From g.etherington at imb.uq.edu.au  Wed Nov  1 03:39:24 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Wed, 1 Nov 2006 18:39:24 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <008901c6fd91$3c415e40$36776682@IMBPC.AD>

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                  
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham



From mark.schreiber at novartis.com  Wed Nov  1 04:53:33 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 1 Nov 2006 17:53:33 +0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <OFC6118B66.DA2E4C19-ON48257219.0036166A-48257219.0036577A@ah.novartis.com>

Hi -

It may not like the command line having spaces in the path. Try installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o 
blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From ayates at ebi.ac.uk  Wed Nov  1 05:00:23 2006
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 01 Nov 2006 10:00:23 +0000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
References: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
Message-ID: <45487037.1090205@ebi.ac.uk>

Hi Graham,

Your problem is probably that you're running this via sh which windows 
does not have. Even if you are running this via cygwin as far as I'm 
aware the JVM will use a normal windows shell/cmd. My advice would be to 
drop the sh and just try running the command as normal and see how that 
goes.

Failing that BioJava has org.biojava.utils.ExecRunner which is quite 
good and takes into account a few lessons learned from this article on 
using runtime:

http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

Hope that helps,

Andy Yates

Graham Etherington wrote:
> Hi,
> I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
> searches on a local BLAST database. Even though I'm not using BioJava
> (intend to use it to parse the results), I thought this formum would be the
> best place to ask for help.
> Even when I hard code a good BLAST search I keep getting the same error when
> I run my search, namely: 
> " java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
> Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
> test.fas -o blast.out" error=2 "
> 
> The pertinent bits of code I'm using are...
> 
> String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
> 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";
> 
> ............
> 
> 
> Runtime r = Runtime.getRuntime ();
> Process runBlast = r.exec (new String[] {"sh","-c",cmd});
>                   
> runBlast.waitFor ();
> out.println ("Waiting for result");
> 
> //Write the results
> BufferedReader br = new BufferedReader (new FileReader (output));
> String line = null;
> String results = "";
> while ( (line = br.readLine ()) != null )
> results = results.concat ("/n" + line);
> 
> .............
> 
> I'm not sure why it give me an IOException. I've checked that the file input
> file exists and that all the paths are correct.
> Any ideas?
> 
> Many thanks,
> Graham
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

From Peter.Ng at bccdc.ca  Wed Nov  1 14:40:53 2006
From: Peter.Ng at bccdc.ca (Ng, Peter)
Date: Wed, 1 Nov 2006 11:40:53 -0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB91E@srvex04.phsabc.ehcnet.ca>

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


From g.etherington at imb.uq.edu.au  Wed Nov  1 16:21:53 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Thu, 2 Nov 2006 07:21:53 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB91E@srvex04.phsabc.ehcnet.ca>
Message-ID: <000301c6fdfb$c0c82a80$36776682@IMBPC.AD>

Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the process
represented by this Process object has terminated. I've used it in my code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From Peter.Ng at bccdc.ca  Wed Nov  1 16:52:42 2006
From: Peter.Ng at bccdc.ca (Ng, Peter)
Date: Wed, 1 Nov 2006 13:52:42 -0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB925@srvex04.phsabc.ehcnet.ca>

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


From g.etherington at imb.uq.edu.au  Wed Nov  1 17:16:38 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Thu, 2 Nov 2006 08:16:38 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB925@srvex04.phsabc.ehcnet.ca>
Message-ID: <001a01c6fe03$6688b4b0$36776682@IMBPC.AD>

Peter,
The method is explained quite well at:

http://java.sun.com/j2se/1.3/docs/api/java/lang/Process.html#waitFor()

Not sure about your threading question, but I'm presuming that the Process
produces and exit value. By convention, 0 indicates normal termination.

Hope this helps a little.
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 7:53 AM
To: Graham Etherington; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From michael.tran at acpfg.com.au  Thu Nov  2 00:43:09 2006
From: michael.tran at acpfg.com.au (Michael Tran)
Date: Thu, 2 Nov 2006 16:13:09 +1030
Subject: [Biojava-l] Can BioJava do Multiple Alignments?
References: <mailman.878.1162373982.2429.biojava-l@lists.open-bio.org>
Message-ID: <D3C986810EBCCE488A9DCA95463794F146F416@kaneda.acpfg.local>

<http://www.acpfg.com.au/profiles/Michael_Tran.html> 
Hi,
 
I know that BioJava 1.5 can do pairwise alignments using algorithms like SmithWaterman and NeedlemanWunch. But can BioJava do multiple alignments like the algorthm used for ClustalW? I have also checked the HMM classes, but they appear to only do pairwise alignments.
 
Michael

________________________________

From: biojava-l-bounces at lists.open-bio.org on behalf of biojava-l-request at lists.open-bio.org
Sent: Wed 1/11/2006 8:09 PM
To: biojava-l at lists.open-bio.org
Subject: Biojava-l Digest, Vol 47, Issue 1



Send Biojava-l mailing list submissions to
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than "Re: Contents of Biojava-l digest..."


Today's Topics:

   1. Re: can BioJava do alignment ? (Ramon Medrado)
   2. Re: can BioJava do alignment ? (mark.schreiber at novartis.com)
   3. More extensive Bioperl-run 1.5.2RC2 tests (Nathan S. Haigh)
   4. Re: More extensive Bioperl-run 1.5.2RC2 tests (Nathan Haigh)
   5. fasta description line (ThorstenInAnger)
   6. pK values (Gerster  Sarah)
   7. Re: fasta description line (Mark Schreiber)
   8. Re: pK values (Mark Schreiber)
   9. Re: pK values (David Huen)
  10. Using Java to create BLAST searches (Graham Etherington)


----------------------------------------------------------------------

Message: 1
Date: Thu, 19 Oct 2006 14:45:24 -0300
From: "Ramon Medrado" <rmedrado at gmail.com>
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <37ba4b050610191045q30a6282bjce052e31e1463cea at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 2
Date: Fri, 20 Oct 2006 09:57:09 +0800
From: mark.schreiber at novartis.com
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: "Ramon Medrado" <rmedrado at gmail.com>, CARMELK at il.ibm.com
Cc: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <OFED374D90.C3E37FD4-ON4825720D.000A9274-4825720D.000AB9F8 at ah.novartis.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi -

You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise).
This is actually the most flexible way to do it.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM


        To:     biojava <Biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] can BioJava do alignment ?


Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





------------------------------

Message: 3
Date: Wed, 25 Oct 2006 13:54:26 +0000
From: "Nathan S. Haigh" <n.haigh at sheffield.ac.uk>
Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <453F6C92.6020207 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1


I have recently installed some more software for which there are
bioperl-run tests and run the test suite with several versions of the
software I could find. I've added info to
http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
fails in any of the versions I tested I've noted them together with
versions that were ok (if any).

There maybe another 6 or so programs I'm trying to get hold of to run
further tests - I'll update when I get them.
Nath


------------------------------

Message: 4
Date: Thu, 26 Oct 2006 09:46:13 +0100
From: Nathan Haigh <n.haigh at sheffield.ac.uk>
Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <454075D5.2030005 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

Nathan S. Haigh wrote:
> I have recently installed some more software for which there are
> bioperl-run tests and run the test suite with several versions of the
> software I could find. I've added info to
> http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
> fails in any of the versions I tested I've noted them together with
> versions that were ok (if any).
>
> There maybe another 6 or so programs I'm trying to get hold of to run
> further tests - I'll update when I get them.
> Nath
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>  

My aplogies, this should have gone to the Bioperl mailing list! :o)


------------------------------

Message: 5
Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT)
From: ThorstenInAnger <henrich at embl.de>
Subject: [Biojava-l] fasta description line
To: biojava-l at lists.open-bio.org
Message-ID: <6950970.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi,

I want to do something very simple:

- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)

this is my code:
                                rs = stmt.executeQuery(query);
                            Feature.Template templ = new Feature.Template();
                       
                            //fill in the template
                            Annotation an = new SimpleAnnotation();
                            templ.location = Location.empty;
                               
                                while (rs.next()) {
                                        mepdId = rs.getInt(1);
                                        mepdName = rs.getString(2);
                                        seq = rs.getString(3);
                                        seqObj =  DNATools.createDNASequence(seq, mepdName);
                                    an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
                                    templ.annotation = an;
                                        seqObj.createFeature(templ);
                                        SeqIOTools.writeFasta(fastaFos, seqObj);
                                        //db.addSequence(seqObj);
                                }

It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?

Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.

Cheers,

Thorsten

--
View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
Sent from the BioJava mailing list archive at Nabble.com.



------------------------------

Message: 6
Date: Tue, 31 Oct 2006 09:04:33 +0100
From: "Gerster  Sarah" <sgerster at student.ethz.ch>
Subject: [Biojava-l] pK values
To: <biojava-l at lists.open-bio.org>
Message-ID: <E9D421793368D44FB81D3C438D300574BC729D at EX5.d.ethz.ch>
Content-Type: text/plain;       charset="iso-8859-1"

Hi!

I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use.

And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own?

Cheers

Sarah



------------------------------

Message: 7
Date: Tue, 31 Oct 2006 17:37:24 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] fasta description line
To: ThorstenInAnger <henrich at embl.de>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310137u68700b06se364f99da69feb47 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

If you are using biojava 1.5 beta (recommended) you should use
RichSequence.IOTools to write the fasta (strongly recommended).

With the new org.biojavax.bio.seq.io.FastaFormat object the
description line is constructed from:

richSequence.getIdentifier()
richSequence.getNamespace().getName();
richSequence.getAccession()
richSequence.getVersion()
richSequence.getName()
richSequence.getDescription()

- Mark


On 10/23/06, ThorstenInAnger <henrich at embl.de> wrote:
>
> Hi,
>
> I want to do something very simple:
>
> - get id and sequence from a database
> - create a sequence object
> - write it out as fasta format file (with a defined description line)
>
> this is my code:
>                                 rs = stmt.executeQuery(query);
>                             Feature.Template templ = new Feature.Template();
>
>                             //fill in the template
>                             Annotation an = new SimpleAnnotation();
>                             templ.location = Location.empty;
>
>                                 while (rs.next()) {
>                                         mepdId = rs.getInt(1);
>                                         mepdName = rs.getString(2);
>                                         seq = rs.getString(3);
>                                         seqObj =  DNATools.createDNASequence(seq, mepdName);
>                                     an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
> here");
>                                     templ.annotation = an;
>                                         seqObj.createFeature(templ);
>                                         SeqIOTools.writeFasta(fastaFos, seqObj);
>                                         //db.addSequence(seqObj);
>                                 }
>
> It works fine, but there is no description line in the resulting file!
> How can I change the fasta description line?
>
> Also I am using deprecated methods, but could not find out what to use
> instead:
> FastaFormat.PROPERTY_DESCRIPTIONLINE
> SeqIOTools.writeFasta
> All tutorials I found are using the deprecated.
>
> Cheers,
>
> Thorsten
>
> --
> View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
> Sent from the BioJava mailing list archive at Nabble.com.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 8
Date: Tue, 31 Oct 2006 17:27:29 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] pK values
To: "Gerster Sarah" <sgerster at student.ethz.ch>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310127h75010e56ne31e188294e23803 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

The values are calculated using the SymbolPropertyTable returned by
ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);

This table gets it's values from the resource file
org/biojava/bio/symbol/ResidueProperties.xml

The pK values were added by david huen (I think).

To read XML sequence files try one of the methods in
RichSequence.IOTools from biojava 1.5 beta.

- Mark

On 10/31/06, Gerster  Sarah <sgerster at student.ethz.ch> wrote:
> Hi!
>
> I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use.
>
> And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 9
Date: 31 Oct 2006 12:21:43 +0000
From: David Huen <smh1008 at cam.ac.uk>
Subject: Re: [Biojava-l] pK values
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-l at lists.open-bio.org
Message-ID: <Prayer.1.0.18.0610311221430.32704 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

On Oct 31 2006, Mark Schreiber wrote:

>Hi -
>
>The values are calculated using the SymbolPropertyTable returned by
>ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
>
>This table gets it's values from the resource file
>org/biojava/bio/symbol/ResidueProperties.xml
>
>The pK values were added by david huen (I think).
>

I used the same pK values as those used by GCG to maintian
cross-compability.

Regards,
David


------------------------------

Message: 10
Date: Wed, 1 Nov 2006 18:39:24 +1000
From: "Graham Etherington" <g.etherington at imb.uq.edu.au>
Subject: [Biojava-l] Using Java to create BLAST searches
To: <biojava-l at lists.open-bio.org>
Message-ID: <008901c6fd91$3c415e40$36776682 at IMBPC.AD>
Content-Type: text/plain;       charset="us-ascii"

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely:
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham




------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


End of Biojava-l Digest, Vol 47, Issue 1
****************************************




From mark.schreiber at novartis.com  Thu Nov  2 01:03:13 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 2 Nov 2006 14:03:13 +0800
Subject: [Biojava-l] Can BioJava do Multiple Alignments?
Message-ID: <OFD4AAB495.DA47C130-ON4825721A.00211B06-4825721A.0021412A@ah.novartis.com>

In short -- No.

The best solution is probably to call ClustalW in a process. You could of 
course reimplement the algorithm in biojava if you wish. The DP library 
could also be extended for MSA but this would be hard work.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Michael Tran" <michael.tran at acpfg.com.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/02/2006 01:43 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Can BioJava do Multiple Alignments?


<http://www.acpfg.com.au/profiles/Michael_Tran.html> 
Hi,
 
I know that BioJava 1.5 can do pairwise alignments using algorithms like 
SmithWaterman and NeedlemanWunch. But can BioJava do multiple alignments 
like the algorthm used for ClustalW? I have also checked the HMM classes, 
but they appear to only do pairwise alignments.
 
Michael

________________________________

From: biojava-l-bounces at lists.open-bio.org on behalf of 
biojava-l-request at lists.open-bio.org
Sent: Wed 1/11/2006 8:09 PM
To: biojava-l at lists.open-bio.org
Subject: Biojava-l Digest, Vol 47, Issue 1



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Today's Topics:

   1. Re: can BioJava do alignment ? (Ramon Medrado)
   2. Re: can BioJava do alignment ? (mark.schreiber at novartis.com)
   3. More extensive Bioperl-run 1.5.2RC2 tests (Nathan S. Haigh)
   4. Re: More extensive Bioperl-run 1.5.2RC2 tests (Nathan Haigh)
   5. fasta description line (ThorstenInAnger)
   6. pK values (Gerster  Sarah)
   7. Re: fasta description line (Mark Schreiber)
   8. Re: pK values (Mark Schreiber)
   9. Re: pK values (David Huen)
  10. Using Java to create BLAST searches (Graham Etherington)


----------------------------------------------------------------------

Message: 1
Date: Thu, 19 Oct 2006 14:45:24 -0300
From: "Ramon Medrado" <rmedrado at gmail.com>
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <37ba4b050610191045q30a6282bjce052e31e1463cea at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it 
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., 
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not 
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 2
Date: Fri, 20 Oct 2006 09:57:09 +0800
From: mark.schreiber at novartis.com
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: "Ramon Medrado" <rmedrado at gmail.com>, CARMELK at il.ibm.com
Cc: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
 
<OFED374D90.C3E37FD4-ON4825720D.000A9274-4825720D.000AB9F8 at ah.novartis.com>
 
Content-Type: text/plain; charset="us-ascii"

Hi -

You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise).
This is actually the most flexible way to do it.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM


        To:     biojava <Biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] can BioJava do alignment ?


Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





------------------------------

Message: 3
Date: Wed, 25 Oct 2006 13:54:26 +0000
From: "Nathan S. Haigh" <n.haigh at sheffield.ac.uk>
Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <453F6C92.6020207 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1


I have recently installed some more software for which there are
bioperl-run tests and run the test suite with several versions of the
software I could find. I've added info to
http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
fails in any of the versions I tested I've noted them together with
versions that were ok (if any).

There maybe another 6 or so programs I'm trying to get hold of to run
further tests - I'll update when I get them.
Nath


------------------------------

Message: 4
Date: Thu, 26 Oct 2006 09:46:13 +0100
From: Nathan Haigh <n.haigh at sheffield.ac.uk>
Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <454075D5.2030005 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

Nathan S. Haigh wrote:
> I have recently installed some more software for which there are
> bioperl-run tests and run the test suite with several versions of the
> software I could find. I've added info to
> http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
> fails in any of the versions I tested I've noted them together with
> versions that were ok (if any).
>
> There maybe another 6 or so programs I'm trying to get hold of to run
> further tests - I'll update when I get them.
> Nath
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

My aplogies, this should have gone to the Bioperl mailing list! :o)


------------------------------

Message: 5
Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT)
From: ThorstenInAnger <henrich at embl.de>
Subject: [Biojava-l] fasta description line
To: biojava-l at lists.open-bio.org
Message-ID: <6950970.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi,

I want to do something very simple:

- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)

this is my code:
                                rs = stmt.executeQuery(query);
                            Feature.Template templ = new 
Feature.Template();
 
                            //fill in the template
                            Annotation an = new SimpleAnnotation();
                            templ.location = Location.empty;
 
                                while (rs.next()) {
                                        mepdId = rs.getInt(1);
                                        mepdName = rs.getString(2);
                                        seq = rs.getString(3);
                                        seqObj = 
DNATools.createDNASequence(seq, mepdName);
 an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
                                    templ.annotation = an;
                                        seqObj.createFeature(templ);
                                        SeqIOTools.writeFasta(fastaFos, 
seqObj);
                                        //db.addSequence(seqObj);
                                }

It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?

Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.

Cheers,

Thorsten

--
View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
Sent from the BioJava mailing list archive at Nabble.com.



------------------------------

Message: 6
Date: Tue, 31 Oct 2006 09:04:33 +0100
From: "Gerster  Sarah" <sgerster at student.ethz.ch>
Subject: [Biojava-l] pK values
To: <biojava-l at lists.open-bio.org>
Message-ID: <E9D421793368D44FB81D3C438D300574BC729D at EX5.d.ethz.ch>
Content-Type: text/plain;       charset="iso-8859-1"

Hi!

I want to compute the pI of some sequences. I looked at 
"IsoelectricPointCalc.java". Where do the values for the pks come from? 
are they defined as constants somewhere? I couldn't find them... I wanted 
to see if the values are the same ones than the ones that I am supposed to 
use.

And another question> reading in sequences from an xml file... Is there 
something that I can use, or do I have to write it on my own?

Cheers

Sarah



------------------------------

Message: 7
Date: Tue, 31 Oct 2006 17:37:24 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] fasta description line
To: ThorstenInAnger <henrich at embl.de>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310137u68700b06se364f99da69feb47 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

If you are using biojava 1.5 beta (recommended) you should use
RichSequence.IOTools to write the fasta (strongly recommended).

