From deniz.koellhofer at cambia.org  Wed Sep  1 02:21:52 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Wed, 1 Sep 2010 16:21:52 +1000
Subject: [Biojava-dev] biojava3 BLAST parser
In-Reply-To: <47FD5948-0439-45C6-A1AB-22E7CC8D17A6@scripps.edu>
References: <AANLkTikkkBhc7EoRDyMcvXww4n9kEbwyYZwKd9s=JJCx@mail.gmail.com>
	<FE9A1C82-E2A1-4A41-94CE-2CFBC0D5E83B@scripps.edu>
	<AANLkTi=sHWMtu8JqPCca3GBeWxN4N2n+0wiSw5y2qxR6@mail.gmail.com>
	<47FD5948-0439-45C6-A1AB-22E7CC8D17A6@scripps.edu>
Message-ID: <AANLkTi=DBJ5_KNqdd8KskFGKi0HO9MYe14iLZ3K=FyT4@mail.gmail.com>

Hi Scooter,

I'm currently parsing the BLAST results into plain data containers, but
wouldn't mind integrating it more with existing BioJava3 modules if I find
some time. Pretty busy at the moment, but I will let you guys know if I get
any further.

Cheers,
Deniz

On Wed, Sep 1, 2010 at 12:11 AM, Scooter Willis <HWillis at scripps.edu> wrote:

> Deniz
>
> It would be great to formalize the XML blast results as Java classes. Do
> you have any interest in taking on the project?
>
> Capturing the blast alignment using the new alignment classes would be a
> very nice feature. I like using XPATH as the query language to select for
> hits of interest which should allow for a SAX based approach to minimize the
> impact of very large XML files. XPATH and SAX does appear to have some
> constraints (
> http://stackoverflow.com/questions/1863250/is-it-there-any-xpath-processor-for-sax-model
> )
>
> Probably makes sense to have a Blast module that would depend on core and
> alignment.
>
> Thanks
>
> Scooter
>
>
>
> On Aug 31, 2010, at 8:49 AM, Deniz Koellhofer wrote:
>
> *Hi Scooter,*
> *
> *
> *Thanks for the reply. I guess the BlastXMLQuery is a good example to show
> how to quickly extract information from a BLAST result. *
> *
> *
> *But in my opinion biojava3 should alo have a Blast parser that generates
> java beans containing the complete Blast result set - similar to what
> biojava1.7.1 was doing. So yeah, I'm after translating the XML elements to
> Java classes.*
> *
> *
> *Would something like that fit into one of the biojava3 modules? homology,
> I/O?*
> *
> *
> *Thanks,*
> *Deniz*
> *
> *
> On Tue, Aug 31, 2010 at 8:43 PM, Scooter Willis <HWillis at scripps.edu>wrote:
>
>> Deniz
>>
>> Can you provide some requirements regarding parsing the Blast XML. I tend
>> to use XPATH and the DOM object to get to the data elements of interest so
>> you already have the ability to load the Blast XML and work with the data.
>> The difficulty of "parsing" is not an issue with XML. The BlastXMLQuery is
>> an example of searching the Blast XML to get results. Are you wanting the
>> XML elements translated to Java classes?
>>
>> Thanks
>>
>> Scooter
>>
>> On Aug 31, 2010, at 2:46 AM, Deniz Koellhofer wrote:
>>
>> > Hi,
>> >
>> > I wanted to find out the current state of blast parsing efforts in
>> biojava3
>> > - especially for ncbi blastxml output?
>> >
>> > I had a quick look and found some DOM based code fragments
>> > in org.biojava3.genome.query.BlastXMLQuery. Is there already anybody
>> working
>> > on a more comprehensive SAX parser?
>> >
>> > The biojava1.7.1 blastxml parser seems to work fine, however some of the
>> > tags in NCBI-BLASTN 2.2.23+ output like Hsp_midline, BlastOutput_param
>> don't
>> > seem to get parsed properly
>> > in org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.
>> >
>> > Cheers,
>> > Deniz
>> >
>> > --
>> > Deniz Koellhofer
>> > Cambia
>> > Initiative for Open Innovation (IOI)
>> > Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> --
> --
> Deniz Koellhofer
> Cambia
> Initiative for Open Innovation (IOI)
> Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>
>
>

From bugzilla-daemon at portal.open-bio.org  Wed Sep  1 13:59:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 1 Sep 2010 13:59:08 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009011759.o81Hx83i005446@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132


darnells at dnastar.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #2 from darnells at dnastar.com  2010-09-01 13:59 EST -------
I have applied the patch Amr sent over the weekend and tested it.  It's looking
pretty good.  I tested structures 3CYT, 4HHB, 3AFA, 1MR1, and 2OHX and the
following functions work as advertised:

Structure: getSites()
PDBSite: getSiteID(), getResidues()
PDBSite.Residue: getResidueName(), getResidueNumber()

I didn't directly test the set* methods, assuming they are working fine since
the get* methods work.

I noticed that PDBSite implements PDBRecord (similarly as SSBond).  The method
PDBSite.toPDB() ends in error:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.Arrays.copyOf(Arrays.java:2882)
        at
java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100)
        at
java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
        at java.lang.StringBuffer.append(StringBuffer.java:224)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:39)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:25)
        at com.dnastar.structureTest.Cookbook.printSiteIDs(Cookbook.java:36)
        at com.dnastar.structureTest.Cookbook.main(Cookbook.java:24)

That should be corrected so that it is consistent with the SSBond class.

I also agree with Jules Jacobsen's comments (via email): "We still need to
hook-up the REMARK 800 parser and make some unit tests for this."


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From jacobsen at ebi.ac.uk  Thu Sep  2 06:27:10 2010
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Thu, 02 Sep 2010 11:27:10 +0100
Subject: [Biojava-dev] Bug 3132: "SITE records in PDBFileReader"???
In-Reply-To: <A4009967D1886D4286A9B7931FD58610025EFB27@FS1.dnastar.com>
References: <A4009967D1886D4286A9B7931FD586100258B7E5@FS1.dnastar.com>
	<4C73A9A8.9010708@ebi.ac.uk>
	<A4009967D1886D4286A9B7931FD586100258B9C9@FS1.dnastar.com>
	<4C7667D8.9030000@ebi.ac.uk>
	<BLU150-ds94DFD18782F5554696C6D8E850@phx.gbl>
	<A4009967D1886D4286A9B7931FD586100258BC3C@FS1.dnastar.com>
	<BLU150-ds218C7A88228EE554DC5098E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD586100258BFCC@FS1.dnastar.com>
	<BLU150-ds18B1C8FDF9A109AE6757978E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EF71F@FS1.dnastar.com>
	<BLU150-ds21B29D475DEE3FD4F54128E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EF78D@FS1.dnastar.com>
	<BLU150-ds5D9BC89E2B67732E9560B8E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EFB27@FS1.dnastar.com>
Message-ID: <4C7F7BFE.6090101@ebi.ac.uk>

Hi Guys,

OK, please don't hack about with this - I'm adding it into the main 
branch of biojava 3, but things are changing a little.

