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
Is it possible to access the line using the xml
parser?
Nicholas Stiffler
Institute of Molecular Biology
University of Oregon
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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
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
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:-)
- 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
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