In the last weeks, we had many discussions on BLAST which shows that
BLAST is of much interest. To my knowledge, there is no class in
Biojava for invoking Blast searches yet.
Therefore I would like to discuss the new BLAST API with you.
It is a Java wrapper for local NCBI and
local WU-blast and
If you installed blast locally you would need a cron job updating the
blast database regularly.
Perhaps it is easier to install a proxy server e.g. tiniproxy on the web
server where the applet is stored. The proxy can redirect the blast
request to any cgi server.
___
java-l@biojava.org
> Subject: [Biojava-l] Blast xml parser question -- new to Biojava
>
>
> Hi,
> I am pretty new to Biojava. I am trying to use the
> blast xml parser. (Specifically, I am using
> org.biojava.bio.program.sax.blastxml.BlastParserFacade
> in biojava v1.4 )
&g
Hi,
I am pretty new to Biojava. I am trying to use the
blast xml parser. (Specifically, I am using
org.biojava.bio.program.sax.blastxml.BlastParserFacade
in biojava v1.4 )
Is it possible to get the accession number from blast
output? (equivalent to in results.xml
from blast results)
Is there ano
t;[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
07/07/2005 01:27 AM
Please respond to Felipe Albrecht
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Blast Format Writer
There was some class in biojava that writes info
There was some class in biojava that writes informations in ASN.1 format?
Thanks.
Felipe Albrecht
___
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
There have been a number of requests to the list (and directly to me) for
increased functionality for the BLAST parsers (eg capturing more of the
information in the report). Originally the design was lightweight and
captured what most people wanted but as always there are always people who
thin
D] On Behalf Of Sébastien PETIT
Sent: Wednesday, 29 June 2005 2:50 a.m.
To: biojava-l@biojava.org
Subject: RE: AW: AW: [Biojava-l] BLAST Parser for extracting all BLAST data?
I try the code you sent me. I just change the path of the XML file.
But, in this file, there is this line :
and I have excep
n PETIT [mailto:[EMAIL PROTECTED]
> Gesendet: Dienstag, 28. Juni 2005 15:00
> An: biojava-l@biojava.org
> Betreff: RE: AW: [Biojava-l] BLAST Parser for extracting all BLAST
> data?
>
>
> Thank you for JDOM and the code...
> But, it generates a ton of exceptions and error be
Thank you for JDOM and the code...
But, it generates a ton of exceptions and error because it doesn't find
a DTD file (NCBI_BlastOutput.dtd) that I don't have...
So, I don't know how to do...
Sebastien
--- "BIBIS, Garnier, Christophe" <[EMAIL PROTECTED]> a écrit
:
>
> if you don't find what yo
+
-Ursprüngliche Nachricht-
Von: Sébastien PETIT [mailto:[EMAIL PROTECTED]
Gesendet: Dienstag, 28. Juni 2005 13:34
An: biojava-l@biojava.org
Betreff: RE: [Biojava-l] BLAST Parser for extracting all BLAST data?
ArgghI didn't find wh
mented ; )
>
> - Mark
>
>
>
>
>
> Sébastien PETIT <[EMAIL PROTECTED]>
> Sent by: [EMAIL PROTECTED]
> 06/28/2005 05:11 PM
>
>
> To: biojava-l@biojava.org
> cc: (bcc: Mark Schreiber/GP/Novartis)
> Subject:R
t the Gaps data.
Fortunately, I don't need it at the moment.
Thanks,
George
>-Original Message-
>From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
>Sent: 27 June 2005 03:25
>To: Y D Sun
>Subject: Re: [Biojava-l] BLAST Parser for extracting all BLAST data?
>
>Hello -
>
&
>
> cheers,
> Richard
>
>
> -Original Message-
> From: [EMAIL PROTECTED] on behalf of Y D Sun
> Sent: Sun 6/26/2005 5:42 PM
> To: biojava-l@biojava.org
> Cc:
> Subject: [Biojava-l] BLAST Parser for extracting all BLAST data?
>
> Hi,
dump them all out to see what you
get.
cheers,
Richard
-Original Message-
From: [EMAIL PROTECTED] on behalf of Y D Sun
Sent: Sun 6/26/2005 5:42 PM
To: biojava-l@biojava.org
Cc:
Subject: [Biojava-l] BLAST Parser for extracting all BLAST data?