PDBSite has been renamed to Site ('PDB' is a redundant)

The Residue inner class in PDBSite I have removed so as to use the Group 
interface which we have already defined.

As Steve says, Site.toPDB() throws an OutOfMemoryError - I'm fixing this 
and adding tests to Site, the PDBFileParser and other classes which have 
been touched.

Also I'm adding the Remark800 parser and minor cosmetic tweaks for 
consistent coding style.

This should be good to go for Mon/Tues next week.

Jules


On 01/09/2010 18:57, Steve Darnell wrote:
> Amr,
>
> I have applied the patch you sent over the weekend and tested it.  It's
> looking pretty good.  I tested structures 3CYT, 4HHB, 3AFA, 1MR1, and
> 2OHX and the following functions work as advertised:
>
> Structure: getSites()
> PDBSite: getSiteID(), getResidues()
> PDBSite.Residue: getResidueName(), getResidueNumber()
>
> I didn't directly test the set* methods, assuming they are working fine
> since the get* methods work.
>
> I noticed that PDBSite implements PDBRecord (similarly as SSBond).  The
> method PDBSite.toPDB() ends in error:
>
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> 	at java.util.Arrays.copyOf(Arrays.java:2882)
> 	at
> java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.jav
> a:100)
> 	at
> java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
> 	at java.lang.StringBuffer.append(StringBuffer.java:224)
> 	at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:39)
> 	at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:25)
> 	at
> com.dnastar.structureTest.Cookbook.printSiteIDs(Cookbook.java:36)
> 	at com.dnastar.structureTest.Cookbook.main(Cookbook.java:24)
>
> That should be corrected so that it is consistent with the SSBond class.
> I'll update the bug in Bugzilla with this information.
>
> Regards,
> Steve
>
> CC: Jules Jacobsen (also looking at SITE patch)
>
> -----Original Message-----
> From: Steve Darnell
> Sent: Tuesday, August 31, 2010 5:52 PM
> To: 'Amr AL-Hossary'
> Subject: RE: Bug 3132: "SITE records in PDBFileReader"???
>
> Amr,
>
>> The configuration is related to the PROJECT PROPERTIES, not to Your
> system.
>
> My project/application is using JDK 1.6.0_20 (Windows/Mac).
>
>
>> so all you need is SITE_IDENTIFIER, you don't need EVIDENCE_CODE, right
> ?
>
> I need the SITE_DESCRIPTION from REMARK 800.  SITE_IDENTIFIER, which is
> the same as the siteID from the SITE record, is not meaningful.
> Correct, I do not need the EVIDENCE_CODE.
>
>
>> Sorry? Isn't it already there in the PDBSite bean?
>> or what is the difference between site name&  site ID?
>
> For example, PDBID: 3CYT
>
> SITE, siteID or REMARK 800, SITE_IDENTIFIER: "AC1"
> REMARK 800, SITE_DESCRIPTION: "BINDING SITE FOR RESIDUE HEM O 104"
>
> The description is meaningful, the identifier is not.
>
>
>> please recheck the date.
>
> My mistake.  Wednesday, September 8th, two days after Labor Day (Monday,
> September 6th).
>
> I hope I addressed your questions.  Let me know if I can clarify
> anything else.
>
> Regards,
> Steve

From bugzilla-daemon at portal.open-bio.org  Thu Sep  2 13:21:39 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Sep 2010 13:21:39 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009021721.o82HLdKj024110@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #3 from jacobsen at ebi.ac.uk  2010-09-02 13:21 EST -------
SITE parser now up and running in DEV - should be available in automated build

- access Site objects from Structure.getSites()
- Output available in standard String and also proper PDB format (with padded
whitespace!) 
- java.lang.OutOfMemoryError fixed.
- tests added to PDBFileParserTest and SiteTest

REMARK 800 is being added too.


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From bugzilla-daemon at portal.open-bio.org  Thu Sep  2 17:32:50 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Sep 2010 17:32:50 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009022132.o82LWoP7005561@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #4 from darnells at dnastar.com  2010-09-02 17:32 EST -------
Using revision 8221 (2010/09/02 17:11:55), I experienced two unit test failures
in org.biojava.bio.structure.SiteTest during the build process.  Both
testToPDB_0args() and testToPDB_StringBuffer() failed because the expected
result did not have whitespace padding the line lengths to 80 characters.

In SiteTest.java, I replaced lines 118-119 and 134-135 with the following:
        String expResult =  "SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403 
HOH H 460                    " + newline +
                            "SITE     2 AC1  6 HOH H 464  HOH H 497            
                             " + newline;

I can successfully build afterwards.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 04:48:01 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 04:48:01 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009030848.o838m1qv018822@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #5 from jacobsen at ebi.ac.uk  2010-09-03 04:48 EST -------
Sorry Steve - I forgot to comment out the wrong bit of the test - the results
are correct, but the test was wrong! This is fixed now. 


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 06:43:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 06:43:08 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009031043.o83Ah8rE008398@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #6 from jacobsen at ebi.ac.uk  2010-09-03 06:43 EST -------
Updated SiteTest and PDBFileParserTest to include REMARK 800 parsing and
functionality - new methods added to Site to get/set and print its related
REMARK 800 section.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 15:55:12 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 15:55:12 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009031955.o83JtCUJ023861@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #7 from darnells at dnastar.com  2010-09-03 15:55 EST -------
There is a defect in PDBFileParser.java regarding sites.

Line 2044: String pdbCode = groupString.substring(4, 10).trim();

This assigns pdbCode to "$CHAIN $RESNUM$INSCODE" (e.g. "H 221A"), where the
Group interface documentation states it should just be $RESNUM$INSCODE (e.g.
"221A").  Also, setParent() is never called and assigned to a chain object.

Currently, to get the chain id for a site residue, you need to use the first
character of pdbCode.  Is it possible to link the site residue groups to their
correct chain?  This is somewhat analogous to SSBond; is a similar approach
appropriate?


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From bugzilla-daemon at portal.open-bio.org  Mon Sep  6 04:06:01 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 6 Sep 2010 04:06:01 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009060806.o86861xr002482@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #8 from amr_alhossary at hotmail.com  2010-09-06 04:06 EST -------
Actually Dr. Andreas idea was to use the PDBResidueNumber bean, and thats what
i did in my implementation.

Any way, we can update everything to use the new bean, but we need first to set
new clear definitions of terms like group, residue, HetAtom, etc. and the
relation between them.