With the new org.biojavax.bio.seq.io.FastaFormat object the
description line is constructed from:

richSequence.getIdentifier()
richSequence.getNamespace().getName();
richSequence.getAccession()
richSequence.getVersion()
richSequence.getName()
richSequence.getDescription()

- Mark


On 10/23/06, ThorstenInAnger <henrich at embl.de> wrote:
>
> Hi,
>
> I want to do something very simple:
>
> - get id and sequence from a database
> - create a sequence object
> - write it out as fasta format file (with a defined description line)
>
> this is my code:
>                                 rs = stmt.executeQuery(query);
>                             Feature.Template templ = new 
Feature.Template();
>
>                             //fill in the template
>                             Annotation an = new SimpleAnnotation();
>                             templ.location = Location.empty;
>
>                                 while (rs.next()) {
>                                         mepdId = rs.getInt(1);
>                                         mepdName = rs.getString(2);
>                                         seq = rs.getString(3);
>                                         seqObj = 
DNATools.createDNASequence(seq, mepdName);
> an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
> here");
>                                     templ.annotation = an;
>                                         seqObj.createFeature(templ);
>                                         SeqIOTools.writeFasta(fastaFos, 
seqObj);
>                                         //db.addSequence(seqObj);
>                                 }
>
> It works fine, but there is no description line in the resulting file!
> How can I change the fasta description line?
>
> Also I am using deprecated methods, but could not find out what to use
> instead:
> FastaFormat.PROPERTY_DESCRIPTIONLINE
> SeqIOTools.writeFasta
> All tutorials I found are using the deprecated.
>
> Cheers,
>
> Thorsten
>
> --
> View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
> Sent from the BioJava mailing list archive at Nabble.com.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 8
Date: Tue, 31 Oct 2006 17:27:29 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] pK values
To: "Gerster Sarah" <sgerster at student.ethz.ch>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310127h75010e56ne31e188294e23803 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

The values are calculated using the SymbolPropertyTable returned by
ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);

This table gets it's values from the resource file
org/biojava/bio/symbol/ResidueProperties.xml

The pK values were added by david huen (I think).

To read XML sequence files try one of the methods in
RichSequence.IOTools from biojava 1.5 beta.

- Mark

On 10/31/06, Gerster  Sarah <sgerster at student.ethz.ch> wrote:
> Hi!
>
> I want to compute the pI of some sequences. I looked at 
"IsoelectricPointCalc.java". Where do the values for the pks come from? 
are they defined as constants somewhere? I couldn't find them... I wanted 
to see if the values are the same ones than the ones that I am supposed to 
use.
>
> And another question> reading in sequences from an xml file... Is there 
something that I can use, or do I have to write it on my own?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 9
Date: 31 Oct 2006 12:21:43 +0000
From: David Huen <smh1008 at cam.ac.uk>
Subject: Re: [Biojava-l] pK values
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-l at lists.open-bio.org
Message-ID: <Prayer.1.0.18.0610311221430.32704 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

On Oct 31 2006, Mark Schreiber wrote:

>Hi -
>
>The values are calculated using the SymbolPropertyTable returned by
>ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
>
>This table gets it's values from the resource file
>org/biojava/bio/symbol/ResidueProperties.xml
>
>The pK values were added by david huen (I think).
>

I used the same pK values as those used by GCG to maintian
cross-compability.

Regards,
David


------------------------------

Message: 10
Date: Wed, 1 Nov 2006 18:39:24 +1000
From: "Graham Etherington" <g.etherington at imb.uq.edu.au>
Subject: [Biojava-l] Using Java to create BLAST searches
To: <biojava-l at lists.open-bio.org>
Message-ID: <008901c6fd91$3c415e40$36776682 at IMBPC.AD>
Content-Type: text/plain;       charset="us-ascii"

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely:
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham




------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


End of Biojava-l Digest, Vol 47, Issue 1
****************************************



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From cezard at nokad-technology.com  Thu Nov  2 03:41:02 2006
From: cezard at nokad-technology.com (=?iso-8859-1?Q?CEZARD_Timoth=E9e?=)
Date: Thu, 2 Nov 2006 09:41:02 +0100
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <001a01c6fe03$6688b4b0$36776682@IMBPC.AD>
Message-ID: <20061102084307.5F9EB75D8E@smtp2-g19.free.fr>

Hi everyone,

I've worked a bit on that point and want to share my view.

When you launch a blast via the Runtime exec command it creates (and
launches) a new thread outside the JVM. 
The Process object allows you to monitor and  wait for the end of this
thread.
I've observed that for obscure reason sometime the thread never finish.
In that case you have to clear the InputStream and the ErrorStream of the
process.

Last point I've worked on is how to notice the GUI of the end of the
process. For that I've used the SwingWorker object and it worked fine.
http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html


Hope this helps someone.


CEZARD Timoth?e Ms
bioinformatics Manager 
NOKAD SA
4 rue Pierre Fontaine 
91058 EVRY cedex
Tel : 01.60.87.89.90
Fax : 01.60.87.89.99
www.nokad-technology.com


-----Message d'origine-----
De?: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] De la part de Graham
Etherington
Envoy??: mercredi 1 novembre 2006 23:17
??: 'Ng, Peter'; mark.schreiber at novartis.com
Cc?: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Objet?: Re: [Biojava-l] Using Java to create BLAST searches

Peter,
The method is explained quite well at:

http://java.sun.com/j2se/1.3/docs/api/java/lang/Process.html#waitFor()

Not sure about your threading question, but I'm presuming that the Process
produces and exit value. By convention, 0 indicates normal termination.

Hope this helps a little.
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 7:53 AM
To: Graham Etherington; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From zagato.gekko at gmail.com  Thu Nov  2 16:37:58 2006
From: zagato.gekko at gmail.com (Alan Acosta)
Date: Thu, 2 Nov 2006 16:37:58 -0500
Subject: [Biojava-l] Reading sequence identifier from file in FASTA format
Message-ID: <98028b00611021337n4b7970d2q76f7a045d634f6c2@mail.gmail.com>

Hello Everybody, this is my first write to the list, i'm a student of
computer science, and a really newbie into this subjects, so i'm
experimenting with BioJava against BioPerl...

My problem is that i'm trying to read FASTA file with
///////////////////
        BufferedReader input = new BufferedReader( new
FileReader("NC_008009.fna") );
        RichSequenceIterator seqIter = RichSequence.IOTools.readFastaDNA(
input, RichObjectFactory.getDefaultNamespace() );
        RichSequence rseq = null;

        if( seqIter.hasNext() )
        {
            rseq = seqIter.nextRichSequence();
            System.out.println("Identifier: "+rseq.getIdentifier() );
            System.out.println("Description: "+rseq.getDescription() );
            System.out.println("SubList: "+rseq.subList(10, 20).seqString()
);
        }
///////////////////
but i'm getting a "identifier: null" into the answer when it had to be a
"Identifier: 94967031", the description and sublist works good... in (
http://biojava.org/wiki/BioJava:BioJavaXDocs#Reading) says that:
>gi|<identifier>|<namespace>|<accession>.<version>|<name> <description>
identifier will be read it with setIdentifier() and will available through
getIdentifier() but i get a null.

Then... this file is really in FASTA format ? or i'm doing into the wrong
way this ?

The test file is:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Acidobacteria_bacterium_Ellin345/NC_008009.fna

And the header is:
>gi|94967031|ref|NC_008009.1| Acidobacteria bacterium Ellin345, complete
genome
CCGTGTGTTGCGCGGCCAGATGAGAAATTTCTATGTCCCTCTCGACCACGACTCCACCAGCTCCGAACCC

Where i can find a newbie tutorial for starter task into BioJava ?

I appreciate any help... thanks.


Farewell
Alan Acosta
Cali - Colombia

From g.etherington at imb.uq.edu.au  Thu Nov  2 19:23:09 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Fri, 3 Nov 2006 10:23:09 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
Message-ID: <000801c6fede$3d540870$36776682@IMBPC.AD>

Hi,
First of all, thanks for the replies and help that everyone sent for my
BLAST query (see below). I figured out what the problems were and thought I
should post the solutions to the forum.
Firstly, as pointed out, when running on Windows the 'sh' and '-c' should be
taken out.
Process runBlast = r.exec (new String[] {cmd});

Secondly, I moved the location of blast to C:/blast/bin/, as to have no
spaces in the path (I didn't try this when everything worked to see if it
had an affect, so I don't know how essential this is)

Thirdly, (and this was one of those real killers that have you kicking
yourself once you realise what the problem was), the location of the
database (ecoli.nt in this case) has to be explicitly set, so
"C:/blast/bin/ecoli.nt"

In the end, I used the org.biojava.utils.ExecRunner 
This handled the query really well and one of the best features is actually
the error reporting. It told me that it couldn't find the ecoli.nt database
which java.lang.Process did not.
My final code looked like this:

String cmd = "C:/blast/bin/blastall -p blastn -d C:/blast/bin/ecoli.nt -i
test.fas -o blast.out";
org.biojava.utils.ExecRunner runner = new org.biojava.utils.ExecRunner ();
runner.exec (cmd);
out.println (runner.getErrString ());


My task for today is working out the best way to display the output/output
file to the current jsp page.
Again, thanks for your help. 


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia
-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Graham
Etherington
Sent: Wednesday, 1 November 2006 6:39 PM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Using Java to create BLAST searches

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                  
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From johnson.biotech at gmail.com  Fri Nov  3 17:31:00 2006
From: johnson.biotech at gmail.com (Seth Johnson)
Date: Fri, 3 Nov 2006 17:31:00 -0500
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access to
	primary keys
Message-ID: <b99962880611031431l17aca93x99bd7840856dc15c@mail.gmail.com>

Hello guys,

I've setup a BioSQL to hold sequences of interest parsed from NCBI
genbank release.  I also have another proprietary schema that holds
experimental and alignment data.  I would like to connect the
proprietary schema to BioSQL one using Hibernate persistence, so that
objects from my database would contain linkages to sequence data in
biosql.  Wiki mentions that one need change "only the mapping files
that tell Hibernate how to translate between objects and tables."  Can
anyone elaborate on that topic a little or point me to a tutorial or
some other place that discusses the concept?

-- 
Best Regards,


Seth Johnson
Senior Bioinformatics Associate

From varvenne at genoway.com  Mon Nov  6 07:57:24 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 06 Nov 2006 13:57:24 +0100
Subject: [Biojava-l] Parsing blast results
Message-ID: <C174EFC4.F68%varvenne@genoway.com>

Hello,

I'm a new user of biojava and i'm trying to use it to parse blast results
(against NCBI nr database). I've tried to do so using biojava1.4 and
biojava1.5-beta but none of these seem to support the latest Blast version.

I'd be very greatful to you if anyone could help me with that...

Thanks,
Best regards,

Benoit Varvenne,
Bioinformatics pearson in charge,
Genoway Lyon (France).
 


From varvenne at genoway.com  Mon Nov  6 08:27:32 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 06 Nov 2006 14:27:32 +0100
Subject: [Biojava-l] Parsing blast results
In-Reply-To: <C174EFC4.F68%varvenne@genoway.com>
Message-ID: <C174F6D4.F6E%varvenne@genoway.com>

I've already found the answer to my question which seems to work in previous
archives (?June 2006).

This archive suggests to replace :
BlastLikeSAXParser parser = new BlastLikeSAXParser();

By :
BlastXMLParserFacade parser = new BlastXMLParserFacade();


And this seems to work well.

So sorry for having posted a bit quickly.

Regards,

Beno?t Varvenne,
Bioinformatics pearson in charge,
Genoway Lyon (France).

Le 6/11/06 13:57, ??Benoit VARVENNE?? <varvenne at genoway.com> a ?crit?:

> Hello,
> 
> I'm a new user of biojava and i'm trying to use it to parse blast results
> (against NCBI nr database). I've tried to do so using biojava1.4 and
> biojava1.5-beta but none of these seem to support the latest Blast version.
> 
> I'd be very greatful to you if anyone could help me with that...
> 
> Thanks,
> Best regards,
> 
> Benoit Varvenne,
> Bioinformatics pearson in charge,
> Genoway Lyon (France).
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 



From johnson.biotech at gmail.com  Mon Nov  6 23:59:01 2006
From: johnson.biotech at gmail.com (Seth Johnson)
Date: Mon, 6 Nov 2006 23:59:01 -0500
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access
	to primary keys
In-Reply-To: <454F07D5.2040001@ebi.ac.uk>
References: <b99962880611031431l17aca93x99bd7840856dc15c@mail.gmail.com>
	<454F07D5.2040001@ebi.ac.uk>
Message-ID: <b99962880611062059r4a0bae8ar3213af5aa7452998@mail.gmail.com>

Thank you Richard.  I am using NetBeans 5.5 and JDK 5.0 that
implements mapping metadata (EJB 3.0) instead of .hbm.xml files.   I
read up on Hibernate from you links and I think that the easiest
solution would be to use RichSequence BioJavaX object as an embeddable
object in my proprietary 'alignment' class.

Basically, my goal is to have access to RichSequence object when I
instantiate 'alignment' object from my 'alignment' table.  That table
contains a column with primary key of the bioentry that was used to
produce that alignment.  Since biosql is in different schema, I don't
believe that cross schema foreign keys are possible in mySQL.  Do you
think that this  is a right strategy?

Seth


On 11/6/06, Richard Holland <holland at ebi.ac.uk> wrote:
>
> If your proprietary database has a similar design to BioSQL, or can
> easily be mapped on an approximately 1:1 basis to the existing BioJavaX
> object model, then all you need to do is edit the .hbm.xml files and
> look for references to table names and column names. Remove any tables
> and columns that don't exist in your schema (including removing the
> files if this leaves them empty), and edit the remaining ones so that
> the table and column names match.
>
> If your new schema contains tables that do not map to existing BioJavaX
> objects, then you'll need to create Java objects for those as well as
> the appropriate mapping files. The easiest way to do this is to
> copy-and-paste both an existing BioJavaX object and the related .hbm.xml
> file - eg. SimpleCrossRef.java and CrossRef.hxm.xml.
>
> Hibernate is best explained through its own documentation at
> http://www.hibernate.org/ . The 'getting started' tutorial they provide
> (here:
> http://www.hibernate.org/hib_docs/v3/reference/en/html/tutorial.html )
> is a good starting point.
>
> cheers,
> Richard
>
>
> Seth Johnson wrote:
> > Hello guys,
> >
> > I've setup a BioSQL to hold sequences of interest parsed from NCBI
> > genbank release.  I also have another proprietary schema that holds
> > experimental and alignment data.  I would like to connect the
> > proprietary schema to BioSQL one using Hibernate persistence, so that
> > objects from my database would contain linkages to sequence data in
> > biosql.  Wiki mentions that one need change "only the mapping files
> > that tell Hibernate how to translate between objects and tables."  Can
> > anyone elaborate on that topic a little or point me to a tutorial or
> > some other place that discusses the concept?
> >

From mark.schreiber at novartis.com  Tue Nov  7 03:57:58 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 7 Nov 2006 16:57:58 +0800
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence
 access	to primary keys
Message-ID: <OFA590830C.937721F7-ON4825721F.0030ABEF-4825721F.00314200@ah.novartis.com>

Hi -

If you are using the JDK5 persistence API you either do your mappings as 
annotations or vendor neutral xml mappings. The vendor you choose for the 
actual ORM is specified in your persistence unit definition (eg Hibernate, 
KODO, TopLink etc).

If you want to do the mapping with annotations you would need to make your 
own implemenation of RichSequence etc as biojava is not yet using JDK5 and 
won't support annotation. Basically you would just copy the appropriate 
"SimpleRich" Objects and pepper them with annotations pointing to the 
correct DB tables etc. Not sure which strategy is more appropriate for 
you.

If MySQL doesn't allow for cross schema keys you may have to extend your 
copy of MySQL to include the extra table/ tables from your proprietary 
schema.

- Mark





"Seth Johnson" <johnson.biotech at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/07/2006 12:59 PM

 
        To:     "Richard Holland" <holland at ebi.ac.uk>
        cc:     biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access      to 
primary keys


Thank you Richard.  I am using NetBeans 5.5 and JDK 5.0 that
implements mapping metadata (EJB 3.0) instead of .hbm.xml files.   I
read up on Hibernate from you links and I think that the easiest
solution would be to use RichSequence BioJavaX object as an embeddable
object in my proprietary 'alignment' class.

Basically, my goal is to have access to RichSequence object when I
instantiate 'alignment' object from my 'alignment' table.  That table
contains a column with primary key of the bioentry that was used to
produce that alignment.  Since biosql is in different schema, I don't
believe that cross schema foreign keys are possible in mySQL.  Do you
think that this  is a right strategy?

Seth


On 11/6/06, Richard Holland <holland at ebi.ac.uk> wrote:
>
> If your proprietary database has a similar design to BioSQL, or can
> easily be mapped on an approximately 1:1 basis to the existing BioJavaX
> object model, then all you need to do is edit the .hbm.xml files and
> look for references to table names and column names. Remove any tables
> and columns that don't exist in your schema (including removing the
> files if this leaves them empty), and edit the remaining ones so that
> the table and column names match.
>
> If your new schema contains tables that do not map to existing BioJavaX
> objects, then you'll need to create Java objects for those as well as
> the appropriate mapping files. The easiest way to do this is to
> copy-and-paste both an existing BioJavaX object and the related .hbm.xml
> file - eg. SimpleCrossRef.java and CrossRef.hxm.xml.
>
> Hibernate is best explained through its own documentation at
> http://www.hibernate.org/ . The 'getting started' tutorial they provide
> (here:
> http://www.hibernate.org/hib_docs/v3/reference/en/html/tutorial.html )
> is a good starting point.
>
> cheers,
> Richard
>
>
> Seth Johnson wrote:
> > Hello guys,
> >
> > I've setup a BioSQL to hold sequences of interest parsed from NCBI
> > genbank release.  I also have another proprietary schema that holds
> > experimental and alignment data.  I would like to connect the
> > proprietary schema to BioSQL one using Hibernate persistence, so that
> > objects from my database would contain linkages to sequence data in
> > biosql.  Wiki mentions that one need change "only the mapping files
> > that tell Hibernate how to translate between objects and tables."  Can
> > anyone elaborate on that topic a little or point me to a tutorial or
> > some other place that discusses the concept?
> >
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From sgerster at student.ethz.ch  Wed Nov  8 03:14:39 2006
From: sgerster at student.ethz.ch (Gerster  Sarah)
Date: Wed, 8 Nov 2006 09:14:39 +0100
Subject: [Biojava-l] reading paptides from a fasta file
Message-ID: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>

Hi!

I'm trying to read peptides from a fasta file:
>id|0|0.9992|1
ASITENGGAEEESVAK
>id|1|0.9953|1
ASITENGGAEEESVAK
>id|2|0.9998|1
ASNASSAGDEVDNVATSSK
>id|3|0.9998|1
EAAAAEEPQPSDEGDVVAK
>id|4|0.9998|1
EAAAAEEPQPSDEGDVVAK
....
I would like to have all peptides somewhere in the memory. I need, their id, the sequence and the 2 numbers at the end (e.g. id = 0, probability = 0.9992, rank = 1 for the first entry in the file).

I tried to use readFastaProtein... but I guess I don't use it right. Anyway, I get the sequences, but I don't get any of the other infomations I want... 

Here is my code:
try
{
  BufferedReader br = new BufferedReader(new FileReader(file_name));
  RichSequenceIterator rich_stream = RichSequence.IOTools.readFastaProtein(br,null);
  while(rich_stream.hasNext())
  {
    RichSequence rich_seq = rich_stream.nextRichSequence();
    System.out.println(rich_seq.toString());
    System.out.println(rich_seq.getAccession());
    System.out.println(rich_seq.getAlphabet());
    System.out.println(rich_seq.getAnnotation());
    System.out.println(rich_seq.getName());
    System.out.println(rich_seq.getDescription());
    System.out.println(rich_seq.getIdentifier());
    System.out.println(rich_seq.seqString());
  }     
}
catch(Exception e) 
{
  System.err.println("Bug while reading the sequences from the FASTA file"); 
} 
 

Here's the output (for the first entry in the fasta file):
id|0:1/0.9992
0
org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper at 1df073d

1
null
null
ASITENGGAEEESVAK


Can anyone tell me what's going wrong? 
Is there already a function to put all the sequences directly in the memory (like a HashSet) while reading them?

