[Biojava-dev] BioJava Development
Jeff Cope
jcope at cableone.net
Wed Jan 9 15:59:16 UTC 2008
Hi,
My name is Jeff Cope, and I'm currently working on a bioinformatics
project for a professor at BSU. What we have so far is mostly in java, but
with the data calculations taking place using functionality found in the
BioPython library (Molecular Weight, Instability Index, Isoelectric Point,
Aromaticity, GRAVY, etc...). Anywho, currently we are only looking at
protein sequences, and thought that we could help you out on the BioJava
project by seeing if that functionality could be added into your library
instead...
So I guess my question is, now that I'm signed up on the developers
mail list, what would I need to do to get started (assuming you want my
help), and what kind of programming ground rules do you have...
I feel pretty comfortable in Java code, and if you would like to see
an example of my source code, and some of the work I've done so far, you can
find it here:
Current project:
http://trac.boisestate.edu/protcalc/
Source Code:
http://trac.boisestate.edu/protcalc/src/
API docs:
http://trac.boisestate.edu/protcalc/docs/
Thanks,
Jeff Cope
-----Original Message-----
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Sent: Tuesday, January 08, 2008 1:52 AM
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Subject: biojava-dev Digest, Vol 59, Issue 2
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Today's Topics:
1. Fwd: bioperl like blastparser (Michael Gang)
2. Re: Error while reading byte data for creating a Trace.
(Richard Holland)
3. Re: Error while reading byte data for creating a Trace.
(Andy Yates)
4. Re: bioperl like blastparser (Andreas Prlic)
5. Re: JUnit (Michael Heuer)
6. Re: JUnit (Mark Schreiber)
7. Re: JUnit (Michael Heuer)
8. read fasta file (Michael Gang)
9. Re: read fasta file (Richard Holland)
----------------------------------------------------------------------
Message: 1
Date: Mon, 7 Jan 2008 12:16:22 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] Fwd: bioperl like blastparser
To: biojava-dev at biojava.org
Message-ID:
<6994d82b0801070216q1df26e72ic131592048100f3f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Andreas,
You are correct.
The junit.jar library was missing in my ant_home.
Eclipse wrote that it was running the tests, but did not run any.
Now I corrected it and see that tests are failing.
I ran the program BlastEcho.java manually on the blast test files and
on the ncbi blast.
Judging after manually curation it worked good but at wu_blast id did
not parse the query length.
The reason is that in wu_blast the query length line has just 8 spaces
at the beginning instead of 9.
So I corrected the line which identifies the querylength at
org.biojava.bio.program.sax.BlastSaxParser
line 68 to: if (poLine.matches("^\\s+\\(\\d+\\sletters\\)\\s*$")) {
Now it works also on wu_blast.
It would be now a good idea to update the blast tests regarding the
number of arguments and see if the fail still.
Thanks in advance,
Michael
On Jan 6, 2008 2:41 PM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi Michael,
>
> I just had a look at your patch for the query length.
> Several of the unit tests are now failing at
>
org.biojava.bio.program.ssbind.SSBindCase.testResultGetAnnotation(SSBindCase
.java:143)
>
> The problem is that most blast related unit tests extend the SSBindCase,
> which expects a fixed number of attributes. With the new patch some of the
> blast-flavors have the additional queryLength attribute.
>
> Could you have a look at the behaviour of the parser for some of the files
> where the tests now fail? If you think the new behaviour of the
> parser is correct, we can simply update the tests to accept the different
> number of attributes.
>
> Thanks,
> Andreas
>
>
> --------------------------------------------------
>
> Andreas Prlic Wellcome Trust Sanger Institute
> Hinxton, Cambridge CB10 1SA, UK
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
------------------------------
Message: 2
Date: Mon, 7 Jan 2008 12:01:55 -0000 (GMT)
From: "Richard Holland" <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
a Trace.