Hi,
I want to extrac
Hi,
I want to extract all data from BLASTP results. In the following hit,
for example, I need to get the lengths of query and subject proteins,
the identities (including all data 54, 124 and 43%), the positives (all
data 79, 124 and 63%), and the gaps (3, 124 and 2%). Can the
BLASTLikeSAXParser fi
30/2004 11:54 AM
To:
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Blast SAX parser output
Is there any way to stop the blast parser code from outputting progress? I
get lots of the following and its clogging up my unix mailbox as the job
is run th
Is there any way to stop the blast parser code from outputting progress? I get
lots of the following and its clogging up my unix mailbox as the job is run
through cron:
obj=score 317
obj=expectValue 7e-86
obj=numberOfIdentities 158
obj=alignmentSize 1
Is it possible to access the line using the xml
parser?
Nicholas Stiffler
Institute of Molecular Biology
University of Oregon
___
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
Hello!
Is there a way to get the middle line of an alignment that I parse out
of the blast output? In the example below, it would be the "S++VGTR..."
line. In the Alignment of the SeqSimilaritySearchSubHit, I only find a
Sequence entry for Query and Sbjct.
Query: 2 SFEVGTRCWYPHKELGWIGAEVIKNEFN
,
-mat
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Christian
> Gruber
> Sent: Friday, April 02, 2004 7:20 AM
> To: [EMAIL PROTECTED]
> Subject: [Biojava-l] Blast Parser oddity
>
>
> Hi!
>
> I am currently evaluati
Hi!
I am currently evaluating the XML output of NCBI Blast, and the ability
of BioJava to parse this output. For this purpose, I have done twice the
identical blastp and blastn (i.e. the same sequence against the same
database with the same parameters), one time with the standard output,
and o
Hi,
I want to run blastall on several databases, so I run it with -d "dbName1 dbName2"...
This work well if I launch the command line in a terminal, but not if I launch it from my java program...
It seems like the "" are not reconized.
Here is what I've done :
Process blastRun;
String pOpt
Hello,
I'm seeing a difference in the data being output by stand-alone blast and
online blast. The identities value are different between the xml output and
the text output. The other difference I see is in the query and hit
sequences. I've included below the outputs using the same input par
f Y D Sun
Sent: Tuesday, December 23, 2003 9:38 AM
To: [EMAIL PROTECTED]
Subject: [Biojava-l] Blast Version
Hi,
What blast version does BlastLikeSAXParser support? I encounter the
following error when running the sample code of BLAST Result Parser in
Biojava In Anger to parse blast 2.2.5 o
Hi,
What blast version does BlastLikeSAXParser support? I encounter the
following error when running the sample code of BLAST Result Parser in
Biojava In Anger to parse blast 2.2.5 output:
org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.5 is not
supported by the biojava blast-like parsi
Thank you guys!
I now have a great looking solution which is lean and fast.
I am definitely a biojava fan.
Regards,
Frans
___
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Hi,
Thanks for the suggestions. I am quite new in the world of Biojava and
basically what I did was copy the example in Biojava in anger and adapt
it to my needs. It seems I now have to adapt it a little more.
One more question. If the blast output is already in XML, how would you
go about it in
> " " == VERHOEF Frans <[EMAIL PROTECTED]> writes:
> Hi Keith, Thanks for your response. I did paste the method
> that's doing the parsing somewhere below. I also ran just now
> this method trying to parse a blast output file with a size of
> approximately 350mb. The output
iption + "\n");
out.flush();
hitAnno = null;description = null;hit=null;
System.gc();
}
out.close();
hits = null; out=null; outFile=null; bsetting=null; lib=null;
database=null; queryID=null; anno=null; result=null;
System.gc();
out.flush();
hitAnno = null;description = null;hit=null;
System.gc();
}
out.close();
hits = null; out=null; outFile=null; bsetting=null; lib=null;
database=null; queryID=null; anno=null; result=null;
System.gc();
}
file.de
> "FV" == VERHOEF Frans <[EMAIL PROTECTED]> writes:
FV> Hi, I am having a problem parsing huge blast
FV> results. Basically I am parsing the blast results pretty much
FV> the same way as in "Biojava in Anger", with as only difference
FV> that I use the setModeLazy() of the Blas
Hi,
I am having a problem parsing huge blast results. Basically I am parsing
the blast results pretty much the same way as in "Biojava in Anger",
with as only difference that I use the setModeLazy() of the
BlastLikeSAXParser, since I am using NCBI Blast version 2.2.4 and that
version is not rec
Hi,
I was wondering if anyone has implemented a blast interface using servlets,
and maybe applied a stylesheet to the XML output.