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From deniz.koellhofer at cambia.org  Tue Sep 21 18:59:27 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Wed, 22 Sep 2010 08:59:27 +1000
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
Message-ID: <AANLkTikFDddZyWnBsYSKOWPx9FnyqxsBeY7ce0VWBUW-@mail.gmail.com>

Hi,

I'm trying to parse EMBL formatted files
with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
lines don't match.

Looks like the parser utilises the EMBLFormat class with the following ID
pattern:

*protected** **static** **final** Pattern **lp** = Pattern.compile(**
"^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
**);*

The ID lines in my files (retrieved from EMBL-EBI) look like *ID   A00197;
SV 1; linear; protein; PRT; SYN; 602 AA.*

Looks like the pattern is specifically written for dna/rna and should more
look like:

*protected** **static** **final** Pattern **lp** = Pattern.compile(**
"^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
**\\s+(\\d+)\\s+(BP|AA)\\.$"**);*

Or am I using he wrong RichSequence.IOTools function?

Cheers,

Deniz
-- 
Deniz Koellhofer
Cambia
Initiative for Open Innovation (IOI)
Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia

From deniz.koellhofer at cambia.org  Wed Sep 22 19:10:58 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Thu, 23 Sep 2010 09:10:58 +1000
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <20100922211815.12439.qmail@mxw1102.verio-web.com>
References: <20100922211815.12439.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTinid6vx5odR9xCMttR7P-P9RhdCYXqg7dUQeo99@mail.gmail.com>

Hi George,

This entry is from the embl patent protein database:
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

Have you used the RichSequence.IOTools successfully for parsing EMBL protein
files before? I assume this should always fail due to the "BP" in the regex?

Deniz

On Thu, Sep 23, 2010 at 7:18 AM, George Waldon <gwaldon at geneinfinity.org>wrote:

> Hi Deniz:
>
> I have a quick question that may be obvious, but which database do you get
> those protein files from?
>
> Thank you,
>
> George
>
> On Tue, Sep 21, 2010 at 3:59 PM, Deniz Koellhofer <
> deniz.koellhofer at cambia.org> wrote:
>
>    Hi,
>
>    I'm trying to parse EMBL formatted files
>    with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
>    lines don't match.
>
>    Looks like the parser utilises the EMBLFormat class with the following
> ID
>    pattern:
>
>    *protected** **static** **final** Pattern **lp** = Pattern.compile(**
>
>  "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
>    **);*
>
>    The ID lines in my files (retrieved from EMBL-EBI) look like *ID
> A00197;
>    SV 1; linear; protein; PRT; SYN; 602 AA.*
>
>    Looks like the pattern is specifically written for dna/rna and should
> more
>    look like:
>
>    *protected** **static** **final** Pattern **lp** = Pattern.compile(**
>
>  "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
>    **\\s+(\\d+)\\s+(BP|AA)\\.$"**);*
>
>    Or am I using he wrong RichSequence.IOTools function?
>
>    Cheers,
>
>    Deniz
>    --
>    Deniz Koellhofer
>    Cambia
>    Initiative for Open Innovation (IOI)
>    Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>    _______________________________________________
>    biojava-dev mailing list
>    biojava-dev at lists.open-bio.org
>    http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>
>


-- 
Deniz Koellhofer
Cambia
Initiative for Open Innovation (IOI)
Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia

From gwaldon at geneinfinity.org  Thu Sep 23 00:23:48 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Thu, 23 Sep 2010 00:23:48 -0400
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
Message-ID: <20100923042349.77746.qmail@mxw1102.verio-web.com>

Curious, this seems to be the only place to find this type of files. Not really an official format, a little bit like GenPept. Your fix should probably work. Can you fill a bug on bugzilla (http://bugzilla.open-bio.org/)?

Best,
George

On Wed, Sep 22, 2010 at 4:10 PM, Deniz Koellhofer <deniz.koellhofer at cambia.org> wrote:

    Hi George,

    This entry is from the embl patent protein database: ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

    Have you used the RichSequence.IOTools successfully for parsing EMBL protein files before? I assume this should always fail due to the "BP" in the regex?

    Deniz

    On Thu, Sep 23, 2010 at 7:18 AM, George Waldon <gwaldon at geneinfinity.org> wrote:

        Hi Deniz:

        I have a quick question that may be obvious, but which database do you get those protein files from?

        Thank you,

        George


        On Tue, Sep 21, 2010 at 3:59 PM, Deniz Koellhofer <deniz.koellhofer at cambia.org> wrote:

           Hi,

           I'm trying to parse EMBL formatted files
           with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
           lines don't match.

           Looks like the parser utilises the EMBLFormat class with the following ID
           pattern:

           *protected** **static** **final** Pattern **lp** = Pattern.compile(**
           "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
           **);*

           The ID lines in my files (retrieved from EMBL-EBI) look like *ID   A00197;
           SV 1; linear; protein; PRT; SYN; 602 AA.*

           Looks like the pattern is specifically written for dna/rna and should more
           look like:

           *protected** **static** **final** Pattern **lp** = Pattern.compile(**
           "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
           **\\s+(\\d+)\\s+(BP|AA)\\.$"**);*

           Or am I using he wrong RichSequence.IOTools function?

           Cheers,

           Deniz
           --
           Deniz Koellhofer
           Cambia
           Initiative for Open Innovation (IOI)
           Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
           _______________________________________________
           biojava-dev mailing list
           biojava-dev at lists.open-bio.org
           http://lists.open-bio.org/mailman/listinfo/biojava-dev





From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 00:35:54 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 00:35:54 -0400
Subject: [Biojava-dev] [Bug 3137] New:
	RichSequence.IOTools.readEMBLProtein() fails on EMBL patent
	protein entries.
Message-ID: <bug-3137-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3137

           Summary: RichSequence.IOTools.readEMBLProtein() fails on EMBL
                    patent protein entries.
           Product: BioJava
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dkoellhofer at gmail.com


Hi,

I'm trying to parse EMBL formatted files with
RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID lines don't
match.

Looks like the parser utilises the EMBLFormat class with the following ID
pattern:
protected static final Pattern lp =
Pattern.compile("^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$");

The ID lines in my files (retrieved from EMBL-EBI) look like ID   A00197; SV 1;
linear; protein; PRT; SYN; 602 AA.

Looks like the pattern is specifically written for dna/rna and should more look
like:

protected static final Pattern lp =
Pattern.compile("^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+(BP|AA)\\.$");

The failing protein sequences come from the embl patent protein database:
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

Cheers,

Deniz


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From biopython at maubp.freeserve.co.uk  Thu Sep 23 05:10:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 10:10:56 +0100
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <20100923042349.77746.qmail@mxw1102.verio-web.com>
References: <20100923042349.77746.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>

On Thu, Sep 23, 2010 at 5:23 AM, George Waldon <gwaldon at geneinfinity.org> wrote:
>
> Curious, this seems to be the only place to find this type of files.
> Not really an official format, a little bit like GenPept. Your fix
> should probably work. Can you fill a bug on bugzilla
> (http://bugzilla.open-bio.org/)?
>
> Best,
> George

Bug filed: http://bugzilla.open-bio.org/show_bug.cgi?id=3137

Interestingly Biopython doesn't support Protein EMBL files either
(I didn't know they existed), I wonder if BioPerl does?