To: "Andy Yates" <ayates at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
abhi232 at cc.gatech.edu
Message-ID: <50442.80.42.95.78.1199707315.squirrel at webmail.ebi.ac.uk>
Content-Type: text/plain;charset=iso-8859-1
This problem was resolved back in November. For some reason during the
last couple of weeks the BioJava mailing list has been sending out
occasional duplicate copies of emails sent several months ago! This was
one of them.
cheers,
Richard
On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
> Hi,
>
> As far as I am aware there isn't a problem with the current ABI parser
> however if you could send a code snippit of reading in the byte array
> & the stack trace of the index out of bounds exception that would be
> most helpful
>
> Andy
>
> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>
>> Hi all,
>> I am having a byte array which is having the data from an .ab1
>> file.The
>> biojava library provides a class called as ABITrace which takes as
>> input
>> either a byte[] array , a file or a url.If i use the later
>> parameters (the
>> file or the url )the program works but if I pass the byte array to the
>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is there a
>> problem with the ABITrace class or how can I bypass this particular
>> error.
>> I am printing the length of the byte array and it comes to
>> 144930...Can
>> that cause a problem in my code?
>>
>> Thanks in advance.
>> Abhinav
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
--
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK
------------------------------
Message: 3
Date: Mon, 7 Jan 2008 12:18:50 +0000
From: Andy Yates <ayates at ebi.ac.uk>
Subject: Re: [Biojava-dev] Error while reading byte data for creating
a Trace.
To: "Richard Holland" <holland at ebi.ac.uk>
Cc: biojava-l at biojava.org, biojava-dev at biojava.org,
abhi232 at cc.gatech.edu
Message-ID: <065714BD-6D4F-4B5F-8AAE-E6C47C9405AB at ebi.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Oh for ... :). Thought I'd seen this one before
Andy
On 7 Jan 2008, at 12:01, Richard Holland wrote:
> This problem was resolved back in November. For some reason during the
> last couple of weeks the BioJava mailing list has been sending out
> occasional duplicate copies of emails sent several months ago! This
> was
> one of them.
>
> cheers,
> Richard
>
> On Mon, January 7, 2008 9:34 am, Andy Yates wrote:
>> Hi,
>>
>> As far as I am aware there isn't a problem with the current ABI
>> parser
>> however if you could send a code snippit of reading in the byte array
>> & the stack trace of the index out of bounds exception that would be
>> most helpful
>>
>> Andy
>>
>> On 5 Nov 2007, at 17:59, abhi232 at cc.gatech.edu wrote:
>>
>>> Hi all,
>>> I am having a byte array which is having the data from an .ab1
>>> file.The
>>> biojava library provides a class called as ABITrace which takes as
>>> input
>>> either a byte[] array , a file or a url.If i use the later
>>> parameters (the
>>> file or the url )the program works but if I pass the byte array to
>>> the
>>> constructor I get java.lang.arrayIndexOutOfBound.Exception.Is
>>> there a
>>> problem with the ABITrace class or how can I bypass this particular
>>> error.
>>> I am printing the length of the byte array and it comes to
>>> 144930...Can
>>> that cause a problem in my code?
>>>
>>> Thanks in advance.
>>> Abhinav
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
> --
> Richard Holland
> BioMart (http://www.biomart.org/)
> EMBL-EBI
> Hinxton, Cambridgeshire CB10 1SD, UK
------------------------------
Message: 4
Date: Mon, 7 Jan 2008 21:54:21 +0000 (GMT)
From: Andreas Prlic <ap3 at sanger.ac.uk>
Subject: Re: [Biojava-dev] bioperl like blastparser
To: michaelgang at gmail.com
Cc: biojava-dev at biojava.org
Message-ID:
<Pine.LNX.4.64.0801072149400.15544 at deskpro349.dynamic.sanger.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi Michael,
thanks for your patch, I commited it to the new svn repository
and updated the unit tests to now either take 4 or 5 args.
Andreas
--------------------------------------------------
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
------------------------------
Message: 5
Date: Mon, 7 Jan 2008 19:36:04 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Andreas Prlic <ap3 at sanger.ac.uk>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801071929590.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Andreas Prlic wrote:
> > What do people think about adding the JUnit jar to the test directory
> > of the biojava-live repository and make the appropriate changes to the
> > ant classpath? This would make it easier for people to test the
> >
>
> I would suggest to move all the jar files where we have dependencies
> on into a common subdirectory.
> e.g something called "libs" or "jars"
Using maven would resolve all of these issues.