If anyone has already done this and can share some source code,that would be
greatly appreciated.
thanks,
Marc Dumontier
Bioinformatics Software Developer
Blueprint I
Once upon a time, Ryan Golhar wrote:
> I'm looking through the documentation for biojava 1.3, and cannot find
> any reference to performing a BLAST search, or performing any type of
> SmithWaterman local alignment. If its there, and I'm just not looking
> in the right place, can someone please dir
I'm looking through the documentation for biojava 1.3, and cannot find
any reference to performing a BLAST search, or performing any type of
SmithWaterman local alignment. If its there, and I'm just not looking
in the right place, can someone please direct me to where I can find
information on thi
On Thu, 26 Jun 2003, Russell Smithies wrote:
I normally use a bash script with sed for this but i think it's still
worth having.
Mind if I stick it into the javadocs somewhere within the blastXML
package?
Regards,
David
> Some people may call this cheating but I wrote a simple utility
> pre-pro
Some people may call this cheating but I wrote a simple utility
pre-processor for blast XML to convert it into something a basic SAX parser
can read :-)
---
import java.io.*;
public class XMLPreProcessor{
/**
* A simple utility method t
Hello all:
Does the bio java handles "no hits" from Blast output? I am trying to
populate the output into a java object "BlastOutput" and trying to display
into a GUI. But I get a null pointer exception when i dont have any hits. I
appreciate if any one provide me with any pointers or code.
Hello,
I'm new in biojava programming.
I'm using biojava 1.3 in order to parse a XML Blast outputwith the Blast parser that I
found in "Biojava in Anger".
Each file I test, I have the same error message:
org.xml.sax.SAXException: Could not recognise the format of this file as one
supported by
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
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.biojava.bio.program.sax.Bl
hi there
I am using HT-blast for SGI IRIX systems. I have been trying to use BLAST2HTML
program of biojava for my output but I think output genrated is not in the
format that BLAST2HTMl program needs. So i tried to used the code given for
blast parsing at "biojava in anger" webiste. I have been
The root cause:
java.lang.NoClassDefFoundError:
org/biojava/bio/program/sax/BlastLikeSAXParser
seems to indicate that the biojava.jar is not available to your webapp.
Make sure its in the WEB-INF/lib directory of your webapp.
Cheers,
Simon
dkabic01 wrote:
hi
I am new to biojava having som
hi
I am new to biojava having some difficulty parsing my output. I am using
HT-BLast which is for SGI computer systems . I am calling HT-BLAST program
from my servlet program and it working fine. Problem arise when i add code for
parsing the output. given below is the code for parsing the outpu
D]]
> Sent: Tuesday, 28 January 2003 11:00 p.m.
> To: Schreiber, Mark
> Cc: staatsb; [EMAIL PROTECTED]; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] BLAST Parser in Anger!
>
>
> Please, let's get it right b4 1.3 goes live - I know we're
> meant to be
> onl
L PROTECTED]
Subject: [Biojava-l] BLAST Parser in Anger!
I was successful in getting the BLAST parser to work outlined by the
"BioJava in Anger" doc by changing the version number too
2.0.11 (thank
you Mark Schreiber X2). However, a few of the APIs dont seem to
function i.e. getSeque
get together over a beer at the hackathon and
nut this one out. It really can't be that hard can it?
Hear endeth the sermon.
- Mark
> -Original Message-
> From: staatsb [mailto:[EMAIL PROTECTED]]
> Sent: Tuesday, 28 January 2003 6:19 a.m.
> To: [EMAIL PROTECTED]
>
I was successful in getting the BLAST parser to work outlined by the
"BioJava in Anger" doc by changing the version number too 2.0.11 (thank
you Mark Schreiber X2). However, a few of the APIs dont seem to
function i.e. getSequenceID() is not recognized, but I dont think
thats due to the versi
Hi all,
Yesterday I used our blast parsing code for the 1st
time. I'm impressed by how painlessly it all works.
Thanks to CAT and KeithJ and everyone else for making
my life easier.
In return, I have tickled it aground the edges. I've
added some convenience search handlers for
implementing filter
: [EMAIL PROTECTED]
Subject:RE: [Biojava-l] blast parsing and empty hits
Hello Doug,
It's probably not best open source etiquette to put down the community
that you're trying to get help from.