Peter

From biopython at maubp.freeserve.co.uk  Thu Sep 23 06:51:35 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 11:51:35 +0100
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>
References: <20100923042349.77746.qmail@mxw1102.verio-web.com>
	<AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>
Message-ID: <AANLkTimpPKyhfpFsXg0E2Qob6rPqeu7aByAi=H2cQ=f4@mail.gmail.com>

Hi BioJava team et al,

Thanks for the indirect alert that protein EMBL files exist, e.g.
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

I've just updated Biopython to support them.

Chris - I've CC'd you in case you want to look at this for BioPerl.

Peter

On Thu, Sep 23, 2010 at 10:10 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Sep 23, 2010 at 5:23 AM, George Waldon <gwaldon at geneinfinity.org> wrote:
>>
>> Curious, this seems to be the only place to find this type of files.
>> Not really an official format, a little bit like GenPept. Your fix
>> should probably work. Can you fill a bug on bugzilla
>> (http://bugzilla.open-bio.org/)?
>>
>> Best,
>> George
>
> Bug filed: http://bugzilla.open-bio.org/show_bug.cgi?id=3137
>
> Interestingly Biopython doesn't support Protein EMBL files either
> (I didn't know they existed), I wonder if BioPerl does?
>
> Peter

From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 18:45:44 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 18:45:44 -0400
Subject: [Biojava-dev] [Bug 3138] New: SeqRes2AtomAligner misaligns Atom
	groups at N-terminus
Message-ID: <bug-3138-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3138

           Summary: SeqRes2AtomAligner misaligns Atom groups at N-terminus
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: structure
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: darnells at dnastar.com


The SeqRes2AtomAligner misaligns the N-terminus residues for 1BKV (Collagen)
and 3NLC (VP0956).  Both structures have SEQRES residues without corresponding
ATOM residues at the N-terminus.  In the case of 3NLC, the observed mapping is
(* = no ATOM group):

SEQRES MGHHHHHHSHMIRINE
ATOM   M**********IRINE

and the correct mapping should be:

SEQRES MGHHHHHHSHMIRINE
ATOM   **********MIRINE

Activating the Chemical Component Dictionary does not help the alignment.  Is
it significant that for 1BKV and 3NLC the first SEQRES group and the first ATOM
group are the same residue (nearly the same for 1BKV, PRO ~ HYP)?  Is this a
situation that is difficult for the Needleman-Wunsch algorithm used by
SeqRes2AtomAligner?


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 18:50:11 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 18:50:11 -0400
Subject: [Biojava-dev] [Bug 3138] SeqRes2AtomAligner misaligns Atom groups
	at N-terminus
In-Reply-To: <bug-3138-485@http.bugzilla.open-bio.org/>
Message-ID: <201009232250.o8NMoBr0029097@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3138


ap3 at sanger.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|biojava-dev at biojava.org     |andreas at sdsc.edu




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From bugzilla-daemon at portal.open-bio.org  Fri Sep 24 01:45:17 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 24 Sep 2010 01:45:17 -0400
Subject: [Biojava-dev] [Bug 3137] RichSequence.IOTools.readEMBLProtein()
	fails on EMBL patent protein entries.
In-Reply-To: <bug-3137-485@http.bugzilla.open-bio.org/>
Message-ID: <201009240545.o8O5jHw9007788@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3137


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2010-09-24 01:45 EST -------
Committed new pattern and added a test. Note that protein sequences from KIPO
have a non-regular ID line that prevent parsing.


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From gindin at gmail.com  Sun Sep 26 19:05:50 2010
From: gindin at gmail.com (Yevgeniy Gindin)
Date: Sun, 26 Sep 2010 19:05:50 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties
Message-ID: <AANLkTikqR=hvwnQOwxbvPTvfEU+QfKLAn18QpPrhYZTd@mail.gmail.com>

There seems to be a bug in
org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties.setBlastProgram(String)
The method throws an exception when a valid program name is given. I
believe that this is due to the fact that two String objects are
tested with the "==" operator rather then equals().

To illustrate:
String a = new String ("a");
String b = new String ("a");
System.out.println (a == b);

The above will return false.

--
Yevgeniy

From pedros at berkeley.edu  Mon Sep 27 15:55:05 2010
From: pedros at berkeley.edu (Pedro Silva)
Date: Mon, 27 Sep 2010 12:55:05 -0700
Subject: [Biojava-dev] BioJava 3 current status
Message-ID: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>

On 30 Jun 2010, at 12:18, Andreas Prlic wrote:

> About BioJava 3: This has made great progress over the last weeks and
> a lot of new functionality has been committed to SVN. To make this
> release ready there are now two new tools:
> 
> * There is now a BioJava Maven repository, which is hosting SNAPSHOT
> builds from the current SVN.

Hi Andreas,

A couple questions about Biojava 3, with which I'm trying to interoperate from Clojure:

1. You mention SVN above, but I also see an active git repository at github. 
   Is that only a mirror, and active development occurs at biojava.org's svn repo?
2. Are all non biojava3-prefixed modules in the Maven repository not suitable to use with Biojava 3?
   Eg., biosql, das, etc.
3. Will the Maven repository eventually also host releases, not just snapshots?
   How far along would a release be?

To provide some context, I've started coding on 'Bioclojure', and my strategy is to position my efforts downstream from Biojava (3).
To that end, I'm trying to figure out the best way to pull development snapshots and stable releases from you guys, as well as
your current state of affairs in the porting of biojava1/biojavax to biojava3.

Thanks for your help. 

Pedro
-- 
Pedro Silva <pedros at berkeley.edu>
UC Berkeley - PMB


From andreas at sdsc.edu  Mon Sep 27 16:40:30 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 27 Sep 2010 13:40:30 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
Message-ID: <AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>

Hi Pedro,


> 1. You mention SVN above, but I also see an active git repository at github.
> ? Is that only a mirror, and active development occurs at biojava.org's svn repo?

Yes, git is only a mirror. The main development happens in an ssh
protected SVN, which is replicated onto the anonymous SVN and git
servers (within one hour after a commit).

> 2. Are all non biojava3-prefixed modules in the Maven repository not suitable to use with Biojava 3?
> ? Eg., biosql, das, etc.

In an ideal world we would have a clear separation of biojava 3 and
biojava 1.  However the way things are at the present there is some
mix and  there is still legacy code in SVN. e.g. the module "core" is
essentially a lot of biojava1.7. It is up to the module maintainers to
upgrade their code. We will need to take a decision soon if we want to
drop all legacy code from SVN and only support biojava3 based code
from that point on. ( need to do a dependency analysis how many
modules are still depending on the old core).