Cheers

Sarah


From dreher at molgen.mpg.de  Wed Nov  8 07:39:20 2006
From: dreher at molgen.mpg.de (Felix Dreher)
Date: Wed, 08 Nov 2006 13:39:20 +0100
Subject: [Biojava-l] reading paptides from a fasta file
In-Reply-To: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>
References: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>
Message-ID: <4551CFF8.9050507@molgen.mpg.de>

Hi Sarah,


just a few comments / guesses:
maybe there are other approaches, but you could follow the FASTA-format 
BioJavaX understands, e.g.:
 
|>gi|<identifier>|<namespace>|<accession>|<name> <description>|

http://biojava.org/wiki/BioJava:BioJavaXDocs#Reading   (chapter 8.2.1)

So, if your file would look like this:

 >gi|0|namespace|null|1 0.9992
ASITENGGAEEESVAK
 >gi|1|namespace|null|1 0.9953
ASITENGGAEEESVAK
.
.
.

you could use:

                System.out.println("id: "+rich_seq.getIdentifier());
                System.out.println("rank: "+rich_seq.getName());
                System.out.println("probability: 
"+rich_seq.getDescription());
                System.out.println("sequence: "+rich_seq.seqString());


to get the data.

However, 'rank' or 'probability' actually would be annotations of the 
sequence, so when processing the data (e.g. storing in a database), one 
would store these data as annotations.

- As for Java-style / naming conventions for variables, the 'Camel-Case' 
is recommended, e.g.richSeq instead of rich_seq.

- To get the alphabet:
System.out.println("alphabet: "+rich_seq.getAlphabet().getName());

- Also maybe you should use the default namespace instead of null:
RichSequenceIterator rich_stream = 
RichSequence.IOTools.readFastaProtein(br,RichObjectFactory.getDefaultNamespace());


Cheers,
Felix



Gerster Sarah wrote:
> Hi!
>
> I'm trying to read peptides from a fasta file:
>   
>> id|0|0.9992|1
>>     
> ASITENGGAEEESVAK
>   
>> id|1|0.9953|1
>>     
> ASITENGGAEEESVAK
>   
>> id|2|0.9998|1
>>     
> ASNASSAGDEVDNVATSSK
>   
>> id|3|0.9998|1
>>     
> EAAAAEEPQPSDEGDVVAK
>   
>> id|4|0.9998|1
>>     
> EAAAAEEPQPSDEGDVVAK
> ....
> I would like to have all peptides somewhere in the memory. I need, their id, the sequence and the 2 numbers at the end (e.g. id = 0, probability = 0.9992, rank = 1 for the first entry in the file).
>
> I tried to use readFastaProtein... but I guess I don't use it right. Anyway, I get the sequences, but I don't get any of the other infomations I want... 
>
> Here is my code:
> try
> {
>   BufferedReader br = new BufferedReader(new FileReader(file_name));
>   RichSequenceIterator rich_stream = RichSequence.IOTools.readFastaProtein(br,null);
>   while(rich_stream.hasNext())
>   {
>     RichSequence rich_seq = rich_stream.nextRichSequence();
>     System.out.println(rich_seq.toString());
>     System.out.println(rich_seq.getAccession());
>     System.out.println(rich_seq.getAlphabet());
>     System.out.println(rich_seq.getAnnotation());
>     System.out.println(rich_seq.getName());
>     System.out.println(rich_seq.getDescription());
>     System.out.println(rich_seq.getIdentifier());
>     System.out.println(rich_seq.seqString());
>   }     
> }
> catch(Exception e) 
> {
>   System.err.println("Bug while reading the sequences from the FASTA file"); 
> } 
>  
>
> Here's the output (for the first entry in the fasta file):
> id|0:1/0.9992
> 0
> org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper at 1df073d
>
> 1
> null
> null
> ASITENGGAEEESVAK
>
>
> Can anyone tell me what's going wrong? 
> Is there already a function to put all the sequences directly in the memory (like a HashSet) while reading them?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>   


-- 
Felix Dreher

Max Planck Institute for Molecular Genetics
Department of Vertebrate Genomics
Bioinformatics Group
Ihnestr. 73
D-14195 Berlin

Phone: +49 30 - 8413 1682
Mobile: +49 163 - 754 24 26
E-mail: dreher at molgen.mpg.de
www.molgen.mpg.de/~lh_bioinf
 


From myammad at gmail.com  Wed Nov  8 09:50:49 2006
From: myammad at gmail.com (Ammad Ud Din)
Date: Wed, 8 Nov 2006 19:50:49 +0500
Subject: [Biojava-l] New To BioJava.org
Message-ID: <887d6f690611080650j3a0f6caah610768dbb7dbe498@mail.gmail.com>

Hi,
    i am a student of bs-bioinformatics from Muhammad Ali Jinnah University,
islamabad Pakistan.I am curently taking a course in Java here at my
university so i want to do work in java particularly in BioJava.I would like
to welcome suggestions regarding my final project in this course and also
would like to contribute as well.
                  take care & best wishes,
-- 
Ammad

From mark.schreiber at novartis.com  Wed Nov  8 20:53:37 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 9 Nov 2006 09:53:37 +0800
Subject: [Biojava-l] New To BioJava.org
Message-ID: <OF9A833ABC.E6074CA4-ON48257221.000A52F9-48257221.000A684A@ah.novartis.com>

Hi -

If you take a look at the API docs and the cookbook in www.biojava.org you 
will get an idea of what biojava can do and probably come up with a 
project from there.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ammad Ud Din" <myammad at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/08/2006 10:50 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] New To BioJava.org


Hi,
    i am a student of bs-bioinformatics from Muhammad Ali Jinnah 
University,
islamabad Pakistan.I am curently taking a course in Java here at my
university so i want to do work in java particularly in BioJava.I would 
like
to welcome suggestions regarding my final project in this course and also
would like to contribute as well.
                  take care & best wishes,
-- 
Ammad
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From varvenne at genoway.com  Mon Nov 13 05:54:07 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 13 Nov 2006 11:54:07 +0100
Subject: [Biojava-l] Any memory-optimised blast parser available ?
Message-ID: <C17E0D5F.102E%varvenne@genoway.com>

Hello,

I'm trying to parse blast result files from a remote blast on NCBI
databases.
In order to do so, i'm using biojava XML parser like this :

-----------
      InputStream is = new FileInputStream(blastFile);
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      parser.setContentHandler(adapter);

      List results = new ArrayList();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      adapter.setSearchContentHandler(builder);

// Here is the method that throws 'OutOfMemoryException'
      parser.parse(new InputSource(is));
-----------

While blasting a genomic sequence (i've tried with 50Kb long sequences max),
I've got an OutOfMemory exception.

Does anyone know a way to resolve this ? (this aim is not to dividde my
genomic locus in too many parts, 50Kb is a quarter of my genomic...)

Thanks,
Regards,

Benoit


-- 
Benoit Varvenne,
Bioinformatics pearson in charge,
GenOway - Lyon (France)


From ayates at ebi.ac.uk  Mon Nov 13 06:28:29 2006
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 13 Nov 2006 11:28:29 +0000
Subject: [Biojava-l] Any memory-optimised blast parser available ?
In-Reply-To: <C17E0D5F.102E%varvenne@genoway.com>
References: <C17E0D5F.102E%varvenne@genoway.com>
Message-ID: <455856DD.9040605@ebi.ac.uk>

Hi,

Have you tried increasing the amount of memory the Java virtual machine 
has available? The problem with Java is that it starts with a default 
memory limit of approx. 128MB which if you've got a memory intensive 
process will not be enough.

When running your program try adding the option

-Xmx256M

So if my class was called Main.class my command line would be:

java -Xmx256M -cp .:biojava.jar Main

Or if you're running this from ant then there is an attribute maxmemory 
which can be specified in the <java/> task.

Hope that helps

Andy

Benoit VARVENNE wrote:
> Hello,
> 
> I'm trying to parse blast result files from a remote blast on NCBI
> databases.
> In order to do so, i'm using biojava XML parser like this :
> 
> -----------
>       InputStream is = new FileInputStream(blastFile);
>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
> 
>       parser.setContentHandler(adapter);
> 
>       List results = new ArrayList();
> 
>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>           new DummySequenceDB("queries"), new
> DummySequenceDBInstallation());
> 
>       adapter.setSearchContentHandler(builder);
> 
> // Here is the method that throws 'OutOfMemoryException'
>       parser.parse(new InputSource(is));
> -----------
> 
> While blasting a genomic sequence (i've tried with 50Kb long sequences max),
> I've got an OutOfMemory exception.
> 
> Does anyone know a way to resolve this ? (this aim is not to dividde my
> genomic locus in too many parts, 50Kb is a quarter of my genomic...)
> 
> Thanks,
> Regards,
> 
> Benoit
> 
> 

From varvenne at genoway.com  Mon Nov 13 07:39:34 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 13 Nov 2006 13:39:34 +0100
Subject: [Biojava-l] Any memory-optimised blast parser available ?
In-Reply-To: <455856DD.9040605@ebi.ac.uk>
Message-ID: <C17E2616.1036%varvenne@genoway.com>

Great ! Thanks a lot to all for your answers.
I hadn't thought to that way of solving the problem.
That runs well with -Xmx option.

Thanks again,
Regards,

Benoit


Le 13/11/06 12:28, ??Andy Yates?? <ayates at ebi.ac.uk> a ?crit?:

> Hi,
> 
> Have you tried increasing the amount of memory the Java virtual machine
> has available? The problem with Java is that it starts with a default
> memory limit of approx. 128MB which if you've got a memory intensive
> process will not be enough.
> 
> When running your program try adding the option
> 
> -Xmx256M
> 
> So if my class was called Main.class my command line would be:
> 
> java -Xmx256M -cp .:biojava.jar Main
> 
> Or if you're running this from ant then there is an attribute maxmemory
> which can be specified in the <java/> task.
> 
> Hope that helps
> 
> Andy
> 
> Benoit VARVENNE wrote:
>> Hello,
>> 
>> I'm trying to parse blast result files from a remote blast on NCBI
>> databases.
>> In order to do so, i'm using biojava XML parser like this :
>> 
>> -----------
>>       InputStream is = new FileInputStream(blastFile);
>>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>> 
>>       parser.setContentHandler(adapter);
>> 
>>       List results = new ArrayList();
>> 
>>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>>           new DummySequenceDB("queries"), new
>> DummySequenceDBInstallation());
>> 
>>       adapter.setSearchContentHandler(builder);
>> 
>> // Here is the method that throws 'OutOfMemoryException'
>>       parser.parse(new InputSource(is));
>> -----------
>> 
>> While blasting a genomic sequence (i've tried with 50Kb long sequences max),
>> I've got an OutOfMemory exception.
>> 
>> Does anyone know a way to resolve this ? (this aim is not to dividde my
>> genomic locus in too many parts, 50Kb is a quarter of my genomic...)
>> 
>> Thanks,
>> Regards,
>> 
>> Benoit
>> 
>> 
> 



From jolyon.holdstock at ogt.co.uk  Mon Nov 13 06:33:43 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Mon, 13 Nov 2006 11:33:43 -0000
Subject: [Biojava-l] Any memory-optimised blast parser available
	?[Scanned]
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0111DCE1@EUCLID.internal.ogtip.com>

Can you use the -Xmx flag to add more memory to the JRE?

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Benoit
VARVENNE
Sent: 13 November 2006 10:54
To: biojava-l
Subject: [Biojava-l] Any memory-optimised blast parser available
?[Scanned]

Hello,

I'm trying to parse blast result files from a remote blast on NCBI
databases.
In order to do so, i'm using biojava XML parser like this :

-----------
      InputStream is = new FileInputStream(blastFile);
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      parser.setContentHandler(adapter);

      List results = new ArrayList();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      adapter.setSearchContentHandler(builder);

// Here is the method that throws 'OutOfMemoryException'
      parser.parse(new InputSource(is));
-----------

While blasting a genomic sequence (i've tried with 50Kb long sequences
max),
I've got an OutOfMemory exception.

Does anyone know a way to resolve this ? (this aim is not to dividde my
genomic locus in too many parts, 50Kb is a quarter of my genomic...)

Thanks,
Regards,

Benoit


-- 
Benoit Varvenne,
Bioinformatics pearson in charge,
GenOway - Lyon (France)

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.



From dunarel at gmx.net  Fri Nov 17 21:48:41 2006
From: dunarel at gmx.net (Dunarel Badescu)
Date: Sat, 18 Nov 2006 03:48:41 +0100
Subject: [Biojava-l] New To BioJava.org, right in the question.
In-Reply-To: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
References: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
Message-ID: <20061118024841.274400@gmx.net>

Hello,

My name is Dunarel Badescu, a student at UQAM University in Montreal,Quebec,Canada in Graduate Diploma of Bioinformatics.

Currently I am using BioJavaX and BioSql for my session project.

I have parsed NCBI GeneBank files using RichSequences.
I then inserted the sequences into the database.

Several problems arise:

1) A bug in the code pulled from CVS:
In class BioSQLRichObjectBuilder: I had to append some code for the program to find the right constructors:

// Get the results
Object result = this.uniqueResult.invoke(query, null);
// Return the found object, if found
if (result!=null) return result;
// Create, persist and return the new object otherwise
else {

/*NEW CODE*/
if (SimpleDocRef.class.isAssignableFrom(clazz)) {
// convert String to List constructor 
      	ourParamsList.set(0,
DocRefAuthor.Tools.parseAuthorString((String)ourParamsList.get(0)));
                }                
             
// Load the class


2) Meny memory problems, after inserting 800 sequences it slows extremely so performance is degraded.
I thought of a hibernate cache problem and tried to turn it off by setting some parameters: 
        <property name="hibernate.jdbc.batch_size">20</property>
        <property name="hibernate.cache.enabled">false</property>
        <property name="hibernate.cache.use_query_cache">false</property>
        <property name="hibernate.cache.use_second_level_cache">false</property>
        <property name="hibernate.connection.aggressive_release">false</property> 
        
        <property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
        <property name="cache.use_query_cache">false</property>
        <property name="cache.use_minimal_puts">false</property>
        <property name="max_fetch_depth">3</property> 
    
to no much benefit.

Then I observed some small performance gain by using :
  session.save("Sequence",rs);  // persist the sequence
  session.getTransaction().commit();
  session.flush();
  session.evict(rs);
The session.evict(rs);

Any atempt to dealocate memory by closing the session, the session factory either generates errors or it will generate on reopening.

So as a last resort I fragmented the original aprox. 130 mb containing one taxon from ncbi in 38 files 1000 sequences each and made a dos batch script executing the program in the commad line for each file.
So that way it works but:

3) Inserting rows sometimes generates exceptions in the references table.
After taking it more closely I found that by disabling the unique constraint on the dbxref_id on references table solves all the remaining problems.

The coment about it on the original code is:
-- No two references can reference the same reference database entry 
-- (dbxref_id). This is where the MEDLINE id goes: PUBMED:123456. 
and the modification is:

--UNIQUE ( dbxref_id ) , 

I must say that the script for creating the biosql schema is version 1.29 from the cvs, the most recent I found.

And I must say that for running the script on Postgresql 8.1.5 I had to modify each create table statement adding with oids at the end, now that 8.1.5 doesn't create oids by default.

It must have be a more elegant aproch to all these problems isn't it?

At least the constraint situation, I mean is it normal to exist or not as it seems.

I wish You all the best and thank you for your work which is most useful and scarce as a resource.



-- 
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! 
Ideal f?r Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

From sanges at biogem.it  Sat Nov 18 06:54:26 2006
From: sanges at biogem.it (Remo Sanges)
Date: Sat, 18 Nov 2006 11:54:26 +0000
Subject: [Biojava-l] Fellowships for Junior Scientists
In-Reply-To: <20061118024841.274400@gmx.net>
References: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
	<20061118024841.274400@gmx.net>
Message-ID: <455EF472.1000903@biogem.it>

Apologies for the off topic post and for the crossposting...

AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/)
and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility
initiative aimed at attracting international scientists to work with
the biomedical research community of Trieste.

Research areas:

     * Biostatistics
     * Systems Biology
     * Algorithm Development

The fellowships are funded by AREA Science Park and the CBM - Consortium
for Molecular Biomedicine as part of an international mobility programme
run by AREA Science Park and the CBM. The programme aims at attracting
young scientists to the Friuli Venezia Giulia Region and adding them to
the community of researchers operating in Trieste in the field of
biomedicine.


CBM and AREA Science Park are two research institutes recognised by the
Ministry of Education, Universities and Research.
Here there are laboratories integrating dry and wet lab research and
developing a wide research program encompassing functional and comparative
genomics, bioinformatics database, software development and algorithm
development.
The laboratories are already integrated in international collaborative
projects tackling non-coding RNA genes, regulatory elements, and
bioinformatics workflow management systems.

For further information:
http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2


Regards

Remo Sanges


From varvenne at genoway.com  Mon Nov 20 11:19:38 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 20 Nov 2006 17:19:38 +0100
Subject: [Biojava-l] Any ORF Finder available ?
Message-ID: <C187942A.1150%varvenne@genoway.com>

Hello,

I'm a working on a biojava project and i'm searching for a way to include an
ORF Finder in my code. The aim is to find ORFs on cDNA sequences (or partial
ORFs on ESTs ones) 

Anyone can help me ?
Is there a module with biojava to do so ? Do you know any free-to-dowload
software (source code or compiled one) ?

Thanks,
Regards   

Beno?t.



From mark.schreiber at novartis.com  Mon Nov 20 22:12:03 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 21 Nov 2006 11:12:03 +0800
Subject: [Biojava-l] Any ORF Finder available ?
Message-ID: <OFC6723038.1FD8CED2-ON4825722D.000FE302-4825722D.00119573@ah.novartis.com>

Hi -

A quick and dirty way is to make a six frame translation 
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames).

Probably a better way is to scan in six frames (using a 
WindowedSymbolList) looking for a start codon and then look for the 
appropriate stop codon. You will want to define the start and stop codons 
as Symbols from the codon (DNAxDNAxDNA) alphabet. You can do this as 
follows:

FiniteAlphabet codonAlpha = DNATools.getCodonAlphabet();

//make a ambiguity symbol for ATG, GTG and TTG codons

//first make the A or G or T ambiguity BasisSymbol
Set syms = new HashSet();
syms.add(DNATools.a()); syms.add(DNATools.t()); syms.add(DNATools.g());
Symbol amb = DNATools.getDNA().getAmbiguity(syms) ;

//now make the [A|G|T] TG codon
List l = new ArrayList();
l.add(amb); l.add(DNATools.t()); l.add(DNATools.g());
Symbol startCodon = codonAlpha.getSymbol(l);

//You would construct the stop codons in a similar manner although you 
probably can't merge them all into one.

The above example shows how you can use a single symbol to represent all 3 
common bacterial start codons. You could also make all 3 seperatly and 
test them individually.

- Mark
 

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





Benoit VARVENNE <varvenne at genoway.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/21/2006 12:19 AM

 
        To:     biojava-l <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Any ORF Finder available ?