Rather, you'd probably get a much warmer reception by providing patches
to t
t; Doug Rusch
> TCAG.org
>
>
> -Original Message-
> From: Wiepert, Mathieu [mailto:[EMAIL PROTECTED]]
> Sent: Thu 10/3/2002 12:34 PM
> To: Doug Rusch; Simon Brocklehurst
> Cc: [EMAIL PROTECTED]
> Subject: RE: [Biojava-l] blast parsing and empty hits
> H
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
PROTECTED]]
Sent: Thu 10/3/2002 12:34 PM
To: Doug Rusch; Simon Brocklehurst
Cc: [EMAIL PROTECTED]
Subject: RE: [Biojava-l] blast parsing and empty hits
Hi,
I might add, that if you are familiar with java, and this is just one use case that
fails, it would probably be easy enough
Doug Rusch
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] blast parsing and empty hits
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
Hi,
I might add, that if you are familiar with java, and this is just one use case that
fails, it would probably be easy enough to enhance the parser? It may not be touched
much because it works as is, sending off SAX events merrily. At least I like to hope
that is the case ;-)
-Mat
___
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
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
questions are : Am I missing something
t; <[EMAIL PROTECTED]>@biojava.org on
08/25/2002 04:57:13 PM
Sent by:[EMAIL PROTECTED]
To:"Brian Gilman" <[EMAIL PROTECTED]>, "Patrick McConnell"
<[EMAIL PROTECTED]>, <[EMAIL PROTECTED]>
cc:
Subject:RE: [Biojava-l] BLAST/Java interfac
Schreiber, Mark wrote:
> I think that a web service of BLAST or a binary installation are
> preferable to submitting BLAST to NCBI for anything over 30 or so
> sequences. You can quite quickly find your domain blocked from NCBI's
> web servers if you send large numbers of messages to NCBI. (Speaki
om: Brian Gilman [mailto:[EMAIL PROTECTED]]
> Sent: Saturday, 24 August 2002 2:02 a.m.
> To: Patrick McConnell; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] BLAST/Java interface
>
>
> On 8/23/02 9:18 AM, "Patrick McConnell" <[EMAIL PROTECTED]> wrote:
>
satyanarayana pasupuleti wrote:
>
> Hello:
>
> I am wondering if there are any examples in the documentation that
> would help me in parsing BLAST output? I appreciate any kind of help
> in this regard.
There is a tutorial about how to parse Blast results with biojava,
http://www.biojava.org/
Hello:
I am wondering if there are any examples in the documentation that would
help me in parsing BLAST output? I appreciate any kind of help in this
regard.
Thanks a lot,
--satya
_
Send and receive Hotmail on your mobile devic
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);
>
On Wed, Mar 06, 2002 at 05:07:17PM +, 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',
> >
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);
>
> my $writer = new Bio::SearchIO::Writ
]
Subject: Re: [Biojava-l] Blast-xml parser
We have a soln for this in bioperl, consider this script in bioperl (using
the live cvs code or 1.0alpha2-rc this weekend)
#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;
my $in = new Bio::SearchIO(-format
t;
> Thanks a lot!
>
> Best wishes
>
> Edda
>
>
>
>
>
> *
> Wiepert, Mathieu [EMAIL PROTECTED]
> Fri, 8 Jun 2001 07:35:26 -0500
>
> Previous message: [Biojava-l] blast xml parser
> Next message
*
Wiepert, Mathieu [EMAIL PROTECTED]
Fri, 8 Jun 2001 07:35:26 -0500
Previous message: [Biojava-l] blast xml parser
Next message: [Biojava-l] LocationTools + Decoratorated Locations = ?
Messages sorted by: [ date ] [ thread
Thomas Down wrote
> I'm not a Windows user. But one thing which occurs to
> me: you're handling the output of the process on the same
> thread as the Process itself. I always use separate threads
> (I don't know if this is the `official' way of doing things,
> but it's a pragmatic approach wh
#x27;s nothing too tricky about running it but being able to use some of
Biojavas other methods on the results might be handy.
Russell
> -Original Message-
> From: Thomas Down [mailto:[EMAIL PROTECTED]]
> Sent: Wednesday, 20 February 2002 9:16 p.m.
> To: Russell Smithies
>
Thomas Down wrote
> I'm not a Windows user. But one thing which occurs to
> me: you're handling the output of the process on the same
> thread as the Process itself. I always use separate threads
> (I don't know if this is the `official' way of doing things,
> but it's a pragmatic approach wh
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
Hmmm, are you saying that the command works okay via
a batch file, but not if you exec it directly? Very strange...
I'm not a Windows user. But one thing which occurs to
me: you're handling the output of the process on the same
thread as the Process itself. I always use separate threads
(I don
Has anyone had any luck running Blast locally from Java using Runtime.exec()
and command array??
I always get an error from Blast and the only reliable way I've found so far
is to write a batch file then delete it as follows:
*
File batFileNa
On Tue, Feb 12, 2002 at 01:44:34PM -0500, Ratiba Terbaoui wrote:
>
> hello,
>
> I'm a new user of Biojava and i want to know if i can run Blast using
> Biojava, which classes i have tu use
Hi...