> 3. Will the Maven repository eventually also host releases, not just snapshots?

yes

> ? How far along would a release be?

We have not set a date at the present.  I will write a proposal about
the next steps to the mailing list soon and then this is up for
discussion. Having said this, several people are using the current SVN
checkouts in production environments and what seems mostly missing is
lots of documentation...

> To provide some context, I've started coding on 'Bioclojure', and my strategy is to position my efforts downstream from Biojava (3).

Excellent! Are you planning to add additional functionality or is it
mainly a wrapper for biojava?

> To that end, I'm trying to figure out the best way to pull development snapshots and stable releases from you guys, as well as
> your current state of affairs in the porting of biojava1/biojavax to biojava3.

The automated build system pushes any successful build to

http://www.biojava.org/download/maven/

This means all libraries that are available from there are guaranteed
to pass the junit tests and compile correctly.

Andreas


From pedros at berkeley.edu  Mon Sep 27 19:13:17 2010
From: pedros at berkeley.edu (Pedro Silva)
Date: Mon, 27 Sep 2010 16:13:17 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
	<AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>
Message-ID: <1285629197.25539.38.camel@dev.dzlab.pmb.berkeley.edu>

On Mon, 2010-09-27 at 13:40 -0700, Andreas Prlic wrote:

> Excellent! Are you planning to add additional functionality or is it
> mainly a wrapper for biojava?

Well, it started as native Clojure all the way, then I figured it would
be a wrapper around Biojava, *then* I figured, Clojure-Java
interoperability is so good, I don't need any wrapper at all.

That leaves adding additional functionality, plus wrapping the more
verbose and/or common Biojava idioms.

Thanks for your answers again. I appreciate it.

Pedro
-- 
Pedro Silva <pedros at berkeley.edu>
UC Berkeley - PMB


From gwaldon at geneinfinity.org  Mon Sep 27 23:34:01 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 27 Sep 2010 23:34:01 -0400
Subject: [Biojava-dev] BioJava 3 current status
Message-ID: <20100928033401.79626.qmail@mxw1102.verio-web.com>

On Mon, Sep 27, 2010 at 1:40 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

>In an ideal world we would have a clear separation of biojava 3 and
>biojava 1.  However the way things are at the present there is some
>mix and  there is still legacy code in SVN. e.g. the module "core" is
>essentially a lot of biojava1.7. It is up to the module maintainers to
>upgrade their code. We will need to take a decision soon if we want to
>drop all legacy code from SVN and only support biojava3 based code
>from that point on. ( need to do a dependency analysis how many
>modules are still depending on the old core).

I see a few (rather lonely) BioException in the biojava3-ws module and a "biojava1-core" dependency in org.biojava3.core.sequence.transcription.DefaultRNAProteinTranscription in the sequence-core module. I also see that many of the classes of the sequence-core module are duplicated in the biojava3-core module. Is-there a meaning for this duplication?

George


From andreas at sdsc.edu  Tue Sep 28 13:17:37 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 28 Sep 2010 10:17:37 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <20100928033401.79626.qmail@mxw1102.verio-web.com>
References: <20100928033401.79626.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTikFqh-Uz4sLj86aOHt2kQFgCq8xuDqrgBXJ7W9m@mail.gmail.com>

>
> I see a few (rather lonely) BioException in the biojava3-ws module and a "biojava1-core" dependency in org.biojava3.core.sequence.transcription.DefaultRNAProteinTranscription in the sequence-core module. I also see that many of the classes of the sequence-core module are duplicated in the biojava3-core module. Is-there a meaning for this duplication?

Andy, Scooter, is this a leftover from the initial days? Can I delete
the sequence module? Is this all biojava3-core now?

On a related matter, is anybody working on genebank and embl file
parsing for biojava3? There were some feature requests for this and
would be nice if this could be done in biojava3 as well...

Andreas



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From sylvain.foisy at inflammgen.org  Tue Sep 28 09:54:43 2010
From: sylvain.foisy at inflammgen.org (Sylvain Foisy)
Date: Tue, 28 Sep 2010 09:54:43 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy
	Gindin)
Message-ID: <C8C76BE3.7499%sylvain.foisy@inflammgen.org>

Hi,

Ok, it should be fixed in SVN. I actually replaced the == by a call to the
Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
the array obsolete.

Thanks for pointing it ;-)

Best regards

Sylvain




From HWillis at scripps.edu  Tue Sep 28 13:30:50 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 28 Sep 2010 13:30:50 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties
	(Yevgeniy	Gindin)
Message-ID: <BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>

Andreas

Yes you can delete the sequence modules. I will add the parsers to the list and will use that to make sure core sequence module properly models the data elements.

Thanks

Scooter

----- Reply message -----
From: "Sylvain Foisy" <sylvain.foisy at inflammgen.org>
Date: Tue, Sep 28, 2010 1:18 pm
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy Gindin)
To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>

Hi,

Ok, it should be fixed in SVN. I actually replaced the == by a call to the
Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
the array obsolete.

Thanks for pointing it ;-)

Best regards

Sylvain



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


From bugzilla-daemon at portal.open-bio.org  Wed Sep 29 00:48:46 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 29 Sep 2010 00:48:46 -0400
Subject: [Biojava-dev] [Bug 3140] New: Required Correction in
	GenbankLocationParser class
Message-ID: <bug-3140-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3140

           Summary: Required Correction in GenbankLocationParser class
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


Reported on behalf of Deepak Sheoran:

Their is problem with GenbankLocationParser class, this class don't process
genbank record with    Accession: M32882. LocationParser class fails at
following line in genbank record:

    gene  </nuccore/150738?itemid=33&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
    mRNA  </nuccore/150738?itemid=15&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
                    /note="alternative transcript"


Exception stack trace is as follows:

       Could not understand position: 10206,1..855
       org.biojava.bio.seq.io.ParseException: Could not understand position:
10206,1..855
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:277)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:244)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131)

I did some investigation in following matter, and found the defect in regular
expression named as "gp" in GenbankLocationParser class.

This error can be fixed by applying attached patch. And then for testing I have
created a method which proves that it can now understand all the possible
combination of location. This test class is also attached so that you can test
my patch before and after its application.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 29 00:52:33 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 29 Sep 2010 00:52:33 -0400
Subject: [Biojava-dev] [Bug 3140] Required Correction in
	GenbankLocationParser class
In-Reply-To: <bug-3140-485@http.bugzilla.open-bio.org/>
Message-ID: <201009290452.o8T4qXkg023352@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3140


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2010-09-29 00:52 EST -------
Applied proposed patch and test case. 