Hello,

I'm a working on a biojava project and i'm searching for a way to include 
an
ORF Finder in my code. The aim is to find ORFs on cDNA sequences (or 
partial
ORFs on ESTs ones) 

Anyone can help me ?
Is there a module with biojava to do so ? Do you know any free-to-dowload
software (source code or compiled one) ?

Thanks,
Regards 

Beno?t.


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From weelainy at hotmail.com  Tue Nov 21 12:44:26 2006
From: weelainy at hotmail.com (Elaine Forbes)
Date: Tue, 21 Nov 2006 17:44:26 +0000
Subject: [Biojava-l] remove me from your list
Message-ID: <BAY117-F3807D23951044A323DAC4ECBEC0@phx.gbl>

Hi
I no longer wish to recieve emails from the biojava email list- please 
remove me.
THanks
Elaine

_________________________________________________________________
Windows Live? Messenger has arrived. Click here to download it for free! 
http://imagine-msn.com/messenger/launch80/?locale=en-gb


From markjschreiber at gmail.com  Wed Nov 22 01:35:54 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 22 Nov 2006 14:35:54 +0800
Subject: [Biojava-l] Open JDK
Message-ID: <93b45ca50611212235r265b4730sea68dfb6b41fb4e0@mail.gmail.com>

Dear All -

Everyone knows that BioJava is open-source but you may not know that
the Java JDK is in the process of being made open-source several parts
already are including the javac and HotSpot runtime.

https://openjdk.dev.java.net/

Next time you think the GenBank parser is slow maybe you could
optimise the HotSpot runtime instead : )

- Mark

From kingsulaman at hotmail.com  Thu Nov 23 08:02:31 2006
From: kingsulaman at hotmail.com (Sulaman Malik)
Date: Thu, 23 Nov 2006 18:02:31 +0500
Subject: [Biojava-l] Looking For Project
Message-ID: <BAY114-DAV106855476E012F01A88F58ADE20@phx.gbl>



hi:
    This is Sulaman Malik BS(Bio-informatics) Student of MAJU,Islamabad Pakistan.

     I am looking for a good semester project which i could impelement using the Java as a platefarm,so give me a lsit of bio-projects or any bio-project so that i could go further. 

From varvenne at genoway.com  Fri Nov 24 11:19:27 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 17:19:27 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN vs. blastP)
Message-ID: <C18CDA1F.11FF%varvenne@genoway.com>

Hello,

I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
the code put at the end of this mail.

I've tried this with a blastN query and there i got no trouble.
However, i've tried to do exactly the same thing with a BlastP query and
i've got the exception cited at the end of this mail.

I've verified and the two infiles (blastn/blastp) seem to have the same
structures (except that one is for prot so data are different). (Please find
them as attached if you're used to this).

Can someone help me ? I don't understand why it works in a case and not in
the other one ...

Thanks a lot,
Cheers,

Beno?t.


-------------------
My code :
-----
InputStream is = new FileInputStream(blastFile);
// blastFile is the xml file, output of my blast

      //make a BlastLikeSAXParser
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      //make the SAX event adapter that will pass events to a Handler.
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      //set the parsers SAX event adapter
      parser.setContentHandler(adapter);

      //The list to hold the SeqSimilaritySearchResults
      List results = new ArrayList();

      //create the SearchContentHandler that will build
SeqSimilaritySearchResults
      //in the results List
      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      //register builder with adapter
      adapter.setSearchContentHandler(builder);

      parser.parse(new InputSource(is)); // From here come the Exception

-------------------


-------------------
The exception :
----
  org.xml.sax.SAXParseException: Une d?claration XML peut commencer des
entit?s uniquement.
        at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3376)
        at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3364)
        at org.apache.crimson.parser.Parser2.maybePI(Parser2.java:1140)
        at org.apache.crimson.parser.Parser2.maybeMisc(Parser2.java:1266)
        at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:671)
        at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
        at 
org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
        at 
org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLPars
erFacade.java:180)



From smh1008 at cam.ac.uk  Fri Nov 24 12:08:54 2006
From: smh1008 at cam.ac.uk (David Huen)
Date: 24 Nov 2006 17:08:54 +0000
Subject: [Biojava-l] A problem parsing Blast XML output (blastN vs.
	blastP)
In-Reply-To: <C18CDA1F.11FF%varvenne@genoway.com>
References: <C18CDA1F.11FF%varvenne@genoway.com>
Message-ID: <Prayer.1.0.18.0611241708540.30878@hermes-1.csi.cam.ac.uk>

On Nov 24 2006, Benoit VARVENNE wrote:

>Hello,
>
>I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>the code put at the end of this mail.
>
>I've tried this with a blastN query and there i got no trouble.
>However, i've tried to do exactly the same thing with a BlastP query and
>i've got the exception cited at the end of this mail.
>
> I've verified and the two infiles (blastn/blastp) seem to have the same 
> structures (except that one is for prot so data are different). (Please 
> find them as attached if you're used to this).
>
>Can someone help me ? I don't understand why it works in a case and not in
>the other one ...
>
I am uncertain whether BlastXMLFacade will actually support a protein 
sequence parse. It was originally developed to handle blastn. Anyone else 
tried it with blastp?

I'm offline till Sunday so I can't reply till then.

Regards,
David Huen

From varvenne at genoway.com  Fri Nov 24 12:53:49 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 18:53:49 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN
	vs.	blastP)
In-Reply-To: <Prayer.1.0.18.0611241708540.30878@hermes-1.csi.cam.ac.uk>
Message-ID: <C18CF03D.120D%varvenne@genoway.com>

Le 24/11/06 18:08, ??David Huen?? <smh1008 at cam.ac.uk> a ?crit?:

> On Nov 24 2006, Benoit VARVENNE wrote:
> 
>> Hello,
>> 
>> I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>> the code put at the end of this mail.
>> 
>> I've tried this with a blastN query and there i got no trouble.
>> However, i've tried to do exactly the same thing with a BlastP query and
>> i've got the exception cited at the end of this mail.
>> 
>> I've verified and the two infiles (blastn/blastp) seem to have the same
>> structures (except that one is for prot so data are different). (Please
>> find them as attached if you're used to this).
>> 
>> Can someone help me ? I don't understand why it works in a case and not in
>> the other one ...
>> 
> I am uncertain whether BlastXMLFacade will actually support a protein
> sequence parse. It was originally developed to handle blastn. Anyone else
> tried it with blastp?
> 
> I'm offline till Sunday so I can't reply till then.
> 
> Regards,
> David Huen
> 

David,

As BlastLikeSAXParser seemed to support older versions of NCBI blastP (see
"http://www.biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book#S
tep_A_-_Create_an_application_that_sets_up_the_parser_and_does_the_parsing")
,  i'll be surprised if BlastXMLParserFacade does not.

However, i'll be very interested if someone's got any information.

Can't it be dtd problem ? If yes, can we update dtd sources ?

Cheers,
Beno?t.




From karl_harvey at hotmail.com  Thu Nov 23 20:40:44 2006
From: karl_harvey at hotmail.com (Karl Harvey)
Date: Thu, 23 Nov 2006 20:40:44 -0500
Subject: [Biojava-l] Query to blast.. on Internet.
Message-ID: <BAY135-F89E1D571DE6EDBB2D4AB795E10@phx.gbl>

An HTML attachment was scrubbed...
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From varvenne at genoway.com  Fri Nov 24 12:04:01 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 18:04:01 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN
	vs.	blastP)
In-Reply-To: <45672448.7060906@ebi.ac.uk>
Message-ID: <C18CE494.1204%varvenne@genoway.com>

Ooooo sorry i hadn't noticed that. Here is the traduction (home made...)

"org.xml.sax.SAXParseException: An XML declaration can only begin with an
entity"

The problem is that my two files (attached this time) don't seem to differ.

Have you got an xml validation tool to recommend me ?

Cheers,

Beno?t 

Le 24/11/06 17:56, ??Richard Holland?? <holland at ebi.ac.uk> a ?crit?:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Unfortunately the exception you are getting is in French and sadly my 1
> year of French lessons in school failed to make any impact on my ability
> to understand it. :)
> 
> But, my guess would be that something is wrong with the BlastP output,
> as the exception is an XML parser one and not a BioJava one. It's most
> likely that the BlastP report is not valid XML. Try running it through
> an XML validation tool to check.
> 
> cheers,
> Richard
> 
> Benoit VARVENNE wrote:
>> Hello,
>> 
>> I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>> the code put at the end of this mail.
>> 
>> I've tried this with a blastN query and there i got no trouble.
>> However, i've tried to do exactly the same thing with a BlastP query and
>> i've got the exception cited at the end of this mail.
>> 
>> I've verified and the two infiles (blastn/blastp) seem to have the same
>> structures (except that one is for prot so data are different). (Please find
>> them as attached if you're used to this).
>> 
>> Can someone help me ? I don't understand why it works in a case and not in
>> the other one ...
>> 
>> Thanks a lot,
>> Cheers,
>> 
>> Beno?t.
>> 
>> 
>> -------------------
>> My code :
>> -----
>> InputStream is = new FileInputStream(blastFile);
>> // blastFile is the xml file, output of my blast
>> 
>>       //make a BlastLikeSAXParser
>>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>>       //make the SAX event adapter that will pass events to a Handler.
>>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>> 
>>       //set the parsers SAX event adapter
>>       parser.setContentHandler(adapter);
>> 
>>       //The list to hold the SeqSimilaritySearchResults
>>       List results = new ArrayList();
>> 
>>       //create the SearchContentHandler that will build
>> SeqSimilaritySearchResults
>>       //in the results List
>>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>>           new DummySequenceDB("queries"), new
>> DummySequenceDBInstallation());
>> 
>>       //register builder with adapter
>>       adapter.setSearchContentHandler(builder);
>> 
>>       parser.parse(new InputSource(is)); // From here come the Exception
>> 
>> -------------------
>> 
>> 
>> -------------------
>> The exception :
>> ----
   org.xml.sax.SAXParseException: An XML declaration can only begin with an
entity
>>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3376)
>>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3364)
>>         at org.apache.crimson.parser.Parser2.maybePI(Parser2.java:1140)
>>         at org.apache.crimson.parser.Parser2.maybeMisc(Parser2.java:1266)
>>         at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:671)
>>         at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
>>         at 
>> org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
>>         at 
>> org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLPars
>> erFacade.java:180)
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> 
> iD8DBQFFZyRI4C5LeMEKA/QRAmQoAJoD1RjbKgqOsiRVW1rPBrYDcaAObgCglHYI
> 48o/exGfv1xSSnLzMMjPKxo=
> =tRNi
> -----END PGP SIGNATURE-----
> 

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From myammad at gmail.com  Mon Nov 27 09:41:39 2006
From: myammad at gmail.com (Ammad Ud Din)
Date: Mon, 27 Nov 2006 19:41:39 +0500
Subject: [Biojava-l] Looking forward for suggestions
Message-ID: <887d6f690611270641x3aeefb63pc537210cda242b30@mail.gmail.com>

Hi EveryBody,

i am a final year Undergraduate student of bioinformatics.I am currently
carrying a course in java so i want to contribute on open source
projects.can anybody suggest me what type of open source projects are going
on and how could i contribute in these....waiting for the
reply..............tc bestwishes

----Ammad

From mittalashr at yahoo.com  Mon Nov 27 23:54:35 2006
From: mittalashr at yahoo.com (ashish mittal)
Date: Mon, 27 Nov 2006 20:54:35 -0800 (PST)
Subject: [Biojava-l] Using REstriction Mapper
Message-ID: <20061128045435.9535.qmail@web52315.mail.yahoo.com>

Hi all, 

I am trying to use restriction mapper to search for a list of resctriction enzymes in a given sequence. Can some one send me some sample code that does the same. I tried following and this code gives exception: 
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException
        at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
        at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
        at org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:52)
        at org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:116)
        at org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:143)
        at org.biojava.bio.molbio.RestrictionMapper.annotate(RestrictionMapper.java:115)
        at seed.rs.rsTry.Searcher.search(Searcher.java:91)
        at seed.rs.rsTry.Searcher.main(Searcher.java:101)


CODE: 

public class Searcher {
    
    ThreadPool tPool = new ThreadPool() {
        public void addRequest(Runnable runnable) {
        }
        public void startThreads() {
        }
        public void stopThreads() {
        }
        public void waitForThreads() {
        }
    };
    
    RestrictionMapper mapper = new RestrictionMapper(tPool);
    
    
    
    /** Creates a new instance of Searcher */
    public Searcher() {
    }
    
    public void search(){
    
        
        try {
            RestrictionEnzyme res1 = new RestrictionEnzyme("enz1",DNATools.createDNA("agtg"),0,0);
            RestrictionEnzyme res2 = new RestrictionEnzyme("enz2",DNATools.createDNA("gatt"),0,0);
            RestrictionEnzyme res3 = new RestrictionEnzyme("enz3",DNATools.createDNA("gatg"),0,0);
            
            mapper.addEnzyme(res1);
            mapper.addEnzyme(res2);
            mapper.addEnzyme(res3);
            
        RestrictionEnzymeManager.register(res1,new TreeSet());
        RestrictionEnzymeManager.register(res2,new TreeSet());
        RestrictionEnzymeManager.register(res3,new TreeSet());
      
            
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        } catch (IllegalAlphabetException ex) {
            ex.printStackTrace();
        }
        
        //RestrictionEnzymeManager  resManager = new RestrictionEnzymeManager();
        
        try {
            
            Sequence dnaSeq = DNATools.createDNASequence("agtgattcgtatcgattcggatggtcattttt","my_dnaseq");
            Sequence newSeq = mapper.annotate(dnaSeq);
            
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        }
    }
    
    public static void main (String args[])
    {
        Searcher searcherObj = new Searcher();
        searcherObj.search();
    }
}



Thanks in Advance. 
Ashish 





 
____________________________________________________________________________________
Yahoo! Music Unlimited
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From mark.schreiber at novartis.com  Tue Nov 28 00:55:43 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 28 Nov 2006 13:55:43 +0800
Subject: [Biojava-l] Using REstriction Mapper
Message-ID: <OFAC89D389.5836515E-ON48257234.0020195B-48257234.00209171@ah.novartis.com>

Hi -

Looks like you forgot to include the bytecode.jar on your classpath. Take 
a look at these instructions : http://biojava.org/wiki/BioJava:GetStarted

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





ashish mittal <mittalashr at yahoo.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/28/2006 12:54 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using REstriction Mapper


Hi all, 

I am trying to use restriction mapper to search for a list of resctriction 
enzymes in a given sequence. Can some one send me some sample code that 
does the same. I tried following and this code gives exception: 
Exception in thread "main" java.lang.NoClassDefFoundError: 
org/biojava/utils/bytecode/CodeException
        at 
org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
        at 
org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
        at 
org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:52)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:116)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:143)
        at 
org.biojava.bio.molbio.RestrictionMapper.annotate(RestrictionMapper.java:115)
        at seed.rs.rsTry.Searcher.search(Searcher.java:91)
        at seed.rs.rsTry.Searcher.main(Searcher.java:101)


CODE: 

public class Searcher {
 
    ThreadPool tPool = new ThreadPool() {
        public void addRequest(Runnable runnable) {
        }
        public void startThreads() {
        }
        public void stopThreads() {
        }
        public void waitForThreads() {
        }
    };
 
    RestrictionMapper mapper = new RestrictionMapper(tPool);
 
 
 
    /** Creates a new instance of Searcher */
    public Searcher() {
    }
 
    public void search(){
 
 
        try {
            RestrictionEnzyme res1 = new 
RestrictionEnzyme("enz1",DNATools.createDNA("agtg"),0,0);
            RestrictionEnzyme res2 = new 
RestrictionEnzyme("enz2",DNATools.createDNA("gatt"),0,0);
            RestrictionEnzyme res3 = new 
RestrictionEnzyme("enz3",DNATools.createDNA("gatg"),0,0);
 
            mapper.addEnzyme(res1);
            mapper.addEnzyme(res2);
            mapper.addEnzyme(res3);
 
        RestrictionEnzymeManager.register(res1,new TreeSet());
        RestrictionEnzymeManager.register(res2,new TreeSet());
        RestrictionEnzymeManager.register(res3,new TreeSet());
 
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        } catch (IllegalAlphabetException ex) {
            ex.printStackTrace();
        }
 
        //RestrictionEnzymeManager  resManager = new 
RestrictionEnzymeManager();
 
        try {
 
            Sequence dnaSeq = 
DNATools.createDNASequence("agtgattcgtatcgattcggatggtcattttt","my_dnaseq");
            Sequence newSeq = mapper.annotate(dnaSeq);
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        }
    }
 
    public static void main (String args[])
    {
        Searcher searcherObj = new Searcher();
        searcherObj.search();
    }
}



Thanks in Advance. 
Ashish 





 
____________________________________________________________________________________
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_______________________________________________
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From kingsulaman at hotmail.com  Mon Nov 27 09:44:11 2006
From: kingsulaman at hotmail.com (Sulaman Nawaz)
Date: Mon, 27 Nov 2006 14:44:11 +0000
Subject: [Biojava-l] Willing to Contribute in  BioJava
In-Reply-To: <mailman.4952.1164431612.2429.biojava-l@lists.open-bio.org>
Message-ID: <BAY114-F29B02F0C2AD422EAB5AD43ADE60@phx.gbl>

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From g.etherington at imb.uq.edu.au  Wed Nov  1 08:39:24 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Wed, 1 Nov 2006 18:39:24 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <008901c6fd91$3c415e40$36776682@IMBPC.AD>

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                  
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham




From mark.schreiber at novartis.com  Wed Nov  1 09:53:33 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 1 Nov 2006 17:53:33 +0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <OFC6118B66.DA2E4C19-ON48257219.0036166A-48257219.0036577A@ah.novartis.com>

Hi -

It may not like the command line having spaces in the path. Try installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o 
blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From ayates at ebi.ac.uk  Wed Nov  1 10:00:23 2006
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 01 Nov 2006 10:00:23 +0000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
References: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
Message-ID: <45487037.1090205@ebi.ac.uk>

Hi Graham,

Your problem is probably that you're running this via sh which windows 
does not have. Even if you are running this via cygwin as far as I'm 
aware the JVM will use a normal windows shell/cmd. My advice would be to 
drop the sh and just try running the command as normal and see how that 
goes.

