.exec()
> and command array??
Yes ;-) Running native executables via Runtime.exec() works fine for us - but
almost all the Runtime.exec() code we have written is designed to run under
Unix.
Runtime.e
Simon Foote wrote:
> Hi Simon,
>
> I've found a bug in the Blast2HTMLHandler code.
You're right ;-) Serves us right for putting code in at the last minute. Not
quite sure if your fix is right or not, we're checking it out. In any case,
expect this to be fixed ASAP.
Simon
--
Simon M. Brockl
"Emig, Robin" wrote:
> Copyright © 2000,2001 Cambridge Antibody Technology. All Rights Reserved
>
> I noticed that many files contain the above copyright notice.
>
> 1) Does this conflict at all with the files being under lgpl
As others have said, this isn't a problem with LGPL
>
> 2) regard
David Huen wrote:
> The software I am attempting to write is now getting beyond the stage
> where I can conveniently keep all key aspects in (my) memory and I am
> looking for affordable development tools to assist me in doing this.
>
> I've considered using UML but cheap tools capable of the f
Anu Padki wrote:
> Hi Gurus at Biojava,
>
> I am trying to find out which one to go for, BioPerl or BioJava?
>
> Can someone tell me why there was a need for BioJava ?
> How is it better/different from BioPerl?
Hi,
I'm not sure that "which is better/different BioJava and BioPerl" is
necessaril
Roy Park wrote:
> Hi there,
>
> I'm trying to write a small program that reads in only the HIT section of
> BLAST output (i.e. starting with ">"), by instantiating a
> HitSectionSAXParser class, and I noticed that the BlastLikeVersionSupport
> variable oVersion needs to be already populated by
Dear All,
FYI, I've just checked the following classes into the cvs.
In package org.biojava.bio.program.sax:
o An update version of PdbSAXParser.java - more robust parsing of 3-D
molecular structure data
o A new class - NeedleAlignmentSAXParser.java - parsing of multiple
alignments from the pr
Petri Pehkonen wrote:
> Hi,
>
> I'm using Java SDK Standard Edition 1.3.1 under Windows 2000. I tried to
> change the virtual machine to "classic" but it didn't help and I got the
> same error message. I wonder if anyone has made parsing with result files
> as big as ours?
Hi,
I just tried the
Petri Pehkonen wrote:
> Hello,
>
> When parsing Blast-result-raport with BlastLikeSAXParser and using
> TutorialEx1Handler shown in demos in cvs.biojava.org as a contenthandler,
> I get errormessage like this:
> ---
> #
> # An EXCEPTION_STACK_OVERFLOW exception has been de
Just taken a look at JFlex, and noticed it's licensed under GPL. In the
way that you've used it, would this contaiminate biojava (which is licensed
under LGPL)?
S.
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Camb
Robert Hubley wrote:
> I have developed a parsing framework called LSAX that I would
> like to submit to BioJava. It was inspired by the work of Cambridge
> Antibody Technology (Simon Brocklehurst et al.) on the BioJava
> BlastLikeSaxParser. The idea is the same -- create a brid
Thomas Down wrote:
> No, I don't think any of our current SeqIO code will handle
> this format. Certainly, I'm amazed that the EmblLikeFormat
> got as far as it did -- STOCKHOLM format really isn't much
> like EMBL at all (even in the headers, there's the
> extra #= stuff, to be confusing).
>
>
Matthew Muller wrote:
> I am using WU-BLAST version 2.0MP and am had some trouble using
> BlastLikeSaxParser to parse the output. A NoSuchElement exception is
> thrown from WuBlastSummaryLineHelper and I think I've figured out
> why. The exception occurs because the class tries to parse out the
Thomas Down wrote:
> No, there isn't a 3d structure object model in BioJava
> at the moment, although there has been a certain amount
> of interest (we do, for instance, have a parser for PDB
> files, contributed by the developers at Cambridge Antibody
> Technology).
Hi,
As stated in the JavaDo
"Emig, Robin" wrote:
> So what your saying is that if you have the sequence ATGGAC, that
> the first A is position 1 in the sequence/symbol list, but position 0 in the
> frame/phase. I realize that 0,1,2 may be the most common convention, but
> does anyone else see how that can get confus
Dear All,
Apologies, for posting this to the list - this message is intended for
people around Cambridge, UK...
It seems that there are quite a few contributers and users of biojava
around Cambridge, UK. We thought it might be fun to get together every
so often to: discuss Java/Bioinformatics;
Johan Hattne wrote:
> Hi, all.