Index: GenbankLocationParser.java
===================================================================
--- GenbankLocationParser.java  (revision 8212)
+++ GenbankLocationParser.java  (working copy)
@@ -133,7 +133,7 @@

     // O beautiful regex, we worship you. (:-)
     // this matches grouped locations
-    private static Pattern gp =
Pattern.compile("^([^\\(\\):]*?:)?(complement|join|order)?\\(*{0,1}(.*?)\\)*{0,1}$");
+    private static Pattern gp =
Pattern.compile("^([^\\(\\):]*?:)?(complement|join|order)?\\({0,1}(.*?\\)*{0,1})$");
     // this matches range locations
     private static Pattern rp =
Pattern.compile("^\\(*(.*?)\\)*(\\.\\.\\(*(.*)\\)*)?$");
     // this matches accession/version pairs


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From chapmanb at 50mail.com  Wed Sep 29 07:49:24 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 29 Sep 2010 07:49:24 -0400
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
Message-ID: <20100929114924.GC8837@sobchak.mgh.harvard.edu>

Pedro;

> To provide some context, I've started coding on 'Bioclojure', and my
> strategy is to position my efforts downstream from Biojava (3).

That's awesome. I've been teaching myself Clojure to be able to
interoperate with Biojava and the GATK/Picard toolkits. Great to
hear you are tackling this.

Have you also seen Jan Aerts work?

http://github.com/jandot/bioclojure

Brad

From andreas at sdsc.edu  Wed Sep 29 22:17:45 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 29 Sep 2010 19:17:45 -0700
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy
	Gindin)
In-Reply-To: <BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>
References: <ActfFLPB8id2wMsHEd+Nfci8yIq+ogAHjHPf>
	<BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>
Message-ID: <AANLkTimvxFXHOuVM_cRdmWGJrABxkMqB4K-okqDA-7sr@mail.gmail.com>

Hi Scooter,

I just deleted the sequence modules in SVN. If it later turns out that
there is some code that was forgotten to be moved to biojava3-core,
there is still a tag in svn to show the status before it got
deleted...

Andreas

On Tue, Sep 28, 2010 at 10:30 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> Andreas
>
> Yes you can delete the sequence modules. I will add the parsers to the list and will use that to make sure core sequence module properly models the data elements.
>
> Thanks
>
> Scooter
>
> ----- Reply message -----
> From: "Sylvain Foisy" <sylvain.foisy at inflammgen.org>
> Date: Tue, Sep 28, 2010 1:18 pm
> Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy Gindin)
> To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
>
> Hi,
>
> Ok, it should be fixed in SVN. I actually replaced the == by a call to the
> Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
> the array obsolete.
>
> Thanks for pointing it ;-)
>
> Best regards
>
> Sylvain
>
>
>
> _______________________________________________
> 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
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

From deniz.koellhofer at cambia.org  Wed Sep  1 06:21:52 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Wed, 1 Sep 2010 16:21:52 +1000
Subject: [Biojava-dev] biojava3 BLAST parser
In-Reply-To: <47FD5948-0439-45C6-A1AB-22E7CC8D17A6@scripps.edu>
References: <AANLkTikkkBhc7EoRDyMcvXww4n9kEbwyYZwKd9s=JJCx@mail.gmail.com>
	<FE9A1C82-E2A1-4A41-94CE-2CFBC0D5E83B@scripps.edu>
	<AANLkTi=sHWMtu8JqPCca3GBeWxN4N2n+0wiSw5y2qxR6@mail.gmail.com>
	<47FD5948-0439-45C6-A1AB-22E7CC8D17A6@scripps.edu>
Message-ID: <AANLkTi=DBJ5_KNqdd8KskFGKi0HO9MYe14iLZ3K=FyT4@mail.gmail.com>

Hi Scooter,

I'm currently parsing the BLAST results into plain data containers, but
wouldn't mind integrating it more with existing BioJava3 modules if I find
some time. Pretty busy at the moment, but I will let you guys know if I get
any further.

Cheers,
Deniz

On Wed, Sep 1, 2010 at 12:11 AM, Scooter Willis <HWillis at scripps.edu> wrote:

> Deniz
>
> It would be great to formalize the XML blast results as Java classes. Do
> you have any interest in taking on the project?
>
> Capturing the blast alignment using the new alignment classes would be a
> very nice feature. I like using XPATH as the query language to select for
> hits of interest which should allow for a SAX based approach to minimize the
> impact of very large XML files. XPATH and SAX does appear to have some
> constraints (
> http://stackoverflow.com/questions/1863250/is-it-there-any-xpath-processor-for-sax-model
> )
>
> Probably makes sense to have a Blast module that would depend on core and
> alignment.
>
> Thanks
>
> Scooter
>
>
>
> On Aug 31, 2010, at 8:49 AM, Deniz Koellhofer wrote:
>
> *Hi Scooter,*
> *
> *
> *Thanks for the reply. I guess the BlastXMLQuery is a good example to show
> how to quickly extract information from a BLAST result. *
> *
> *
> *But in my opinion biojava3 should alo have a Blast parser that generates
> java beans containing the complete Blast result set - similar to what
> biojava1.7.1 was doing. So yeah, I'm after translating the XML elements to
> Java classes.*
> *
> *
> *Would something like that fit into one of the biojava3 modules? homology,
> I/O?*
> *
> *
> *Thanks,*
> *Deniz*
> *
> *
> On Tue, Aug 31, 2010 at 8:43 PM, Scooter Willis <HWillis at scripps.edu>wrote:
>
>> Deniz
>>
>> Can you provide some requirements regarding parsing the Blast XML. I tend
>> to use XPATH and the DOM object to get to the data elements of interest so
>> you already have the ability to load the Blast XML and work with the data.
>> The difficulty of "parsing" is not an issue with XML. The BlastXMLQuery is
>> an example of searching the Blast XML to get results. Are you wanting the
>> XML elements translated to Java classes?
>>
>> Thanks
>>
>> Scooter
>>
>> On Aug 31, 2010, at 2:46 AM, Deniz Koellhofer wrote:
>>
>> > Hi,
>> >
>> > I wanted to find out the current state of blast parsing efforts in
>> biojava3
>> > - especially for ncbi blastxml output?
>> >
>> > I had a quick look and found some DOM based code fragments
>> > in org.biojava3.genome.query.BlastXMLQuery. Is there already anybody
>> working
>> > on a more comprehensive SAX parser?
>> >
>> > The biojava1.7.1 blastxml parser seems to work fine, however some of the
>> > tags in NCBI-BLASTN 2.2.23+ output like Hsp_midline, BlastOutput_param
>> don't
>> > seem to get parsed properly
>> > in org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.
>> >
>> > Cheers,
>> > Deniz
>> >
>> > --
>> > Deniz Koellhofer
>> > Cambia
>> > Initiative for Open Innovation (IOI)
>> > Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> --
> --
> Deniz Koellhofer
> Cambia
> Initiative for Open Innovation (IOI)
> Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>
>
>


From bugzilla-daemon at portal.open-bio.org  Wed Sep  1 17:59:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 1 Sep 2010 13:59:08 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009011759.o81Hx83i005446@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132


darnells at dnastar.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #2 from darnells at dnastar.com  2010-09-01 13:59 EST -------
I have applied the patch Amr sent over the weekend and tested it.  It's looking
pretty good.  I tested structures 3CYT, 4HHB, 3AFA, 1MR1, and 2OHX and the
following functions work as advertised:

Structure: getSites()
PDBSite: getSiteID(), getResidues()
PDBSite.Residue: getResidueName(), getResidueNumber()

I didn't directly test the set* methods, assuming they are working fine since
the get* methods work.