Failing that BioJava has org.biojava.utils.ExecRunner which is quite 
good and takes into account a few lessons learned from this article on 
using runtime:

http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html

Hope that helps,

Andy Yates

Graham Etherington wrote:
> Hi,
> I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
> searches on a local BLAST database. Even though I'm not using BioJava
> (intend to use it to parse the results), I thought this formum would be the
> best place to ask for help.
> Even when I hard code a good BLAST search I keep getting the same error when
> I run my search, namely: 
> " java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
> Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
> test.fas -o blast.out" error=2 "
> 
> The pertinent bits of code I'm using are...
> 
> String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
> 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";
> 
> ............
> 
> 
> Runtime r = Runtime.getRuntime ();
> Process runBlast = r.exec (new String[] {"sh","-c",cmd});
>                   
> runBlast.waitFor ();
> out.println ("Waiting for result");
> 
> //Write the results
> BufferedReader br = new BufferedReader (new FileReader (output));
> String line = null;
> String results = "";
> while ( (line = br.readLine ()) != null )
> results = results.concat ("/n" + line);
> 
> .............
> 
> I'm not sure why it give me an IOException. I've checked that the file input
> file exists and that all the paths are correct.
> Any ideas?
> 
> Many thanks,
> Graham
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From Peter.Ng at bccdc.ca  Wed Nov  1 19:40:53 2006
From: Peter.Ng at bccdc.ca (Ng, Peter)
Date: Wed, 1 Nov 2006 11:40:53 -0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB91E@srvex04.phsabc.ehcnet.ca>

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From g.etherington at imb.uq.edu.au  Wed Nov  1 21:21:53 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Thu, 2 Nov 2006 07:21:53 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB91E@srvex04.phsabc.ehcnet.ca>
Message-ID: <000301c6fdfb$c0c82a80$36776682@IMBPC.AD>

Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the process
represented by this Process object has terminated. I've used it in my code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From Peter.Ng at bccdc.ca  Wed Nov  1 21:52:42 2006
From: Peter.Ng at bccdc.ca (Ng, Peter)
Date: Wed, 1 Nov 2006 13:52:42 -0800
Subject: [Biojava-l] Using Java to create BLAST searches
Message-ID: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB925@srvex04.phsabc.ehcnet.ca>

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From g.etherington at imb.uq.edu.au  Wed Nov  1 22:16:38 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Thu, 2 Nov 2006 08:16:38 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <C04143BBDB37E24E820B5B6CE3EE1C6A061CB925@srvex04.phsabc.ehcnet.ca>
Message-ID: <001a01c6fe03$6688b4b0$36776682@IMBPC.AD>

Peter,
The method is explained quite well at:

http://java.sun.com/j2se/1.3/docs/api/java/lang/Process.html#waitFor()

Not sure about your threading question, but I'm presuming that the Process
produces and exit value. By convention, 0 indicates normal termination.

Hope this helps a little.
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 7:53 AM
To: Graham Etherington; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From michael.tran at acpfg.com.au  Thu Nov  2 05:43:09 2006
From: michael.tran at acpfg.com.au (Michael Tran)
Date: Thu, 2 Nov 2006 16:13:09 +1030
Subject: [Biojava-l] Can BioJava do Multiple Alignments?
References: <mailman.878.1162373982.2429.biojava-l@lists.open-bio.org>
Message-ID: <D3C986810EBCCE488A9DCA95463794F146F416@kaneda.acpfg.local>

<http://www.acpfg.com.au/profiles/Michael_Tran.html> 
Hi,
 
I know that BioJava 1.5 can do pairwise alignments using algorithms like SmithWaterman and NeedlemanWunch. But can BioJava do multiple alignments like the algorthm used for ClustalW? I have also checked the HMM classes, but they appear to only do pairwise alignments.
 
Michael

________________________________

From: biojava-l-bounces at lists.open-bio.org on behalf of biojava-l-request at lists.open-bio.org
Sent: Wed 1/11/2006 8:09 PM
To: biojava-l at lists.open-bio.org
Subject: Biojava-l Digest, Vol 47, Issue 1



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Today's Topics:

   1. Re: can BioJava do alignment ? (Ramon Medrado)
   2. Re: can BioJava do alignment ? (mark.schreiber at novartis.com)
   3. More extensive Bioperl-run 1.5.2RC2 tests (Nathan S. Haigh)
   4. Re: More extensive Bioperl-run 1.5.2RC2 tests (Nathan Haigh)
   5. fasta description line (ThorstenInAnger)
   6. pK values (Gerster  Sarah)
   7. Re: fasta description line (Mark Schreiber)
   8. Re: pK values (Mark Schreiber)
   9. Re: pK values (David Huen)
  10. Using Java to create BLAST searches (Graham Etherington)


----------------------------------------------------------------------

Message: 1
Date: Thu, 19 Oct 2006 14:45:24 -0300
From: "Ramon Medrado" <rmedrado at gmail.com>
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <37ba4b050610191045q30a6282bjce052e31e1463cea at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 2
Date: Fri, 20 Oct 2006 09:57:09 +0800
From: mark.schreiber at novartis.com
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: "Ramon Medrado" <rmedrado at gmail.com>, CARMELK at il.ibm.com
Cc: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <OFED374D90.C3E37FD4-ON4825720D.000A9274-4825720D.000AB9F8 at ah.novartis.com>
       
Content-Type: text/plain; charset="us-ascii"

Hi -

You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise).
This is actually the most flexible way to do it.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM


        To:     biojava <Biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] can BioJava do alignment ?


Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





------------------------------

Message: 3
Date: Wed, 25 Oct 2006 13:54:26 +0000
From: "Nathan S. Haigh" <n.haigh at sheffield.ac.uk>
Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <453F6C92.6020207 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1


I have recently installed some more software for which there are
bioperl-run tests and run the test suite with several versions of the
software I could find. I've added info to
http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
fails in any of the versions I tested I've noted them together with
versions that were ok (if any).

There maybe another 6 or so programs I'm trying to get hold of to run
further tests - I'll update when I get them.
Nath


------------------------------

Message: 4
Date: Thu, 26 Oct 2006 09:46:13 +0100
From: Nathan Haigh <n.haigh at sheffield.ac.uk>
Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <454075D5.2030005 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

Nathan S. Haigh wrote:
> I have recently installed some more software for which there are
> bioperl-run tests and run the test suite with several versions of the
> software I could find. I've added info to
> http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
> fails in any of the versions I tested I've noted them together with
> versions that were ok (if any).
>
> There maybe another 6 or so programs I'm trying to get hold of to run
> further tests - I'll update when I get them.
> Nath
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>  

My aplogies, this should have gone to the Bioperl mailing list! :o)


------------------------------

Message: 5
Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT)
From: ThorstenInAnger <henrich at embl.de>
Subject: [Biojava-l] fasta description line
To: biojava-l at lists.open-bio.org
Message-ID: <6950970.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi,

I want to do something very simple:

- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)

this is my code:
                                rs = stmt.executeQuery(query);
                            Feature.Template templ = new Feature.Template();
                       
                            //fill in the template
                            Annotation an = new SimpleAnnotation();
                            templ.location = Location.empty;
                               
                                while (rs.next()) {
                                        mepdId = rs.getInt(1);
                                        mepdName = rs.getString(2);
                                        seq = rs.getString(3);
                                        seqObj =  DNATools.createDNASequence(seq, mepdName);
                                    an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
                                    templ.annotation = an;
                                        seqObj.createFeature(templ);
                                        SeqIOTools.writeFasta(fastaFos, seqObj);
                                        //db.addSequence(seqObj);
                                }

It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?

Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.

Cheers,

Thorsten

--
View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
Sent from the BioJava mailing list archive at Nabble.com.



------------------------------

Message: 6
Date: Tue, 31 Oct 2006 09:04:33 +0100
From: "Gerster  Sarah" <sgerster at student.ethz.ch>
Subject: [Biojava-l] pK values
To: <biojava-l at lists.open-bio.org>
Message-ID: <E9D421793368D44FB81D3C438D300574BC729D at EX5.d.ethz.ch>
Content-Type: text/plain;       charset="iso-8859-1"

Hi!

I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use.

And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own?

Cheers

Sarah



------------------------------

Message: 7
Date: Tue, 31 Oct 2006 17:37:24 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] fasta description line
To: ThorstenInAnger <henrich at embl.de>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310137u68700b06se364f99da69feb47 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

If you are using biojava 1.5 beta (recommended) you should use
RichSequence.IOTools to write the fasta (strongly recommended).

With the new org.biojavax.bio.seq.io.FastaFormat object the
description line is constructed from:

richSequence.getIdentifier()
richSequence.getNamespace().getName();
richSequence.getAccession()
richSequence.getVersion()
richSequence.getName()
richSequence.getDescription()

- Mark


On 10/23/06, ThorstenInAnger <henrich at embl.de> wrote:
>
> Hi,
>
> I want to do something very simple:
>
> - get id and sequence from a database
> - create a sequence object
> - write it out as fasta format file (with a defined description line)
>
> this is my code:
>                                 rs = stmt.executeQuery(query);
>                             Feature.Template templ = new Feature.Template();
>
>                             //fill in the template
>                             Annotation an = new SimpleAnnotation();
>                             templ.location = Location.empty;
>
>                                 while (rs.next()) {
>                                         mepdId = rs.getInt(1);
>                                         mepdName = rs.getString(2);
>                                         seq = rs.getString(3);
>                                         seqObj =  DNATools.createDNASequence(seq, mepdName);
>                                     an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
> here");
>                                     templ.annotation = an;
>                                         seqObj.createFeature(templ);
>                                         SeqIOTools.writeFasta(fastaFos, seqObj);
>                                         //db.addSequence(seqObj);
>                                 }
>
> It works fine, but there is no description line in the resulting file!
> How can I change the fasta description line?
>
> Also I am using deprecated methods, but could not find out what to use
> instead:
> FastaFormat.PROPERTY_DESCRIPTIONLINE
> SeqIOTools.writeFasta
> All tutorials I found are using the deprecated.
>
> Cheers,
>
> Thorsten
>
> --
> View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
> Sent from the BioJava mailing list archive at Nabble.com.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 8
Date: Tue, 31 Oct 2006 17:27:29 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] pK values
To: "Gerster Sarah" <sgerster at student.ethz.ch>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310127h75010e56ne31e188294e23803 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

The values are calculated using the SymbolPropertyTable returned by
ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);

This table gets it's values from the resource file
org/biojava/bio/symbol/ResidueProperties.xml

The pK values were added by david huen (I think).

To read XML sequence files try one of the methods in
RichSequence.IOTools from biojava 1.5 beta.

- Mark

On 10/31/06, Gerster  Sarah <sgerster at student.ethz.ch> wrote:
> Hi!
>
> I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use.
>
> And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 9
Date: 31 Oct 2006 12:21:43 +0000
From: David Huen <smh1008 at cam.ac.uk>
Subject: Re: [Biojava-l] pK values
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-l at lists.open-bio.org
Message-ID: <Prayer.1.0.18.0610311221430.32704 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

On Oct 31 2006, Mark Schreiber wrote:

>Hi -
>
>The values are calculated using the SymbolPropertyTable returned by
>ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
>
>This table gets it's values from the resource file
>org/biojava/bio/symbol/ResidueProperties.xml
>
>The pK values were added by david huen (I think).
>

I used the same pK values as those used by GCG to maintian
cross-compability.

Regards,
David


------------------------------

Message: 10
Date: Wed, 1 Nov 2006 18:39:24 +1000
From: "Graham Etherington" <g.etherington at imb.uq.edu.au>
Subject: [Biojava-l] Using Java to create BLAST searches
To: <biojava-l at lists.open-bio.org>
Message-ID: <008901c6fd91$3c415e40$36776682 at IMBPC.AD>
Content-Type: text/plain;       charset="us-ascii"

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely:
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham




------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


End of Biojava-l Digest, Vol 47, Issue 1
****************************************





From mark.schreiber at novartis.com  Thu Nov  2 06:03:13 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 2 Nov 2006 14:03:13 +0800
Subject: [Biojava-l] Can BioJava do Multiple Alignments?
Message-ID: <OFD4AAB495.DA47C130-ON4825721A.00211B06-4825721A.0021412A@ah.novartis.com>

In short -- No.

The best solution is probably to call ClustalW in a process. You could of 
course reimplement the algorithm in biojava if you wish. The DP library 
could also be extended for MSA but this would be hard work.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Michael Tran" <michael.tran at acpfg.com.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/02/2006 01:43 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Can BioJava do Multiple Alignments?


<http://www.acpfg.com.au/profiles/Michael_Tran.html> 
Hi,
 
I know that BioJava 1.5 can do pairwise alignments using algorithms like 
SmithWaterman and NeedlemanWunch. But can BioJava do multiple alignments 
like the algorthm used for ClustalW? I have also checked the HMM classes, 
but they appear to only do pairwise alignments.
 
Michael

________________________________

From: biojava-l-bounces at lists.open-bio.org on behalf of 
biojava-l-request at lists.open-bio.org
Sent: Wed 1/11/2006 8:09 PM
To: biojava-l at lists.open-bio.org
Subject: Biojava-l Digest, Vol 47, Issue 1



Send Biojava-l mailing list submissions to
        biojava-l at lists.open-bio.org

To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Biojava-l digest..."


Today's Topics:

   1. Re: can BioJava do alignment ? (Ramon Medrado)
   2. Re: can BioJava do alignment ? (mark.schreiber at novartis.com)
   3. More extensive Bioperl-run 1.5.2RC2 tests (Nathan S. Haigh)
   4. Re: More extensive Bioperl-run 1.5.2RC2 tests (Nathan Haigh)
   5. fasta description line (ThorstenInAnger)
   6. pK values (Gerster  Sarah)
   7. Re: fasta description line (Mark Schreiber)
   8. Re: pK values (Mark Schreiber)
   9. Re: pK values (David Huen)
  10. Using Java to create BLAST searches (Graham Etherington)


----------------------------------------------------------------------

Message: 1
Date: Thu, 19 Oct 2006 14:45:24 -0300
From: "Ramon Medrado" <rmedrado at gmail.com>
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
        <37ba4b050610191045q30a6282bjce052e31e1463cea at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it 
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g., 
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not 
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 2
Date: Fri, 20 Oct 2006 09:57:09 +0800
From: mark.schreiber at novartis.com
Subject: Re: [Biojava-l] can BioJava do alignment ?
To: "Ramon Medrado" <rmedrado at gmail.com>, CARMELK at il.ibm.com
Cc: biojava <Biojava-l at lists.open-bio.org>
Message-ID:
 
<OFED374D90.C3E37FD4-ON4825720D.000A9274-4825720D.000AB9F8 at ah.novartis.com>
 
Content-Type: text/plain; charset="us-ascii"

Hi -

You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See
the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise).
This is actually the most flexible way to do it.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ramon Medrado" <rmedrado at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
10/20/2006 01:45 AM


        To:     biojava <Biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] can BioJava do alignment ?


Hi,

The information is true. Biojava 1.5  has the main algorithms of alignment
as NeedlemanWunch, SmithWaterman and other implementations that are
encapsulated on package org.biojava.bio.alignment
All source is disponible in this link :
http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz

and the jar file is disponible in:
http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar

and the javadoc:
http://www.biojava.org/download/bj15b/doc/doc.tar.gz

I wait to have helped

--
Ramon
Undergraduate Student of Computer Science
Universidade Estadual de Santa Cruz - Brasil



2006/10/19, Carmel Kent <CARMELK at il.ibm.com>:
>
>
> Hello,
>
> I'm interested in a Java package for sequence alignment.
> I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it
can
> only create objects that are representations of alignments generated by
> third-party software.
>
> I had an impression that      BioJava 1.5 can do alignment itself (e.g.,
I
> saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class
> named org.biojava.bio.alignment.NeedlemanWunch)
>
> I have two questions:
>
>    is this true ? I mean, does BioJava 1.5 contain the alignment
> algorithm,
>    itself ?

   if it does, I downloaded the CVS view of BioJava 1.5, but could not
find

>    any javadocs or the alignment package source. Where can I find it ?
>
>
> Thanks very much,
>
>
> Carmel Kent
> Research Staff Member
> Healthcare I/T Research
> IBM Research Laboratory in Haifa
> Tel. +972-4-8281059
> Email: carmelk at il.ibm.com
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





------------------------------

Message: 3
Date: Wed, 25 Oct 2006 13:54:26 +0000
From: "Nathan S. Haigh" <n.haigh at sheffield.ac.uk>
Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <453F6C92.6020207 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1


I have recently installed some more software for which there are
bioperl-run tests and run the test suite with several versions of the
software I could find. I've added info to
http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
fails in any of the versions I tested I've noted them together with
versions that were ok (if any).

There maybe another 6 or so programs I'm trying to get hold of to run
further tests - I'll update when I get them.
Nath


------------------------------

Message: 4
Date: Thu, 26 Oct 2006 09:46:13 +0100
From: Nathan Haigh <n.haigh at sheffield.ac.uk>
Subject: Re: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests
To: biojava-l at lists.open-bio.org
Message-ID: <454075D5.2030005 at sheffield.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1

Nathan S. Haigh wrote:
> I have recently installed some more software for which there are
> bioperl-run tests and run the test suite with several versions of the
> software I could find. I've added info to
> http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any
> fails in any of the versions I tested I've noted them together with
> versions that were ok (if any).
>
> There maybe another 6 or so programs I'm trying to get hold of to run
> further tests - I'll update when I get them.
> Nath
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

My aplogies, this should have gone to the Bioperl mailing list! :o)


------------------------------

Message: 5
Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT)
From: ThorstenInAnger <henrich at embl.de>
Subject: [Biojava-l] fasta description line
To: biojava-l at lists.open-bio.org
Message-ID: <6950970.post at talk.nabble.com>
Content-Type: text/plain; charset=us-ascii


Hi,

I want to do something very simple:

- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)

this is my code:
                                rs = stmt.executeQuery(query);
                            Feature.Template templ = new 
Feature.Template();
 
                            //fill in the template
                            Annotation an = new SimpleAnnotation();
                            templ.location = Location.empty;
 
                                while (rs.next()) {
                                        mepdId = rs.getInt(1);
                                        mepdName = rs.getString(2);
                                        seq = rs.getString(3);
                                        seqObj = 
DNATools.createDNASequence(seq, mepdName);
 an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
                                    templ.annotation = an;
                                        seqObj.createFeature(templ);
                                        SeqIOTools.writeFasta(fastaFos, 
seqObj);
                                        //db.addSequence(seqObj);
                                }

It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?

Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.

Cheers,

Thorsten

--
View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
Sent from the BioJava mailing list archive at Nabble.com.



------------------------------

Message: 6
Date: Tue, 31 Oct 2006 09:04:33 +0100
From: "Gerster  Sarah" <sgerster at student.ethz.ch>
Subject: [Biojava-l] pK values
To: <biojava-l at lists.open-bio.org>
Message-ID: <E9D421793368D44FB81D3C438D300574BC729D at EX5.d.ethz.ch>
Content-Type: text/plain;       charset="iso-8859-1"

Hi!

I want to compute the pI of some sequences. I looked at 
"IsoelectricPointCalc.java". Where do the values for the pks come from? 
are they defined as constants somewhere? I couldn't find them... I wanted 
to see if the values are the same ones than the ones that I am supposed to 
use.

And another question> reading in sequences from an xml file... Is there 
something that I can use, or do I have to write it on my own?

Cheers

Sarah



------------------------------

Message: 7
Date: Tue, 31 Oct 2006 17:37:24 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] fasta description line
To: ThorstenInAnger <henrich at embl.de>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310137u68700b06se364f99da69feb47 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

If you are using biojava 1.5 beta (recommended) you should use
RichSequence.IOTools to write the fasta (strongly recommended).