>
> Has anybody had any luck in parsing output from ClustalW using biojava's
> ClustalWAlignmentSAXParser? I can get it to return the sequences' names,
> but I'm hoping to get at the sequence's symbols. I've looped through the
> attribute lists sent to my handler'
Dear All,
We've finally got around to adding pretty full support for parsing HMMER
output in the BlastLikeSAXParser. Specifically, HmmerSearch and
HmmerPfam. It should just work out of the box - i.e. you throw HMMER
output at the BlastLikeSAXParser, and it should deal with it.
As a consequence
"Wiepert, Mathieu" wrote:
> Simon,
> Awhile ago you had mentioned changing from the DTD to a schema.
> Have you put any work into that? Schema is now a w3C recommendation, so we
> should probably move over to that soon. I did try a simple conversion from
> the DTD to schema with XML S
Keith,
Glad you brought this up - we have recently completed full support for
HMMER, and need to make some minor changes also. We will be putting this
code into the cvs on Friday (tomorrow). Whilst we're doing that, we'll take
a look at the changes you propose (from cursory glance, I think they
Hi,
xling wrote:
> Hi,
>
> I just came back from San Francisco JAVA ONE conference. One of the talk is
> about xml java binding.
>
> Sun has just released the http://java.sun.com/xml/jaxb/index.html which is
> trying to do the xml java binding.
>
> This makes me think of the biojava blast pars
"Wiepert, Mathieu" wrote:
> It would be very easy to do, I haven't done that yet. Which reminds me, I
> have some other code I better put soon. All that needs to be done is to add
> a few if checks to 2 or 3 modules. Then see if it breaks. If it doesn't
> then the format didn't change. Any
"Cox, Greg" wrote:
> The docs for the BlastLikeSAXParser specify that NCBI Blast version 2.0.11
> is the only one that's supported. The current version is 2.1.3; is anyone
> upgrading the parser, or have some feel for how difficult this would be?
Hi,
We are getting ready a bunch of stuff to ch
Arnon Klein wrote:
> Seems to me that most people working on non-unix platforms use IDEs.
> I haven't seen anyone writing java code with notepad (or other text
> editors), and then run javac from the command line... I myself have
> been converted from being an Emacs enthusiast to preaching the g
Keith James wrote:
> Hi all,
>
> I'm keen to set up unit tests for the core classes. A few bugs
> surfaced at the bootcamp which we should have been aware of some time
> ago (and I'm guilty of leaving a bug in the EMBL-like Location parser,
> which I've just fixed).
>
> Some ideas:
>
> * Using
Keith James wrote:
> Inspired by the bootcamp, I've added a SAX2 event emitter for Fasta
> searches. This may be used in the same way as the others. It's backed
> by the same Fasta parser as the
> org.biojava.bio.program.search.FastaSearchBuilder, i.e. uses 'm 10'
> output.
Excellent!
> Thanks
Subba_Raju wrote:
> dear biojava associates,
> iam very new to biojava i need to know is there any class or interface which
> can read content(line by line or charecter by charecter) of flat file/text
> file(blast output) and allow me to manipulate programmatically
> i apologize if it is too much
"Wiepert, Mathieu" wrote:
> I have made some minor changes (I hope) to the sax package. I did this to
> add preliminary support for GCG blastn, and to make the BlastLikeSAXParser
> XSLT processor compliant.
I just wanted to say a public "Thank you" to Mat for adding in this new
functionality.
Matthew Pocock wrote:
> Arnon Klein wrote:
>
> > Hi,
> > Is there existing code that parses/analyzes Pfam libraries?
> >
> > Arnon
> >
> > --
> >
> >
> > ___
> > Biojava-l mailing list - [EMAIL PROTECTED]
> > http://biojava.org/mailman/listinfo/bio
Ramkumar N wrote:
> I apologize for the newbie question upfront.
>
> I tried the tutorial on Blast Parsing found on the web site, using the code
> found in the demos/eventbasedhandling/TutorialEx1.java directory and get the
> following error:
>
> >javac TutorialEx1.java
> Tutori
"Schreiber, Mark" wrote:
> Hi,
>
> How much varience is there between blast versions and how well does the
> SaxLikeBlastParser cope? Is there a way to produce a "standard" blast
> output?
>
Hi,
That's BlastLikeSAXParser ;-) There are significant differences in the output
for blastn, blastp, t
Hi Mark,
"Schreiber, Mark" wrote:
> Hi,
>
> Am I correct in thinking that to parse a blast output all I need to do is
> make a content handler by extending default handler and defining
> characters(), startElement() and endElement?
Absolutely.
> Also can any of the Qnames in BlastSAXParser be
Hi Mathieu,
"Wiepert, Mathieu" wrote:
> I currently have so .csh scripts that fork off as many blasts as there are
> sequences or sequence files in a list.
I don't think you have to do this - you can simply throw all the sequences at
blast in one go i.e. one blast process.
> Anybody doing som
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