I noticed that PDBSite implements PDBRecord (similarly as SSBond).  The method
PDBSite.toPDB() ends in error:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.Arrays.copyOf(Arrays.java:2882)
        at
java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100)
        at
java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
        at java.lang.StringBuffer.append(StringBuffer.java:224)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:39)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:25)
        at com.dnastar.structureTest.Cookbook.printSiteIDs(Cookbook.java:36)
        at com.dnastar.structureTest.Cookbook.main(Cookbook.java:24)

That should be corrected so that it is consistent with the SSBond class.

I also agree with Jules Jacobsen's comments (via email): "We still need to
hook-up the REMARK 800 parser and make some unit tests for this."


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From jacobsen at ebi.ac.uk  Thu Sep  2 10:27:10 2010
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Thu, 02 Sep 2010 11:27:10 +0100
Subject: [Biojava-dev] Bug 3132: "SITE records in PDBFileReader"???
In-Reply-To: <A4009967D1886D4286A9B7931FD58610025EFB27@FS1.dnastar.com>
References: <A4009967D1886D4286A9B7931FD586100258B7E5@FS1.dnastar.com>
	<4C73A9A8.9010708@ebi.ac.uk>
	<A4009967D1886D4286A9B7931FD586100258B9C9@FS1.dnastar.com>
	<4C7667D8.9030000@ebi.ac.uk>
	<BLU150-ds94DFD18782F5554696C6D8E850@phx.gbl>
	<A4009967D1886D4286A9B7931FD586100258BC3C@FS1.dnastar.com>
	<BLU150-ds218C7A88228EE554DC5098E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD586100258BFCC@FS1.dnastar.com>
	<BLU150-ds18B1C8FDF9A109AE6757978E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EF71F@FS1.dnastar.com>
	<BLU150-ds21B29D475DEE3FD4F54128E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EF78D@FS1.dnastar.com>
	<BLU150-ds5D9BC89E2B67732E9560B8E890@phx.gbl>
	<A4009967D1886D4286A9B7931FD58610025EFB27@FS1.dnastar.com>
Message-ID: <4C7F7BFE.6090101@ebi.ac.uk>

Hi Guys,

OK, please don't hack about with this - I'm adding it into the main 
branch of biojava 3, but things are changing a little.

PDBSite has been renamed to Site ('PDB' is a redundant)

The Residue inner class in PDBSite I have removed so as to use the Group 
interface which we have already defined.

As Steve says, Site.toPDB() throws an OutOfMemoryError - I'm fixing this 
and adding tests to Site, the PDBFileParser and other classes which have 
been touched.

Also I'm adding the Remark800 parser and minor cosmetic tweaks for 
consistent coding style.

This should be good to go for Mon/Tues next week.

Jules


On 01/09/2010 18:57, Steve Darnell wrote:
> Amr,
>
> I have applied the patch you sent over the weekend and tested it.  It's
> looking pretty good.  I tested structures 3CYT, 4HHB, 3AFA, 1MR1, and
> 2OHX and the following functions work as advertised:
>
> Structure: getSites()
> PDBSite: getSiteID(), getResidues()
> PDBSite.Residue: getResidueName(), getResidueNumber()
>
> I didn't directly test the set* methods, assuming they are working fine
> since the get* methods work.
>
> I noticed that PDBSite implements PDBRecord (similarly as SSBond).  The
> method PDBSite.toPDB() ends in error:
>
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> 	at java.util.Arrays.copyOf(Arrays.java:2882)
> 	at
> java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.jav
> a:100)
> 	at
> java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
> 	at java.lang.StringBuffer.append(StringBuffer.java:224)
> 	at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:39)
> 	at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:25)
> 	at
> com.dnastar.structureTest.Cookbook.printSiteIDs(Cookbook.java:36)
> 	at com.dnastar.structureTest.Cookbook.main(Cookbook.java:24)
>
> That should be corrected so that it is consistent with the SSBond class.
> I'll update the bug in Bugzilla with this information.
>
> Regards,
> Steve
>
> CC: Jules Jacobsen (also looking at SITE patch)
>
> -----Original Message-----
> From: Steve Darnell
> Sent: Tuesday, August 31, 2010 5:52 PM
> To: 'Amr AL-Hossary'
> Subject: RE: Bug 3132: "SITE records in PDBFileReader"???
>
> Amr,
>
>> The configuration is related to the PROJECT PROPERTIES, not to Your
> system.
>
> My project/application is using JDK 1.6.0_20 (Windows/Mac).
>
>
>> so all you need is SITE_IDENTIFIER, you don't need EVIDENCE_CODE, right
> ?
>
> I need the SITE_DESCRIPTION from REMARK 800.  SITE_IDENTIFIER, which is
> the same as the siteID from the SITE record, is not meaningful.
> Correct, I do not need the EVIDENCE_CODE.
>
>
>> Sorry? Isn't it already there in the PDBSite bean?
>> or what is the difference between site name&  site ID?
>
> For example, PDBID: 3CYT
>
> SITE, siteID or REMARK 800, SITE_IDENTIFIER: "AC1"
> REMARK 800, SITE_DESCRIPTION: "BINDING SITE FOR RESIDUE HEM O 104"
>
> The description is meaningful, the identifier is not.
>
>
>> please recheck the date.
>
> My mistake.  Wednesday, September 8th, two days after Labor Day (Monday,
> September 6th).
>
> I hope I addressed your questions.  Let me know if I can clarify
> anything else.
>
> Regards,
> Steve


From bugzilla-daemon at portal.open-bio.org  Thu Sep  2 17:21:39 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Sep 2010 13:21:39 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009021721.o82HLdKj024110@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #3 from jacobsen at ebi.ac.uk  2010-09-02 13:21 EST -------
SITE parser now up and running in DEV - should be available in automated build

- access Site objects from Structure.getSites()
- Output available in standard String and also proper PDB format (with padded
whitespace!) 
- java.lang.OutOfMemoryError fixed.
- tests added to PDBFileParserTest and SiteTest

REMARK 800 is being added too.