Or alternatively, a maven build can create an ant build.xml that downloads
its dependencies from the maven central repository
http://maven.apache.org/plugins/maven-ant-plugin/
or there is Ivy for ant, which can be configured to use the maven central
repository
http://ant.apache.org/ivy/
The 'lib' directory doesn't really have a place any more.
michael
------------------------------
Message: 6
Date: Tue, 8 Jan 2008 11:17:35 +0800
From: "Mark Schreiber" <markjschreiber at gmail.com>
Subject: Re: [Biojava-dev] JUnit
To: "Michael Heuer" <heuermh at acm.org>
Cc: biojava-dev at biojava.org
Message-ID:
<93b45ca50801071917t1cef45epf8772b4370ef3f97 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi -
I have added the junit jar and modified the build.xml
I will leave the decision about a lib directory etc for some more debate.
- Mark
On Jan 8, 2008 8:36 AM, Michael Heuer <heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
> > > What do people think about adding the JUnit jar to the test directory
> > > of the biojava-live repository and make the appropriate changes to the
> > > ant classpath? This would make it easier for people to test the
> > >
> >
> > I would suggest to move all the jar files where we have dependencies
> > on into a common subdirectory.
> > e.g something called "libs" or "jars"
>
> Using maven would resolve all of these issues.
>
> Or alternatively, a maven build can create an ant build.xml that downloads
> its dependencies from the maven central repository
>
> http://maven.apache.org/plugins/maven-ant-plugin/
>
> or there is Ivy for ant, which can be configured to use the maven central
> repository
>
> http://ant.apache.org/ivy/
>
> The 'lib' directory doesn't really have a place any more.
>
> michael
>
>
------------------------------
Message: 7
Date: Mon, 7 Jan 2008 23:55:42 -0500 (EST)
From: Michael Heuer <heuermh at acm.org>
Subject: Re: [Biojava-dev] JUnit
To: Mark Schreiber <markjschreiber at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <Pine.GSO.4.44.0801072342240.4891-100000 at shell3.shore.net>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Mark Schreiber wrote:
> I will leave the decision about a lib directory etc for some more debate.
Now that we have a subversion repository in place, I would be happy to
create a maven-based build out on branch for consideration at some point.
Ideally this would happen after refactoring/cleanup/purge so I have less
work to do. ;)
michael
------------------------------
Message: 8
Date: Tue, 8 Jan 2008 10:23:56 +0200
From: "Michael Gang" <michaelgang at gmail.com>
Subject: [Biojava-dev] read fasta file
To: biojava-dev at biojava.org
Message-ID:
<6994d82b0801080023y3cdcc005g57b08c6566c37445 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear All,
I want to read a fasta file of dna (the accessions are internal to our
company and may not be like the convention), make manipulations on it
and write it to another file.
When i take the example from the book "Biojava in Anger" it works
fine, but I get warnings that the SeqIOTools type is deprecated.
When using the RichSequence.IOTools package I have problems that when
writing the fasta it changes the fasta header (it adds the lcl:
prefix).
I want that the fasta header will be in the output file like in the input
file.
Will the SeqIOTools type supported further ?
If not, is there another way to solve the problem ?
Thanks in advance,
Michael
------------------------------
Message: 9
Date: Tue, 08 Jan 2008 08:51:32 +0000
From: Richard Holland <holland at ebi.ac.uk>
Subject: Re: [Biojava-dev] read fasta file
To: Michael Gang <michaelgang at gmail.com>
Cc: biojava-dev at biojava.org
Message-ID: <47833994.7090608 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
SeqIOTools is deprecated - this means that it _may_ get dropped in a
future release and so you can't rely on it being present in any future
release.
RichSequence.IOTools follows the FASTA format exactly, which requires a
namespace prefix in the header, and it will change the existing header
if it does not already meet the FASTA standard. There is currently no
way to stop it from doing that, although you might want to raise a bug
report so that it goes on our list of things to change. You can do that
here: http://bugzilla.open-bio.org/enter_bug.cgi?product=BioJava
cheers,
Richard
Michael Gang wrote:
> Dear All,
>
> I want to read a fasta file of dna (the accessions are internal to our
> company and may not be like the convention), make manipulations on it
> and write it to another file.
> When i take the example from the book "Biojava in Anger" it works
> fine, but I get warnings that the SeqIOTools type is deprecated.
> When using the RichSequence.IOTools package I have problems that when
> writing the fasta it changes the fasta header (it adds the lcl:
> prefix).
> I want that the fasta header will be in the output file like in the input
file.
> Will the SeqIOTools type supported further ?
> If not, is there another way to solve the problem ?
>
> Thanks in advance,
> Michael
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416
http://www.biomart.org/
http://www.biojava.org/
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