BioJava includes some a fairly advanced parser for output
from the `blast' family of programs. The
hello,
I'm a new user of Biojava and i want to know if i can run Blast using
Biojava, which classes i have tu use
thanks.
Ratiba.
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Hi,
I have done some
work on the top of current biojava blast parser. The implementation of the
BlastContentHandler class allows to use the eventbased parser in biojava to
instantiate blast/hit/hsp/hspsummary/blastlikealignment objects.
It is a very quick
implem
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
On Thu, 12 Jul 2001, Wiepert, Mathieu wrote:
> So it's the same but with missing sections. Interesting! That should
> easily be accommodated codewise then, is it something that people would use,
> or was this a one-off situation for you?
I would expect to use it extensively for our current pro
Hello, All.
Is there a way to parse the output from bl2seq with biojava? I can't get
the Blast parsers to handle it and I've looked around some, but without
finding anything.
// Rgds; Johan Hattne
___
Johan Hattne * R
:-)
- bruce
-Original Message-
From: Wiepert, Mathieu [mailto:[EMAIL PROTECTED]]
Sent: Monday, June 11, 2001 5:24 AM
To: '[EMAIL PROTECTED]'
Cc: [EMAIL PROTECTED]
Subject: RE: [Biojava-l] blast xml parser
You know, you are more than welcome to add any functionality you d
Thought I'd jump in here as I've found the blast xml parser quite useful
and have created a partial blast object backend to it. It was one of those
quick and dirty implementations as I needed it quickly, so the code isn't
of biojava quality at the moment, but I plan to fix it up once I get more
On Mon, 11 Jun 2001, Ewan Birney wrote:
> On Mon, 11 Jun 2001, Wiepert, Mathieu wrote:
>
> > You know, you are more than welcome to add any functionality you desire.
> > You have made a good point (as supported by Ewan), and besides that, no one
> > is going to stop you from adding functionality
On Mon, 11 Jun 2001, Wiepert, Mathieu wrote:
> You know, you are more than welcome to add any functionality you desire.
> You have made a good point (as supported by Ewan), and besides that, no one
> is going to stop you from adding functionality to the code base. This is
> open source code, so
You know, you are more than welcome to add any functionality you desire.
You have made a good point (as supported by Ewan), and besides that, no one
is going to stop you from adding functionality to the code base. This is
open source code, so be open and code...
-mat
___
f its performance.
Thanks.
Bruce Ling, Ph.D.
Tularik, Inc
http://www.tularik.com
-Original Message-
From: Ewan Birney [mailto:[EMAIL PROTECTED]]
Sent: Saturday, June 09, 2001 2:35 AM
To: xling
Cc: Simon Brocklehurst; '[EMAIL PROTECTED]'
Subject: RE: [Biojava-l] blast xml parser
A view from bioperl:
I would claim that you do need layered levels of abstraction. The event
parsing SAX model is something we are very jealous of in bioperl because
we understand its flexibility and the ease of writing seriously
lean-and-mean parsers by experts.
maintaince of parsers is one
comments see below:
>> Compare to bioperl, the demo code is just a "proof of concept" rather
than
>> the implementation library can be of real use. Correct me if I am wrong.
>You are wrong. The biojava Blast-like parsing package is scalable ways
that
>the bioperl library is not. I think yo
nteer to look into this? :)
-mat
-Original Message-
From: Simon Brocklehurst [mailto:[EMAIL PROTECTED]]
Sent: Friday, June 08, 2001 3:34 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject:Re: [Biojava-l] blast xml parser
Hi,
xling wrote:
> Hi,
>
> I
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
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 parser. I have to admit that there
is
"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
t changed?
-Mat
Mathieu Wiepert
Medical Information Resources
Mayo Foundation
(507) 266-2317
[EMAIL PROTECTED]
-Original Message-
From: Cox, Greg [mailto:[EMAIL PROTECTED]]
Sent: Tuesday, June 05, 2001 3:22 PM
To: '[EMAIL PROTECTED]'
Subject:[Biojava-l] Blast
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?
Greg
___
Biojava-l mailing lis
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
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
TutorialEx1.java:72: cannot resolve symbo
> I have a few questions about the Blast parsing process. Blast > can
output the ASN.1 or XML, as I understand it. Do we have any parsers > that
use that as a starting point, to then fill blast objects? I asked on the
perl side, should have asked here to.
- Mat
> Any better solutions, anyone change the blast itself?
I've done this before, to try to get it to output better formatted
alignments. However, that ended up being a huge exercise in tracing
through arcane, poorly documented c code, decomposed in non-obvious ways.
My conclusion is that it's prob
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