With the new org.biojavax.bio.seq.io.FastaFormat object the
description line is constructed from:

richSequence.getIdentifier()
richSequence.getNamespace().getName();
richSequence.getAccession()
richSequence.getVersion()
richSequence.getName()
richSequence.getDescription()

- Mark


On 10/23/06, ThorstenInAnger <henrich at embl.de> wrote:
>
> Hi,
>
> I want to do something very simple:
>
> - get id and sequence from a database
> - create a sequence object
> - write it out as fasta format file (with a defined description line)
>
> this is my code:
>                                 rs = stmt.executeQuery(query);
>                             Feature.Template templ = new 
Feature.Template();
>
>                             //fill in the template
>                             Annotation an = new SimpleAnnotation();
>                             templ.location = Location.empty;
>
>                                 while (rs.next()) {
>                                         mepdId = rs.getInt(1);
>                                         mepdName = rs.getString(2);
>                                         seq = rs.getString(3);
>                                         seqObj = 
DNATools.createDNASequence(seq, mepdName);
> an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
> here");
>                                     templ.annotation = an;
>                                         seqObj.createFeature(templ);
>                                         SeqIOTools.writeFasta(fastaFos, 
seqObj);
>                                         //db.addSequence(seqObj);
>                                 }
>
> It works fine, but there is no description line in the resulting file!
> How can I change the fasta description line?
>
> Also I am using deprecated methods, but could not find out what to use
> instead:
> FastaFormat.PROPERTY_DESCRIPTIONLINE
> SeqIOTools.writeFasta
> All tutorials I found are using the deprecated.
>
> Cheers,
>
> Thorsten
>
> --
> View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970
> Sent from the BioJava mailing list archive at Nabble.com.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 8
Date: Tue, 31 Oct 2006 17:27:29 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-l] pK values
To: "Gerster Sarah" <sgerster at student.ethz.ch>
Cc: biojava-l at lists.open-bio.org
Message-ID:
        <93b45ca50610310127h75010e56ne31e188294e23803 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi -

The values are calculated using the SymbolPropertyTable returned by
ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);

This table gets it's values from the resource file
org/biojava/bio/symbol/ResidueProperties.xml

The pK values were added by david huen (I think).

To read XML sequence files try one of the methods in
RichSequence.IOTools from biojava 1.5 beta.

- Mark

On 10/31/06, Gerster  Sarah <sgerster at student.ethz.ch> wrote:
> Hi!
>
> I want to compute the pI of some sequences. I looked at 
"IsoelectricPointCalc.java". Where do the values for the pks come from? 
are they defined as constants somewhere? I couldn't find them... I wanted 
to see if the values are the same ones than the ones that I am supposed to 
use.
>
> And another question> reading in sequences from an xml file... Is there 
something that I can use, or do I have to write it on my own?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


------------------------------

Message: 9
Date: 31 Oct 2006 12:21:43 +0000
From: David Huen <smh1008 at cam.ac.uk>
Subject: Re: [Biojava-l] pK values
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-l at lists.open-bio.org
Message-ID: <Prayer.1.0.18.0610311221430.32704 at hermes-1.csi.cam.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

On Oct 31 2006, Mark Schreiber wrote:

>Hi -
>
>The values are calculated using the SymbolPropertyTable returned by
>ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK);
>
>This table gets it's values from the resource file
>org/biojava/bio/symbol/ResidueProperties.xml
>
>The pK values were added by david huen (I think).
>

I used the same pK values as those used by GCG to maintian
cross-compability.

Regards,
David


------------------------------

Message: 10
Date: Wed, 1 Nov 2006 18:39:24 +1000
From: "Graham Etherington" <g.etherington at imb.uq.edu.au>
Subject: [Biojava-l] Using Java to create BLAST searches
To: <biojava-l at lists.open-bio.org>
Message-ID: <008901c6fd91$3c415e40$36776682 at IMBPC.AD>
Content-Type: text/plain;       charset="us-ascii"

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely:
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham




------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


End of Biojava-l Digest, Vol 47, Issue 1
****************************************



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From cezard at nokad-technology.com  Thu Nov  2 08:41:02 2006
From: cezard at nokad-technology.com (=?iso-8859-1?Q?CEZARD_Timoth=E9e?=)
Date: Thu, 2 Nov 2006 09:41:02 +0100
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <001a01c6fe03$6688b4b0$36776682@IMBPC.AD>
Message-ID: <20061102084307.5F9EB75D8E@smtp2-g19.free.fr>

Hi everyone,

I've worked a bit on that point and want to share my view.

When you launch a blast via the Runtime exec command it creates (and
launches) a new thread outside the JVM. 
The Process object allows you to monitor and  wait for the end of this
thread.
I've observed that for obscure reason sometime the thread never finish.
In that case you have to clear the InputStream and the ErrorStream of the
process.

Last point I've worked on is how to notice the GUI of the end of the
process. For that I've used the SwingWorker object and it worked fine.
http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html


Hope this helps someone.


CEZARD Timoth?e Ms
bioinformatics Manager 
NOKAD SA
4 rue Pierre Fontaine 
91058 EVRY cedex
Tel : 01.60.87.89.90
Fax : 01.60.87.89.99
www.nokad-technology.com


-----Message d'origine-----
De?: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] De la part de Graham
Etherington
Envoy??: mercredi 1 novembre 2006 23:17
??: 'Ng, Peter'; mark.schreiber at novartis.com
Cc?: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Objet?: Re: [Biojava-l] Using Java to create BLAST searches

Peter,
The method is explained quite well at:

http://java.sun.com/j2se/1.3/docs/api/java/lang/Process.html#waitFor()

Not sure about your threading question, but I'm presuming that the Process
produces and exit value. By convention, 0 indicates normal termination.

Hope this helps a little.
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 7:53 AM
To: Graham Etherington; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Graham,
thanks for the info!  I have two instances of Runtime.getRuntime().exec
going, should I be putting these into two threads?  also, when does java
see the process actually being finished?  how does java know when blastn
is done at the unix or window level?

thanks,
peter

-----Original Message-----
From: Graham Etherington [mailto:g.etherington at imb.uq.edu.au] 
Sent: November 1, 2006 1:22 PM
To: Ng, Peter; mark.schreiber at novartis.com
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches


Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the
process
represented by this Process object has terminated. I've used it in my
code
that I posted and have snippeted it below.

Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
runBlast.waitFor ();

Hope this is of some help.
Cheers,
Graham


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org



-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches


Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

 
        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches


Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create 
BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be 
the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error 
when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt
-i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
 
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file 
input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From zagato.gekko at gmail.com  Thu Nov  2 21:37:58 2006
From: zagato.gekko at gmail.com (Alan Acosta)
Date: Thu, 2 Nov 2006 16:37:58 -0500
Subject: [Biojava-l] Reading sequence identifier from file in FASTA format
Message-ID: <98028b00611021337n4b7970d2q76f7a045d634f6c2@mail.gmail.com>

Hello Everybody, this is my first write to the list, i'm a student of
computer science, and a really newbie into this subjects, so i'm
experimenting with BioJava against BioPerl...

My problem is that i'm trying to read FASTA file with
///////////////////
        BufferedReader input = new BufferedReader( new
FileReader("NC_008009.fna") );
        RichSequenceIterator seqIter = RichSequence.IOTools.readFastaDNA(
input, RichObjectFactory.getDefaultNamespace() );
        RichSequence rseq = null;

        if( seqIter.hasNext() )
        {
            rseq = seqIter.nextRichSequence();
            System.out.println("Identifier: "+rseq.getIdentifier() );
            System.out.println("Description: "+rseq.getDescription() );
            System.out.println("SubList: "+rseq.subList(10, 20).seqString()
);
        }
///////////////////
but i'm getting a "identifier: null" into the answer when it had to be a
"Identifier: 94967031", the description and sublist works good... in (
http://biojava.org/wiki/BioJava:BioJavaXDocs#Reading) says that:
>gi|<identifier>|<namespace>|<accession>.<version>|<name> <description>
identifier will be read it with setIdentifier() and will available through
getIdentifier() but i get a null.

Then... this file is really in FASTA format ? or i'm doing into the wrong
way this ?

The test file is:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Acidobacteria_bacterium_Ellin345/NC_008009.fna

And the header is:
>gi|94967031|ref|NC_008009.1| Acidobacteria bacterium Ellin345, complete
genome
CCGTGTGTTGCGCGGCCAGATGAGAAATTTCTATGTCCCTCTCGACCACGACTCCACCAGCTCCGAACCC

Where i can find a newbie tutorial for starter task into BioJava ?

I appreciate any help... thanks.


Farewell
Alan Acosta
Cali - Colombia


From g.etherington at imb.uq.edu.au  Fri Nov  3 00:23:09 2006
From: g.etherington at imb.uq.edu.au (Graham Etherington)
Date: Fri, 3 Nov 2006 10:23:09 +1000
Subject: [Biojava-l] Using Java to create BLAST searches
In-Reply-To: <008901c6fd91$3c415e40$36776682@IMBPC.AD>
Message-ID: <000801c6fede$3d540870$36776682@IMBPC.AD>

Hi,
First of all, thanks for the replies and help that everyone sent for my
BLAST query (see below). I figured out what the problems were and thought I
should post the solutions to the forum.
Firstly, as pointed out, when running on Windows the 'sh' and '-c' should be
taken out.
Process runBlast = r.exec (new String[] {cmd});

Secondly, I moved the location of blast to C:/blast/bin/, as to have no
spaces in the path (I didn't try this when everything worked to see if it
had an affect, so I don't know how essential this is)

Thirdly, (and this was one of those real killers that have you kicking
yourself once you realise what the problem was), the location of the
database (ecoli.nt in this case) has to be explicitly set, so
"C:/blast/bin/ecoli.nt"

In the end, I used the org.biojava.utils.ExecRunner 
This handled the query really well and one of the best features is actually
the error reporting. It told me that it couldn't find the ecoli.nt database
which java.lang.Process did not.
My final code looked like this:

String cmd = "C:/blast/bin/blastall -p blastn -d C:/blast/bin/ecoli.nt -i
test.fas -o blast.out";
org.biojava.utils.ExecRunner runner = new org.biojava.utils.ExecRunner ();
runner.exec (cmd);
out.println (runner.getErrString ());


My task for today is working out the best way to display the output/output
file to the current jsp page.
Again, thanks for your help. 


Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia
-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Graham
Etherington
Sent: Wednesday, 1 November 2006 6:39 PM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Using Java to create BLAST searches

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                  
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l




From johnson.biotech at gmail.com  Fri Nov  3 22:31:00 2006
From: johnson.biotech at gmail.com (Seth Johnson)
Date: Fri, 3 Nov 2006 17:31:00 -0500
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access to
	primary keys
Message-ID: <b99962880611031431l17aca93x99bd7840856dc15c@mail.gmail.com>

Hello guys,

I've setup a BioSQL to hold sequences of interest parsed from NCBI
genbank release.  I also have another proprietary schema that holds
experimental and alignment data.  I would like to connect the
proprietary schema to BioSQL one using Hibernate persistence, so that
objects from my database would contain linkages to sequence data in
biosql.  Wiki mentions that one need change "only the mapping files
that tell Hibernate how to translate between objects and tables."  Can
anyone elaborate on that topic a little or point me to a tutorial or
some other place that discusses the concept?

-- 
Best Regards,


Seth Johnson
Senior Bioinformatics Associate


From varvenne at genoway.com  Mon Nov  6 12:57:24 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 06 Nov 2006 13:57:24 +0100
Subject: [Biojava-l] Parsing blast results
Message-ID: <C174EFC4.F68%varvenne@genoway.com>

Hello,

I'm a new user of biojava and i'm trying to use it to parse blast results
(against NCBI nr database). I've tried to do so using biojava1.4 and
biojava1.5-beta but none of these seem to support the latest Blast version.

I'd be very greatful to you if anyone could help me with that...

Thanks,
Best regards,

Benoit Varvenne,
Bioinformatics pearson in charge,
Genoway Lyon (France).
 



From varvenne at genoway.com  Mon Nov  6 13:27:32 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 06 Nov 2006 14:27:32 +0100
Subject: [Biojava-l] Parsing blast results
In-Reply-To: <C174EFC4.F68%varvenne@genoway.com>
Message-ID: <C174F6D4.F6E%varvenne@genoway.com>

I've already found the answer to my question which seems to work in previous
archives (?June 2006).

This archive suggests to replace :
BlastLikeSAXParser parser = new BlastLikeSAXParser();

By :
BlastXMLParserFacade parser = new BlastXMLParserFacade();


And this seems to work well.

So sorry for having posted a bit quickly.

Regards,

Beno?t Varvenne,
Bioinformatics pearson in charge,
Genoway Lyon (France).

Le 6/11/06 13:57, ??Benoit VARVENNE?? <varvenne at genoway.com> a ?crit?:

> Hello,
> 
> I'm a new user of biojava and i'm trying to use it to parse blast results
> (against NCBI nr database). I've tried to do so using biojava1.4 and
> biojava1.5-beta but none of these seem to support the latest Blast version.
> 
> I'd be very greatful to you if anyone could help me with that...
> 
> Thanks,
> Best regards,
> 
> Benoit Varvenne,
> Bioinformatics pearson in charge,
> Genoway Lyon (France).
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 




From johnson.biotech at gmail.com  Tue Nov  7 04:59:01 2006
From: johnson.biotech at gmail.com (Seth Johnson)
Date: Mon, 6 Nov 2006 23:59:01 -0500
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access
	to primary keys
In-Reply-To: <454F07D5.2040001@ebi.ac.uk>
References: <b99962880611031431l17aca93x99bd7840856dc15c@mail.gmail.com>
	<454F07D5.2040001@ebi.ac.uk>
Message-ID: <b99962880611062059r4a0bae8ar3213af5aa7452998@mail.gmail.com>

Thank you Richard.  I am using NetBeans 5.5 and JDK 5.0 that
implements mapping metadata (EJB 3.0) instead of .hbm.xml files.   I
read up on Hibernate from you links and I think that the easiest
solution would be to use RichSequence BioJavaX object as an embeddable
object in my proprietary 'alignment' class.

Basically, my goal is to have access to RichSequence object when I
instantiate 'alignment' object from my 'alignment' table.  That table
contains a column with primary key of the bioentry that was used to
produce that alignment.  Since biosql is in different schema, I don't
believe that cross schema foreign keys are possible in mySQL.  Do you
think that this  is a right strategy?

Seth


On 11/6/06, Richard Holland <holland at ebi.ac.uk> wrote:
>
> If your proprietary database has a similar design to BioSQL, or can
> easily be mapped on an approximately 1:1 basis to the existing BioJavaX
> object model, then all you need to do is edit the .hbm.xml files and
> look for references to table names and column names. Remove any tables
> and columns that don't exist in your schema (including removing the
> files if this leaves them empty), and edit the remaining ones so that
> the table and column names match.
>
> If your new schema contains tables that do not map to existing BioJavaX
> objects, then you'll need to create Java objects for those as well as
> the appropriate mapping files. The easiest way to do this is to
> copy-and-paste both an existing BioJavaX object and the related .hbm.xml
> file - eg. SimpleCrossRef.java and CrossRef.hxm.xml.
>
> Hibernate is best explained through its own documentation at
> http://www.hibernate.org/ . The 'getting started' tutorial they provide
> (here:
> http://www.hibernate.org/hib_docs/v3/reference/en/html/tutorial.html )
> is a good starting point.
>
> cheers,
> Richard
>
>
> Seth Johnson wrote:
> > Hello guys,
> >
> > I've setup a BioSQL to hold sequences of interest parsed from NCBI
> > genbank release.  I also have another proprietary schema that holds
> > experimental and alignment data.  I would like to connect the
> > proprietary schema to BioSQL one using Hibernate persistence, so that
> > objects from my database would contain linkages to sequence data in
> > biosql.  Wiki mentions that one need change "only the mapping files
> > that tell Hibernate how to translate between objects and tables."  Can
> > anyone elaborate on that topic a little or point me to a tutorial or
> > some other place that discusses the concept?
> >


From mark.schreiber at novartis.com  Tue Nov  7 08:57:58 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 7 Nov 2006 16:57:58 +0800
Subject: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence
 access	to primary keys
Message-ID: <OFA590830C.937721F7-ON4825721F.0030ABEF-4825721F.00314200@ah.novartis.com>

Hi -

If you are using the JDK5 persistence API you either do your mappings as 
annotations or vendor neutral xml mappings. The vendor you choose for the 
actual ORM is specified in your persistence unit definition (eg Hibernate, 
KODO, TopLink etc).

If you want to do the mapping with annotations you would need to make your 
own implemenation of RichSequence etc as biojava is not yet using JDK5 and 
won't support annotation. Basically you would just copy the appropriate 
"SimpleRich" Objects and pepper them with annotations pointing to the 
correct DB tables etc. Not sure which strategy is more appropriate for 
you.

If MySQL doesn't allow for cross schema keys you may have to extend your 
copy of MySQL to include the extra table/ tables from your proprietary 
schema.

- Mark





"Seth Johnson" <johnson.biotech at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/07/2006 12:59 PM

 
        To:     "Richard Holland" <holland at ebi.ac.uk>
        cc:     biojava-l at biojava.org, (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-l] BioSQL -> BioJava Hibernate -> RichSequence access      to 
primary keys


Thank you Richard.  I am using NetBeans 5.5 and JDK 5.0 that
implements mapping metadata (EJB 3.0) instead of .hbm.xml files.   I
read up on Hibernate from you links and I think that the easiest
solution would be to use RichSequence BioJavaX object as an embeddable
object in my proprietary 'alignment' class.

Basically, my goal is to have access to RichSequence object when I
instantiate 'alignment' object from my 'alignment' table.  That table
contains a column with primary key of the bioentry that was used to
produce that alignment.  Since biosql is in different schema, I don't
believe that cross schema foreign keys are possible in mySQL.  Do you
think that this  is a right strategy?

Seth


On 11/6/06, Richard Holland <holland at ebi.ac.uk> wrote:
>
> If your proprietary database has a similar design to BioSQL, or can
> easily be mapped on an approximately 1:1 basis to the existing BioJavaX
> object model, then all you need to do is edit the .hbm.xml files and
> look for references to table names and column names. Remove any tables
> and columns that don't exist in your schema (including removing the
> files if this leaves them empty), and edit the remaining ones so that
> the table and column names match.
>
> If your new schema contains tables that do not map to existing BioJavaX
> objects, then you'll need to create Java objects for those as well as
> the appropriate mapping files. The easiest way to do this is to
> copy-and-paste both an existing BioJavaX object and the related .hbm.xml
> file - eg. SimpleCrossRef.java and CrossRef.hxm.xml.
>
> Hibernate is best explained through its own documentation at
> http://www.hibernate.org/ . The 'getting started' tutorial they provide
> (here:
> http://www.hibernate.org/hib_docs/v3/reference/en/html/tutorial.html )
> is a good starting point.
>
> cheers,
> Richard
>
>
> Seth Johnson wrote:
> > Hello guys,
> >
> > I've setup a BioSQL to hold sequences of interest parsed from NCBI
> > genbank release.  I also have another proprietary schema that holds
> > experimental and alignment data.  I would like to connect the
> > proprietary schema to BioSQL one using Hibernate persistence, so that
> > objects from my database would contain linkages to sequence data in
> > biosql.  Wiki mentions that one need change "only the mapping files
> > that tell Hibernate how to translate between objects and tables."  Can
> > anyone elaborate on that topic a little or point me to a tutorial or
> > some other place that discusses the concept?
> >
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From sgerster at student.ethz.ch  Wed Nov  8 08:14:39 2006
From: sgerster at student.ethz.ch (Gerster  Sarah)
Date: Wed, 8 Nov 2006 09:14:39 +0100
Subject: [Biojava-l] reading paptides from a fasta file
Message-ID: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>

Hi!

I'm trying to read peptides from a fasta file:
>id|0|0.9992|1
ASITENGGAEEESVAK
>id|1|0.9953|1
ASITENGGAEEESVAK
>id|2|0.9998|1
ASNASSAGDEVDNVATSSK
>id|3|0.9998|1
EAAAAEEPQPSDEGDVVAK
>id|4|0.9998|1
EAAAAEEPQPSDEGDVVAK
....
I would like to have all peptides somewhere in the memory. I need, their id, the sequence and the 2 numbers at the end (e.g. id = 0, probability = 0.9992, rank = 1 for the first entry in the file).

