[Biojava-dev] BioJava Development
Jeff Cope
jcope at cableone.net
Tue Jan 15 16:27:38 UTC 2008
Hi Richard and Mark,
Thanks for the quick response, and help in pointing out where the
new classes should go. Here are the classes I wanted to propose and where I
thought they should be. Due time constraints, this would probably be
something that I could put into BioJava 2, and would be willing to translate
to BioJava 3 when time came around.
As Mark had suggested it appears that the org.biojava.bio.proteomics
package would be the ideal area for the added classes, so I would be
interpreting functionality for most of the classes from the BioPython
library.
AromaticityCalc.java - Returns the sum of the percentage of the AA
sequence that is made up of the AA's Tyrosine, Tryptophan, and
Phenylalanine.
GRAVYCalc.java (Grand Average of Hydropathy) - Returns the average
sum of hydropathy of the AA sequence
InstabilityIndexCalc.java - Returns an estimated stability for a
protein sequence (<= 40 is considered stable)
AACompositionCalc.java - Breaks down protein sequences, and returns
the percent that individual AA's make up the sequence.
The functionality for Aromaticity, GRAVY, and Instability Index
would all come from the biopython library
(biopython-1.43/Bio/SeqUtils/ProtParam.py), and AAComposition is something
that we worked together that was useful for our application.
Most of the classes are pretty simple for the most part, I think the
most difficult part would be figuring out how the strings of characters are
translated to protein sequences in BioJava.
Anyway, Let me know if this sounds like it would be useful...
Thanks,
Jeff
-----Original Message-----
From: Mark Schreiber [mailto:markjschreiber at gmail.com]
Sent: Thursday, January 10, 2008 12:04 AM
To: Richard Holland
Cc: Jeff Cope; biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] BioJava Development
Hi Jeff -
I think the type of functionality you describe would be best placed in
the proteomic package where there is already some stuff for
calculating MW and PI.
Probably the reorganisation for BJ3 won't mean much change for your
code as these types of algorithms can usually be readily ported to any
new system.
- Mark
On Jan 10, 2008 1:09 AM, Richard Holland <holland at ebi.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Jeff.
>
> Thanks for volunteering! Sounds like you've got a useful set of tools
> which we would definitely appreciate as new BioJava features.
>
> We're currently planning a Big Reorganisation for a new BioJava 3 from
> the ground-up. Details will be published some time in February I expect,
> if not then early March. See this Wiki for things that are currently
> being considered (most will make it into the plan, some may not, but I
> won't know until I've written it up and identified the conflicting areas):
>
> http://www.biojava.org/wiki/BioJava3_Proposal
>
> (also see the associated Discussion page for further comments)
>
> If I were you, I'd hang on until the final plan is published. It will
> contain everything you need to know on how to write modules for the new
> BioJava 3.
>
> However, if you're in a rush to get it into the current BioJava 2
> release, then take a look round the JavaDocs to see what is present and
> what is not. You'll soon get a good idea of how things are organised and
> what features are absent. We also have a bugzilla page with some
> unresolved bugs - always a good starting point to learn how a system
> works and where the opportunities for development are!
>
http://bugzilla.open-bio.org/buglist.cgi?product=BioJava&bug_status=NEW&bug_
status=ASSIGNED&bug_status=REOPENED
>
> cheers,
> Richard
>
>
> Jeff Cope wrote:
> > 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-----
> > From: biojava-dev-bounces at lists.open-bio.org
> > [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
> > biojava-dev-request at lists.open-bio.org
> > Sent: Tuesday, January 08, 2008 1:52 AM
> > To: biojava-dev at lists.open-bio.org
> > Subject: biojava-dev Digest, Vol 59, Issue 2
> >
> > Send biojava-dev mailing list submissions to
> > biojava-dev 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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> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of biojava-dev digest..."
> >
> >
> > 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)
> 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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