I tried to use readFastaProtein... but I guess I don't use it right. Anyway, I get the sequences, but I don't get any of the other infomations I want... 

Here is my code:
try
{
  BufferedReader br = new BufferedReader(new FileReader(file_name));
  RichSequenceIterator rich_stream = RichSequence.IOTools.readFastaProtein(br,null);
  while(rich_stream.hasNext())
  {
    RichSequence rich_seq = rich_stream.nextRichSequence();
    System.out.println(rich_seq.toString());
    System.out.println(rich_seq.getAccession());
    System.out.println(rich_seq.getAlphabet());
    System.out.println(rich_seq.getAnnotation());
    System.out.println(rich_seq.getName());
    System.out.println(rich_seq.getDescription());
    System.out.println(rich_seq.getIdentifier());
    System.out.println(rich_seq.seqString());
  }     
}
catch(Exception e) 
{
  System.err.println("Bug while reading the sequences from the FASTA file"); 
} 
 

Here's the output (for the first entry in the fasta file):
id|0:1/0.9992
0
org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper at 1df073d

1
null
null
ASITENGGAEEESVAK


Can anyone tell me what's going wrong? 
Is there already a function to put all the sequences directly in the memory (like a HashSet) while reading them?

Cheers

Sarah



From dreher at molgen.mpg.de  Wed Nov  8 12:39:20 2006
From: dreher at molgen.mpg.de (Felix Dreher)
Date: Wed, 08 Nov 2006 13:39:20 +0100
Subject: [Biojava-l] reading paptides from a fasta file
In-Reply-To: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>
References: <E9D421793368D44FB81D3C438D300574BC72B6@EX5.d.ethz.ch>
Message-ID: <4551CFF8.9050507@molgen.mpg.de>

Hi Sarah,


just a few comments / guesses:
maybe there are other approaches, but you could follow the FASTA-format 
BioJavaX understands, e.g.:
 
|>gi|<identifier>|<namespace>|<accession>|<name> <description>|

http://biojava.org/wiki/BioJava:BioJavaXDocs#Reading   (chapter 8.2.1)

So, if your file would look like this:

 >gi|0|namespace|null|1 0.9992
ASITENGGAEEESVAK
 >gi|1|namespace|null|1 0.9953
ASITENGGAEEESVAK
.
.
.

you could use:

                System.out.println("id: "+rich_seq.getIdentifier());
                System.out.println("rank: "+rich_seq.getName());
                System.out.println("probability: 
"+rich_seq.getDescription());
                System.out.println("sequence: "+rich_seq.seqString());


to get the data.

However, 'rank' or 'probability' actually would be annotations of the 
sequence, so when processing the data (e.g. storing in a database), one 
would store these data as annotations.

- As for Java-style / naming conventions for variables, the 'Camel-Case' 
is recommended, e.g.richSeq instead of rich_seq.

- To get the alphabet:
System.out.println("alphabet: "+rich_seq.getAlphabet().getName());

- Also maybe you should use the default namespace instead of null:
RichSequenceIterator rich_stream = 
RichSequence.IOTools.readFastaProtein(br,RichObjectFactory.getDefaultNamespace());


Cheers,
Felix



Gerster Sarah wrote:
> Hi!
>
> I'm trying to read peptides from a fasta file:
>   
>> id|0|0.9992|1
>>     
> ASITENGGAEEESVAK
>   
>> id|1|0.9953|1
>>     
> ASITENGGAEEESVAK
>   
>> id|2|0.9998|1
>>     
> ASNASSAGDEVDNVATSSK
>   
>> id|3|0.9998|1
>>     
> EAAAAEEPQPSDEGDVVAK
>   
>> id|4|0.9998|1
>>     
> EAAAAEEPQPSDEGDVVAK
> ....
> I would like to have all peptides somewhere in the memory. I need, their id, the sequence and the 2 numbers at the end (e.g. id = 0, probability = 0.9992, rank = 1 for the first entry in the file).
>
> I tried to use readFastaProtein... but I guess I don't use it right. Anyway, I get the sequences, but I don't get any of the other infomations I want... 
>
> Here is my code:
> try
> {
>   BufferedReader br = new BufferedReader(new FileReader(file_name));
>   RichSequenceIterator rich_stream = RichSequence.IOTools.readFastaProtein(br,null);
>   while(rich_stream.hasNext())
>   {
>     RichSequence rich_seq = rich_stream.nextRichSequence();
>     System.out.println(rich_seq.toString());
>     System.out.println(rich_seq.getAccession());
>     System.out.println(rich_seq.getAlphabet());
>     System.out.println(rich_seq.getAnnotation());
>     System.out.println(rich_seq.getName());
>     System.out.println(rich_seq.getDescription());
>     System.out.println(rich_seq.getIdentifier());
>     System.out.println(rich_seq.seqString());
>   }     
> }
> catch(Exception e) 
> {
>   System.err.println("Bug while reading the sequences from the FASTA file"); 
> } 
>  
>
> Here's the output (for the first entry in the fasta file):
> id|0:1/0.9992
> 0
> org.biojava.bio.symbol.AlphabetManager$ImmutableWellKnownAlphabetWrapper at 1df073d
>
> 1
> null
> null
> ASITENGGAEEESVAK
>
>
> Can anyone tell me what's going wrong? 
> Is there already a function to put all the sequences directly in the memory (like a HashSet) while reading them?
>
> Cheers
>
> Sarah
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>   


-- 
Felix Dreher

Max Planck Institute for Molecular Genetics
Department of Vertebrate Genomics
Bioinformatics Group
Ihnestr. 73
D-14195 Berlin

Phone: +49 30 - 8413 1682
Mobile: +49 163 - 754 24 26
E-mail: dreher at molgen.mpg.de
www.molgen.mpg.de/~lh_bioinf
 



From myammad at gmail.com  Wed Nov  8 14:50:49 2006
From: myammad at gmail.com (Ammad Ud Din)
Date: Wed, 8 Nov 2006 19:50:49 +0500
Subject: [Biojava-l] New To BioJava.org
Message-ID: <887d6f690611080650j3a0f6caah610768dbb7dbe498@mail.gmail.com>

Hi,
    i am a student of bs-bioinformatics from Muhammad Ali Jinnah University,
islamabad Pakistan.I am curently taking a course in Java here at my
university so i want to do work in java particularly in BioJava.I would like
to welcome suggestions regarding my final project in this course and also
would like to contribute as well.
                  take care & best wishes,
-- 
Ammad


From mark.schreiber at novartis.com  Thu Nov  9 01:53:37 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 9 Nov 2006 09:53:37 +0800
Subject: [Biojava-l] New To BioJava.org
Message-ID: <OF9A833ABC.E6074CA4-ON48257221.000A52F9-48257221.000A684A@ah.novartis.com>

Hi -

If you take a look at the API docs and the cookbook in www.biojava.org you 
will get an idea of what biojava can do and probably come up with a 
project from there.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





"Ammad Ud Din" <myammad at gmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/08/2006 10:50 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] New To BioJava.org


Hi,
    i am a student of bs-bioinformatics from Muhammad Ali Jinnah 
University,
islamabad Pakistan.I am curently taking a course in Java here at my
university so i want to do work in java particularly in BioJava.I would 
like
to welcome suggestions regarding my final project in this course and also
would like to contribute as well.
                  take care & best wishes,
-- 
Ammad
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l





From varvenne at genoway.com  Mon Nov 13 10:54:07 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 13 Nov 2006 11:54:07 +0100
Subject: [Biojava-l] Any memory-optimised blast parser available ?
Message-ID: <C17E0D5F.102E%varvenne@genoway.com>

Hello,

I'm trying to parse blast result files from a remote blast on NCBI
databases.
In order to do so, i'm using biojava XML parser like this :

-----------
      InputStream is = new FileInputStream(blastFile);
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      parser.setContentHandler(adapter);

      List results = new ArrayList();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      adapter.setSearchContentHandler(builder);

// Here is the method that throws 'OutOfMemoryException'
      parser.parse(new InputSource(is));
-----------

While blasting a genomic sequence (i've tried with 50Kb long sequences max),
I've got an OutOfMemory exception.

Does anyone know a way to resolve this ? (this aim is not to dividde my
genomic locus in too many parts, 50Kb is a quarter of my genomic...)

Thanks,
Regards,

Benoit


-- 
Benoit Varvenne,
Bioinformatics pearson in charge,
GenOway - Lyon (France)



From ayates at ebi.ac.uk  Mon Nov 13 11:28:29 2006
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 13 Nov 2006 11:28:29 +0000
Subject: [Biojava-l] Any memory-optimised blast parser available ?
In-Reply-To: <C17E0D5F.102E%varvenne@genoway.com>
References: <C17E0D5F.102E%varvenne@genoway.com>
Message-ID: <455856DD.9040605@ebi.ac.uk>

Hi,

Have you tried increasing the amount of memory the Java virtual machine 
has available? The problem with Java is that it starts with a default 
memory limit of approx. 128MB which if you've got a memory intensive 
process will not be enough.

When running your program try adding the option

-Xmx256M

So if my class was called Main.class my command line would be:

java -Xmx256M -cp .:biojava.jar Main

Or if you're running this from ant then there is an attribute maxmemory 
which can be specified in the <java/> task.

Hope that helps

Andy

Benoit VARVENNE wrote:
> Hello,
> 
> I'm trying to parse blast result files from a remote blast on NCBI
> databases.
> In order to do so, i'm using biojava XML parser like this :
> 
> -----------
>       InputStream is = new FileInputStream(blastFile);
>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
> 
>       parser.setContentHandler(adapter);
> 
>       List results = new ArrayList();
> 
>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>           new DummySequenceDB("queries"), new
> DummySequenceDBInstallation());
> 
>       adapter.setSearchContentHandler(builder);
> 
> // Here is the method that throws 'OutOfMemoryException'
>       parser.parse(new InputSource(is));
> -----------
> 
> While blasting a genomic sequence (i've tried with 50Kb long sequences max),
> I've got an OutOfMemory exception.
> 
> Does anyone know a way to resolve this ? (this aim is not to dividde my
> genomic locus in too many parts, 50Kb is a quarter of my genomic...)
> 
> Thanks,
> Regards,
> 
> Benoit
> 
> 


From varvenne at genoway.com  Mon Nov 13 12:39:34 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 13 Nov 2006 13:39:34 +0100
Subject: [Biojava-l] Any memory-optimised blast parser available ?
In-Reply-To: <455856DD.9040605@ebi.ac.uk>
Message-ID: <C17E2616.1036%varvenne@genoway.com>

Great ! Thanks a lot to all for your answers.
I hadn't thought to that way of solving the problem.
That runs well with -Xmx option.

Thanks again,
Regards,

Benoit


Le 13/11/06 12:28, ??Andy Yates?? <ayates at ebi.ac.uk> a ?crit?:

> Hi,
> 
> Have you tried increasing the amount of memory the Java virtual machine
> has available? The problem with Java is that it starts with a default
> memory limit of approx. 128MB which if you've got a memory intensive
> process will not be enough.
> 
> When running your program try adding the option
> 
> -Xmx256M
> 
> So if my class was called Main.class my command line would be:
> 
> java -Xmx256M -cp .:biojava.jar Main
> 
> Or if you're running this from ant then there is an attribute maxmemory
> which can be specified in the <java/> task.
> 
> Hope that helps
> 
> Andy
> 
> Benoit VARVENNE wrote:
>> Hello,
>> 
>> I'm trying to parse blast result files from a remote blast on NCBI
>> databases.
>> In order to do so, i'm using biojava XML parser like this :
>> 
>> -----------
>>       InputStream is = new FileInputStream(blastFile);
>>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>> 
>>       parser.setContentHandler(adapter);
>> 
>>       List results = new ArrayList();
>> 
>>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>>           new DummySequenceDB("queries"), new
>> DummySequenceDBInstallation());
>> 
>>       adapter.setSearchContentHandler(builder);
>> 
>> // Here is the method that throws 'OutOfMemoryException'
>>       parser.parse(new InputSource(is));
>> -----------
>> 
>> While blasting a genomic sequence (i've tried with 50Kb long sequences max),
>> I've got an OutOfMemory exception.
>> 
>> Does anyone know a way to resolve this ? (this aim is not to dividde my
>> genomic locus in too many parts, 50Kb is a quarter of my genomic...)
>> 
>> Thanks,
>> Regards,
>> 
>> Benoit
>> 
>> 
> 




From jolyon.holdstock at ogt.co.uk  Mon Nov 13 11:33:43 2006
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Mon, 13 Nov 2006 11:33:43 -0000
Subject: [Biojava-l] Any memory-optimised blast parser available
	?[Scanned]
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F0111DCE1@EUCLID.internal.ogtip.com>

Can you use the -Xmx flag to add more memory to the JRE?

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Benoit
VARVENNE
Sent: 13 November 2006 10:54
To: biojava-l
Subject: [Biojava-l] Any memory-optimised blast parser available
?[Scanned]

Hello,

I'm trying to parse blast result files from a remote blast on NCBI
databases.
In order to do so, i'm using biojava XML parser like this :

-----------
      InputStream is = new FileInputStream(blastFile);
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      parser.setContentHandler(adapter);

      List results = new ArrayList();

      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      adapter.setSearchContentHandler(builder);

// Here is the method that throws 'OutOfMemoryException'
      parser.parse(new InputSource(is));
-----------

While blasting a genomic sequence (i've tried with 50Kb long sequences
max),
I've got an OutOfMemory exception.

Does anyone know a way to resolve this ? (this aim is not to dividde my
genomic locus in too many parts, 50Kb is a quarter of my genomic...)

Thanks,
Regards,

Benoit


-- 
Benoit Varvenne,
Bioinformatics pearson in charge,
GenOway - Lyon (France)

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l











This email has been scanned by Oxford Gene Technology Security Systems.




From dunarel at gmx.net  Sat Nov 18 02:48:41 2006
From: dunarel at gmx.net (Dunarel Badescu)
Date: Sat, 18 Nov 2006 03:48:41 +0100
Subject: [Biojava-l] New To BioJava.org, right in the question.
In-Reply-To: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
References: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
Message-ID: <20061118024841.274400@gmx.net>

Hello,

My name is Dunarel Badescu, a student at UQAM University in Montreal,Quebec,Canada in Graduate Diploma of Bioinformatics.

Currently I am using BioJavaX and BioSql for my session project.

I have parsed NCBI GeneBank files using RichSequences.
I then inserted the sequences into the database.

Several problems arise:

1) A bug in the code pulled from CVS:
In class BioSQLRichObjectBuilder: I had to append some code for the program to find the right constructors:

// Get the results
Object result = this.uniqueResult.invoke(query, null);
// Return the found object, if found
if (result!=null) return result;
// Create, persist and return the new object otherwise
else {

/*NEW CODE*/
if (SimpleDocRef.class.isAssignableFrom(clazz)) {
// convert String to List constructor 
      	ourParamsList.set(0,
DocRefAuthor.Tools.parseAuthorString((String)ourParamsList.get(0)));
                }                
             
// Load the class


2) Meny memory problems, after inserting 800 sequences it slows extremely so performance is degraded.
I thought of a hibernate cache problem and tried to turn it off by setting some parameters: 
        <property name="hibernate.jdbc.batch_size">20</property>
        <property name="hibernate.cache.enabled">false</property>
        <property name="hibernate.cache.use_query_cache">false</property>
        <property name="hibernate.cache.use_second_level_cache">false</property>
        <property name="hibernate.connection.aggressive_release">false</property> 
        
        <property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
        <property name="cache.use_query_cache">false</property>
        <property name="cache.use_minimal_puts">false</property>
        <property name="max_fetch_depth">3</property> 
    
to no much benefit.

Then I observed some small performance gain by using :
  session.save("Sequence",rs);  // persist the sequence
  session.getTransaction().commit();
  session.flush();
  session.evict(rs);
The session.evict(rs);

Any atempt to dealocate memory by closing the session, the session factory either generates errors or it will generate on reopening.

So as a last resort I fragmented the original aprox. 130 mb containing one taxon from ncbi in 38 files 1000 sequences each and made a dos batch script executing the program in the commad line for each file.
So that way it works but:

3) Inserting rows sometimes generates exceptions in the references table.
After taking it more closely I found that by disabling the unique constraint on the dbxref_id on references table solves all the remaining problems.

The coment about it on the original code is:
-- No two references can reference the same reference database entry 
-- (dbxref_id). This is where the MEDLINE id goes: PUBMED:123456. 
and the modification is:

--UNIQUE ( dbxref_id ) , 

I must say that the script for creating the biosql schema is version 1.29 from the cvs, the most recent I found.

And I must say that for running the script on Postgresql 8.1.5 I had to modify each create table statement adding with oids at the end, now that 8.1.5 doesn't create oids by default.

It must have be a more elegant aproch to all these problems isn't it?

At least the constraint situation, I mean is it normal to exist or not as it seems.

I wish You all the best and thank you for your work which is most useful and scarce as a resource.



-- 
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! 
Ideal f?r Modem und ISDN: http://www.gmx.net/de/go/smartsurfer


From sanges at biogem.it  Sat Nov 18 11:54:26 2006
From: sanges at biogem.it (Remo Sanges)
Date: Sat, 18 Nov 2006 11:54:26 +0000
Subject: [Biojava-l] Fellowships for Junior Scientists
In-Reply-To: <20061118024841.274400@gmx.net>
References: <mailman.3788.1163421612.2429.biojava-l@lists.open-bio.org>
	<20061118024841.274400@gmx.net>
Message-ID: <455EF472.1000903@biogem.it>

Apologies for the off topic post and for the crossposting...

AREA Science Park (http://www.area.trieste.it/opencms/opencms/area/en/)
and CBM (http://www.cbm.fvg.it/?lang=en_US) are launching a mobility
initiative aimed at attracting international scientists to work with
the biomedical research community of Trieste.

Research areas:

     * Biostatistics
     * Systems Biology
     * Algorithm Development

The fellowships are funded by AREA Science Park and the CBM - Consortium
for Molecular Biomedicine as part of an international mobility programme
run by AREA Science Park and the CBM. The programme aims at attracting
young scientists to the Friuli Venezia Giulia Region and adding them to
the community of researchers operating in Trieste in the field of
biomedicine.


CBM and AREA Science Park are two research institutes recognised by the
Ministry of Education, Universities and Research.
Here there are laboratories integrating dry and wet lab research and
developing a wide research program encompassing functional and comparative
genomics, bioinformatics database, software development and algorithm
development.
The laboratories are already integrated in international collaborative
projects tackling non-coding RNA genes, regulatory elements, and
bioinformatics workflow management systems.

For further information:
http://www.cbm.fvg.it/?page=mobility&lang=en_US&id=2


Regards

Remo Sanges



From varvenne at genoway.com  Mon Nov 20 16:19:38 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Mon, 20 Nov 2006 17:19:38 +0100
Subject: [Biojava-l] Any ORF Finder available ?
Message-ID: <C187942A.1150%varvenne@genoway.com>

Hello,

I'm a working on a biojava project and i'm searching for a way to include an
ORF Finder in my code. The aim is to find ORFs on cDNA sequences (or partial
ORFs on ESTs ones) 

Anyone can help me ?
Is there a module with biojava to do so ? Do you know any free-to-dowload
software (source code or compiled one) ?

Thanks,
Regards   

Beno?t.




From mark.schreiber at novartis.com  Tue Nov 21 03:12:03 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 21 Nov 2006 11:12:03 +0800
Subject: [Biojava-l] Any ORF Finder available ?
Message-ID: <OFC6723038.1FD8CED2-ON4825722D.000FE302-4825722D.00119573@ah.novartis.com>

Hi -

A quick and dirty way is to make a six frame translation 
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames).

Probably a better way is to scan in six frames (using a 
WindowedSymbolList) looking for a start codon and then look for the 
appropriate stop codon. You will want to define the start and stop codons 
as Symbols from the codon (DNAxDNAxDNA) alphabet. You can do this as 
follows:

FiniteAlphabet codonAlpha = DNATools.getCodonAlphabet();

//make a ambiguity symbol for ATG, GTG and TTG codons

//first make the A or G or T ambiguity BasisSymbol
Set syms = new HashSet();
syms.add(DNATools.a()); syms.add(DNATools.t()); syms.add(DNATools.g());
Symbol amb = DNATools.getDNA().getAmbiguity(syms) ;

//now make the [A|G|T] TG codon
List l = new ArrayList();
l.add(amb); l.add(DNATools.t()); l.add(DNATools.g());
Symbol startCodon = codonAlpha.getSymbol(l);

//You would construct the stop codons in a similar manner although you 
probably can't merge them all into one.

The above example shows how you can use a single symbol to represent all 3 
common bacterial start codons. You could also make all 3 seperatly and 
test them individually.

- Mark
 

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





Benoit VARVENNE <varvenne at genoway.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/21/2006 12:19 AM

 
        To:     biojava-l <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Any ORF Finder available ?


Hello,

I'm a working on a biojava project and i'm searching for a way to include 
an
ORF Finder in my code. The aim is to find ORFs on cDNA sequences (or 
partial
ORFs on ESTs ones) 

Anyone can help me ?
Is there a module with biojava to do so ? Do you know any free-to-dowload
software (source code or compiled one) ?

Thanks,
Regards 

Beno?t.


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l






From weelainy at hotmail.com  Tue Nov 21 17:44:26 2006
From: weelainy at hotmail.com (Elaine Forbes)
Date: Tue, 21 Nov 2006 17:44:26 +0000
Subject: [Biojava-l] remove me from your list
Message-ID: <BAY117-F3807D23951044A323DAC4ECBEC0@phx.gbl>

Hi
I no longer wish to recieve emails from the biojava email list- please 
remove me.
THanks
Elaine

_________________________________________________________________
Windows Live? Messenger has arrived. Click here to download it for free! 
http://imagine-msn.com/messenger/launch80/?locale=en-gb



From markjschreiber at gmail.com  Wed Nov 22 06:35:54 2006
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 22 Nov 2006 14:35:54 +0800
Subject: [Biojava-l] Open JDK
Message-ID: <93b45ca50611212235r265b4730sea68dfb6b41fb4e0@mail.gmail.com>

Dear All -

Everyone knows that BioJava is open-source but you may not know that
the Java JDK is in the process of being made open-source several parts
already are including the javac and HotSpot runtime.

https://openjdk.dev.java.net/

Next time you think the GenBank parser is slow maybe you could
optimise the HotSpot runtime instead : )

- Mark


From kingsulaman at hotmail.com  Thu Nov 23 13:02:31 2006
From: kingsulaman at hotmail.com (Sulaman Malik)
Date: Thu, 23 Nov 2006 18:02:31 +0500
Subject: [Biojava-l] Looking For Project
Message-ID: <BAY114-DAV106855476E012F01A88F58ADE20@phx.gbl>



hi:
    This is Sulaman Malik BS(Bio-informatics) Student of MAJU,Islamabad Pakistan.

     I am looking for a good semester project which i could impelement using the Java as a platefarm,so give me a lsit of bio-projects or any bio-project so that i could go further. 


From varvenne at genoway.com  Fri Nov 24 16:19:27 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 17:19:27 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN vs. blastP)
Message-ID: <C18CDA1F.11FF%varvenne@genoway.com>

Hello,

I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
the code put at the end of this mail.

I've tried this with a blastN query and there i got no trouble.
However, i've tried to do exactly the same thing with a BlastP query and
i've got the exception cited at the end of this mail.

I've verified and the two infiles (blastn/blastp) seem to have the same
structures (except that one is for prot so data are different). (Please find
them as attached if you're used to this).

Can someone help me ? I don't understand why it works in a case and not in
the other one ...

Thanks a lot,
Cheers,

Beno?t.


-------------------
My code :
-----
InputStream is = new FileInputStream(blastFile);
// blastFile is the xml file, output of my blast

      //make a BlastLikeSAXParser
      BlastXMLParserFacade parser = new BlastXMLParserFacade();
      //make the SAX event adapter that will pass events to a Handler.
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      //set the parsers SAX event adapter
      parser.setContentHandler(adapter);

      //The list to hold the SeqSimilaritySearchResults
      List results = new ArrayList();

      //create the SearchContentHandler that will build
SeqSimilaritySearchResults
      //in the results List
      SearchContentHandler builder = new BlastLikeSearchBuilder(results,
          new DummySequenceDB("queries"), new
DummySequenceDBInstallation());

      //register builder with adapter
      adapter.setSearchContentHandler(builder);

      parser.parse(new InputSource(is)); // From here come the Exception

-------------------


-------------------
The exception :
----
  org.xml.sax.SAXParseException: Une d?claration XML peut commencer des
entit?s uniquement.
        at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3376)
        at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3364)
        at org.apache.crimson.parser.Parser2.maybePI(Parser2.java:1140)
        at org.apache.crimson.parser.Parser2.maybeMisc(Parser2.java:1266)
        at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:671)
        at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
        at 
org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
        at 
org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLPars
erFacade.java:180)




From smh1008 at cam.ac.uk  Fri Nov 24 17:08:54 2006
From: smh1008 at cam.ac.uk (David Huen)
Date: 24 Nov 2006 17:08:54 +0000
Subject: [Biojava-l] A problem parsing Blast XML output (blastN vs.
	blastP)
In-Reply-To: <C18CDA1F.11FF%varvenne@genoway.com>
References: <C18CDA1F.11FF%varvenne@genoway.com>
Message-ID: <Prayer.1.0.18.0611241708540.30878@hermes-1.csi.cam.ac.uk>

On Nov 24 2006, Benoit VARVENNE wrote:

>Hello,
>
>I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>the code put at the end of this mail.
>
>I've tried this with a blastN query and there i got no trouble.
>However, i've tried to do exactly the same thing with a BlastP query and
>i've got the exception cited at the end of this mail.
>
> I've verified and the two infiles (blastn/blastp) seem to have the same 
> structures (except that one is for prot so data are different). (Please 
> find them as attached if you're used to this).
>
>Can someone help me ? I don't understand why it works in a case and not in
>the other one ...
>
I am uncertain whether BlastXMLFacade will actually support a protein 
sequence parse. It was originally developed to handle blastn. Anyone else 
tried it with blastp?

I'm offline till Sunday so I can't reply till then.

Regards,
David Huen


From varvenne at genoway.com  Fri Nov 24 17:53:49 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 18:53:49 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN
	vs.	blastP)
In-Reply-To: <Prayer.1.0.18.0611241708540.30878@hermes-1.csi.cam.ac.uk>
Message-ID: <C18CF03D.120D%varvenne@genoway.com>

Le 24/11/06 18:08, ??David Huen?? <smh1008 at cam.ac.uk> a ?crit?:

> On Nov 24 2006, Benoit VARVENNE wrote:
> 
>> Hello,
>> 
>> I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>> the code put at the end of this mail.
>> 
>> I've tried this with a blastN query and there i got no trouble.
>> However, i've tried to do exactly the same thing with a BlastP query and
>> i've got the exception cited at the end of this mail.
>> 
>> I've verified and the two infiles (blastn/blastp) seem to have the same
>> structures (except that one is for prot so data are different). (Please
>> find them as attached if you're used to this).
>> 
>> Can someone help me ? I don't understand why it works in a case and not in
>> the other one ...
>> 
> I am uncertain whether BlastXMLFacade will actually support a protein
> sequence parse. It was originally developed to handle blastn. Anyone else
> tried it with blastp?
> 
> I'm offline till Sunday so I can't reply till then.
> 
> Regards,
> David Huen
> 

David,

As BlastLikeSAXParser seemed to support older versions of NCBI blastP (see
"http://www.biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book#S
tep_A_-_Create_an_application_that_sets_up_the_parser_and_does_the_parsing")
,  i'll be surprised if BlastXMLParserFacade does not.

However, i'll be very interested if someone's got any information.

Can't it be dtd problem ? If yes, can we update dtd sources ?

Cheers,
Beno?t.





From karl_harvey at hotmail.com  Fri Nov 24 01:40:44 2006
From: karl_harvey at hotmail.com (Karl Harvey)
Date: Thu, 23 Nov 2006 20:40:44 -0500
Subject: [Biojava-l] Query to blast.. on Internet.
Message-ID: <BAY135-F89E1D571DE6EDBB2D4AB795E10@phx.gbl>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20061123/ee5052ec/attachment-0002.html>

From varvenne at genoway.com  Fri Nov 24 17:04:01 2006
From: varvenne at genoway.com (Benoit VARVENNE)
Date: Fri, 24 Nov 2006 18:04:01 +0100
Subject: [Biojava-l] A problem parsing Blast XML output (blastN
	vs.	blastP)
In-Reply-To: <45672448.7060906@ebi.ac.uk>
Message-ID: <C18CE494.1204%varvenne@genoway.com>

Ooooo sorry i hadn't noticed that. Here is the traduction (home made...)

"org.xml.sax.SAXParseException: An XML declaration can only begin with an
entity"

The problem is that my two files (attached this time) don't seem to differ.

Have you got an xml validation tool to recommend me ?

Cheers,

Beno?t 

Le 24/11/06 17:56, ??Richard Holland?? <holland at ebi.ac.uk> a ?crit?:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> Unfortunately the exception you are getting is in French and sadly my 1
> year of French lessons in school failed to make any impact on my ability
> to understand it. :)
> 
> But, my guess would be that something is wrong with the BlastP output,
> as the exception is an XML parser one and not a BioJava one. It's most
> likely that the BlastP report is not valid XML. Try running it through
> an XML validation tool to check.
> 
> cheers,
> Richard
> 
> Benoit VARVENNE wrote:
>> Hello,
>> 
>> I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>> the code put at the end of this mail.
>> 
>> I've tried this with a blastN query and there i got no trouble.
>> However, i've tried to do exactly the same thing with a BlastP query and
>> i've got the exception cited at the end of this mail.
>> 
>> I've verified and the two infiles (blastn/blastp) seem to have the same
>> structures (except that one is for prot so data are different). (Please find
>> them as attached if you're used to this).
>> 
>> Can someone help me ? I don't understand why it works in a case and not in
>> the other one ...
>> 
>> Thanks a lot,
>> Cheers,
>> 
>> Beno?t.
>> 
>> 
>> -------------------
>> My code :
>> -----
>> InputStream is = new FileInputStream(blastFile);
>> // blastFile is the xml file, output of my blast
>> 
>>       //make a BlastLikeSAXParser
>>       BlastXMLParserFacade parser = new BlastXMLParserFacade();
>>       //make the SAX event adapter that will pass events to a Handler.
>>       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
>> 
>>       //set the parsers SAX event adapter
>>       parser.setContentHandler(adapter);
>> 
>>       //The list to hold the SeqSimilaritySearchResults
>>       List results = new ArrayList();
>> 
>>       //create the SearchContentHandler that will build
>> SeqSimilaritySearchResults
>>       //in the results List
>>       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
>>           new DummySequenceDB("queries"), new
>> DummySequenceDBInstallation());
>> 
>>       //register builder with adapter
>>       adapter.setSearchContentHandler(builder);
>> 
>>       parser.parse(new InputSource(is)); // From here come the Exception
>> 
>> -------------------
>> 
>> 
>> -------------------
>> The exception :
>> ----
   org.xml.sax.SAXParseException: An XML declaration can only begin with an
entity
>>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3376)
>>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3364)
>>         at org.apache.crimson.parser.Parser2.maybePI(Parser2.java:1140)
>>         at org.apache.crimson.parser.Parser2.maybeMisc(Parser2.java:1266)
>>         at org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:671)
>>         at org.apache.crimson.parser.Parser2.parse(Parser2.java:337)
>>         at 
>> org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:448)
>>         at 
>> org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.parse(BlastXMLPars
>> erFacade.java:180)
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
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> 
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> 48o/exGfv1xSSnLzMMjPKxo=
> =tRNi
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> 

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From myammad at gmail.com  Mon Nov 27 14:41:39 2006
From: myammad at gmail.com (Ammad Ud Din)
Date: Mon, 27 Nov 2006 19:41:39 +0500
Subject: [Biojava-l] Looking forward for suggestions
Message-ID: <887d6f690611270641x3aeefb63pc537210cda242b30@mail.gmail.com>

Hi EveryBody,

i am a final year Undergraduate student of bioinformatics.I am currently
carrying a course in java so i want to contribute on open source
projects.can anybody suggest me what type of open source projects are going
on and how could i contribute in these....waiting for the
reply..............tc bestwishes

----Ammad


From mittalashr at yahoo.com  Tue Nov 28 04:54:35 2006
From: mittalashr at yahoo.com (ashish mittal)
Date: Mon, 27 Nov 2006 20:54:35 -0800 (PST)
Subject: [Biojava-l] Using REstriction Mapper
Message-ID: <20061128045435.9535.qmail@web52315.mail.yahoo.com>

Hi all, 

I am trying to use restriction mapper to search for a list of resctriction enzymes in a given sequence. Can some one send me some sample code that does the same. I tried following and this code gives exception: 
Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException
        at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
        at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
        at org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:52)
        at org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:116)
        at org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:143)
        at org.biojava.bio.molbio.RestrictionMapper.annotate(RestrictionMapper.java:115)
        at seed.rs.rsTry.Searcher.search(Searcher.java:91)
        at seed.rs.rsTry.Searcher.main(Searcher.java:101)


CODE: 

public class Searcher {
    
    ThreadPool tPool = new ThreadPool() {
        public void addRequest(Runnable runnable) {
        }
        public void startThreads() {
        }
        public void stopThreads() {
        }
        public void waitForThreads() {
        }
    };
    
    RestrictionMapper mapper = new RestrictionMapper(tPool);
    
    
    
    /** Creates a new instance of Searcher */
    public Searcher() {
    }
    
    public void search(){
    
        
        try {
            RestrictionEnzyme res1 = new RestrictionEnzyme("enz1",DNATools.createDNA("agtg"),0,0);
            RestrictionEnzyme res2 = new RestrictionEnzyme("enz2",DNATools.createDNA("gatt"),0,0);
            RestrictionEnzyme res3 = new RestrictionEnzyme("enz3",DNATools.createDNA("gatg"),0,0);
            
            mapper.addEnzyme(res1);
            mapper.addEnzyme(res2);
            mapper.addEnzyme(res3);
            
        RestrictionEnzymeManager.register(res1,new TreeSet());
        RestrictionEnzymeManager.register(res2,new TreeSet());
        RestrictionEnzymeManager.register(res3,new TreeSet());
      
            
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        } catch (IllegalAlphabetException ex) {
            ex.printStackTrace();
        }
        
        //RestrictionEnzymeManager  resManager = new RestrictionEnzymeManager();
        
        try {
            
            Sequence dnaSeq = DNATools.createDNASequence("agtgattcgtatcgattcggatggtcattttt","my_dnaseq");
            Sequence newSeq = mapper.annotate(dnaSeq);
            
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        }
    }
    
    public static void main (String args[])
    {
        Searcher searcherObj = new Searcher();
        searcherObj.search();
    }
}



Thanks in Advance. 
Ashish 





 
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From mark.schreiber at novartis.com  Tue Nov 28 05:55:43 2006
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Tue, 28 Nov 2006 13:55:43 +0800
Subject: [Biojava-l] Using REstriction Mapper
Message-ID: <OFAC89D389.5836515E-ON48257234.0020195B-48257234.00209171@ah.novartis.com>

Hi -

Looks like you forgot to include the bytecode.jar on your classpath. Take 
a look at these instructions : http://biojava.org/wiki/BioJava:GetStarted

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





ashish mittal <mittalashr at yahoo.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/28/2006 12:54 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using REstriction Mapper


Hi all, 

I am trying to use restriction mapper to search for a list of resctriction 
enzymes in a given sequence. Can some one send me some sample code that 
does the same. I tried following and this code gives exception: 
Exception in thread "main" java.lang.NoClassDefFoundError: 
org/biojava/utils/bytecode/CodeException
        at 
org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
        at 
org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
        at 
org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:52)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:116)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:143)
        at 
org.biojava.bio.molbio.RestrictionMapper.annotate(RestrictionMapper.java:115)
        at seed.rs.rsTry.Searcher.search(Searcher.java:91)
        at seed.rs.rsTry.Searcher.main(Searcher.java:101)


CODE: 

public class Searcher {
 
    ThreadPool tPool = new ThreadPool() {
        public void addRequest(Runnable runnable) {
        }
        public void startThreads() {
        }
        public void stopThreads() {
        }
        public void waitForThreads() {
        }
    };
 
    RestrictionMapper mapper = new RestrictionMapper(tPool);
 
 
 
    /** Creates a new instance of Searcher */
    public Searcher() {
    }
 
    public void search(){
 
 
        try {
            RestrictionEnzyme res1 = new 
RestrictionEnzyme("enz1",DNATools.createDNA("agtg"),0,0);
            RestrictionEnzyme res2 = new 
RestrictionEnzyme("enz2",DNATools.createDNA("gatt"),0,0);
            RestrictionEnzyme res3 = new 
RestrictionEnzyme("enz3",DNATools.createDNA("gatg"),0,0);
 
            mapper.addEnzyme(res1);
            mapper.addEnzyme(res2);
            mapper.addEnzyme(res3);
 
        RestrictionEnzymeManager.register(res1,new TreeSet());
        RestrictionEnzymeManager.register(res2,new TreeSet());
        RestrictionEnzymeManager.register(res3,new TreeSet());
 
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        } catch (IllegalAlphabetException ex) {
            ex.printStackTrace();
        }
 
        //RestrictionEnzymeManager  resManager = new 
RestrictionEnzymeManager();
 
        try {
 
            Sequence dnaSeq = 
DNATools.createDNASequence("agtgattcgtatcgattcggatggtcattttt","my_dnaseq");
            Sequence newSeq = mapper.annotate(dnaSeq);
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        }
    }
 
    public static void main (String args[])
    {
        Searcher searcherObj = new Searcher();
        searcherObj.search();
    }
}



Thanks in Advance. 
Ashish 





 
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Access over 1 million songs.
http://music.yahoo.com/unlimited
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From kingsulaman at hotmail.com  Mon Nov 27 14:44:11 2006
From: kingsulaman at hotmail.com (Sulaman Nawaz)
Date: Mon, 27 Nov 2006 14:44:11 +0000
Subject: [Biojava-l] Willing to Contribute in  BioJava
In-Reply-To: <mailman.4952.1164431612.2429.biojava-l@lists.open-bio.org>
Message-ID: <BAY114-F29B02F0C2AD422EAB5AD43ADE60@phx.gbl>

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