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From bugzilla-daemon at portal.open-bio.org  Thu Sep  2 21:32:50 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 2 Sep 2010 17:32:50 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009022132.o82LWoP7005561@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #4 from darnells at dnastar.com  2010-09-02 17:32 EST -------
Using revision 8221 (2010/09/02 17:11:55), I experienced two unit test failures
in org.biojava.bio.structure.SiteTest during the build process.  Both
testToPDB_0args() and testToPDB_StringBuffer() failed because the expected
result did not have whitespace padding the line lengths to 80 characters.

In SiteTest.java, I replaced lines 118-119 and 134-135 with the following:
        String expResult =  "SITE     1 AC1  6 ARG H 221A LYS H 224  HOH H 403 
HOH H 460                    " + newline +
                            "SITE     2 AC1  6 HOH H 464  HOH H 497            
                             " + newline;

I can successfully build afterwards.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 08:48:01 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 04:48:01 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009030848.o838m1qv018822@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #5 from jacobsen at ebi.ac.uk  2010-09-03 04:48 EST -------
Sorry Steve - I forgot to comment out the wrong bit of the test - the results
are correct, but the test was wrong! This is fixed now. 


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 10:43:08 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 06:43:08 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009031043.o83Ah8rE008398@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #6 from jacobsen at ebi.ac.uk  2010-09-03 06:43 EST -------
Updated SiteTest and PDBFileParserTest to include REMARK 800 parsing and
functionality - new methods added to Site to get/set and print its related
REMARK 800 section.


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From bugzilla-daemon at portal.open-bio.org  Fri Sep  3 19:55:12 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 3 Sep 2010 15:55:12 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009031955.o83JtCUJ023861@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #7 from darnells at dnastar.com  2010-09-03 15:55 EST -------
There is a defect in PDBFileParser.java regarding sites.

Line 2044: String pdbCode = groupString.substring(4, 10).trim();

This assigns pdbCode to "$CHAIN $RESNUM$INSCODE" (e.g. "H 221A"), where the
Group interface documentation states it should just be $RESNUM$INSCODE (e.g.
"221A").  Also, setParent() is never called and assigned to a chain object.

Currently, to get the chain id for a site residue, you need to use the first
character of pdbCode.  Is it possible to link the site residue groups to their
correct chain?  This is somewhat analogous to SSBond; is a similar approach
appropriate?


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From bugzilla-daemon at portal.open-bio.org  Mon Sep  6 08:06:01 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 6 Sep 2010 04:06:01 -0400
Subject: [Biojava-dev] [Bug 3132] SITE records in PDBFileReader
In-Reply-To: <bug-3132-485@http.bugzilla.open-bio.org/>
Message-ID: <201009060806.o86861xr002482@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3132





------- Comment #8 from amr_alhossary at hotmail.com  2010-09-06 04:06 EST -------
Actually Dr. Andreas idea was to use the PDBResidueNumber bean, and thats what
i did in my implementation.

Any way, we can update everything to use the new bean, but we need first to set
new clear definitions of terms like group, residue, HetAtom, etc. and the
relation between them.


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From deniz.koellhofer at cambia.org  Tue Sep 21 22:59:27 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Wed, 22 Sep 2010 08:59:27 +1000
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
Message-ID: <AANLkTikFDddZyWnBsYSKOWPx9FnyqxsBeY7ce0VWBUW-@mail.gmail.com>

Hi,

I'm trying to parse EMBL formatted files
with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
lines don't match.

Looks like the parser utilises the EMBLFormat class with the following ID
pattern:

*protected** **static** **final** Pattern **lp** = Pattern.compile(**
"^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
**);*

The ID lines in my files (retrieved from EMBL-EBI) look like *ID   A00197;
SV 1; linear; protein; PRT; SYN; 602 AA.*

Looks like the pattern is specifically written for dna/rna and should more
look like:

*protected** **static** **final** Pattern **lp** = Pattern.compile(**
"^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
**\\s+(\\d+)\\s+(BP|AA)\\.$"**);*

Or am I using he wrong RichSequence.IOTools function?

Cheers,

Deniz
-- 
Deniz Koellhofer
Cambia
Initiative for Open Innovation (IOI)
Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia


From deniz.koellhofer at cambia.org  Wed Sep 22 23:10:58 2010
From: deniz.koellhofer at cambia.org (Deniz Koellhofer)
Date: Thu, 23 Sep 2010 09:10:58 +1000
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <20100922211815.12439.qmail@mxw1102.verio-web.com>
References: <20100922211815.12439.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTinid6vx5odR9xCMttR7P-P9RhdCYXqg7dUQeo99@mail.gmail.com>

Hi George,

This entry is from the embl patent protein database:
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

Have you used the RichSequence.IOTools successfully for parsing EMBL protein
files before? I assume this should always fail due to the "BP" in the regex?

Deniz

On Thu, Sep 23, 2010 at 7:18 AM, George Waldon <gwaldon at geneinfinity.org>wrote:

> Hi Deniz:
>
> I have a quick question that may be obvious, but which database do you get
> those protein files from?
>
> Thank you,
>
> George
>
> On Tue, Sep 21, 2010 at 3:59 PM, Deniz Koellhofer <
> deniz.koellhofer at cambia.org> wrote:
>
>    Hi,
>
>    I'm trying to parse EMBL formatted files
>    with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
>    lines don't match.
>
>    Looks like the parser utilises the EMBLFormat class with the following
> ID
>    pattern:
>
>    *protected** **static** **final** Pattern **lp** = Pattern.compile(**
>
>  "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
>    **);*
>
>    The ID lines in my files (retrieved from EMBL-EBI) look like *ID
> A00197;
>    SV 1; linear; protein; PRT; SYN; 602 AA.*
>
>    Looks like the pattern is specifically written for dna/rna and should
> more
>    look like:
>
>    *protected** **static** **final** Pattern **lp** = Pattern.compile(**
>
>  "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
>    **\\s+(\\d+)\\s+(BP|AA)\\.$"**);*
>
>    Or am I using he wrong RichSequence.IOTools function?
>
>    Cheers,
>
>    Deniz
>    --
>    Deniz Koellhofer
>    Cambia
>    Initiative for Open Innovation (IOI)
>    Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
>    _______________________________________________
>    biojava-dev mailing list
>    biojava-dev at lists.open-bio.org
>    http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>
>


-- 
Deniz Koellhofer
Cambia
Initiative for Open Innovation (IOI)
Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia


From gwaldon at geneinfinity.org  Thu Sep 23 04:23:48 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Thu, 23 Sep 2010 00:23:48 -0400
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
Message-ID: <20100923042349.77746.qmail@mxw1102.verio-web.com>

Curious, this seems to be the only place to find this type of files. Not really an official format, a little bit like GenPept. Your fix should probably work. Can you fill a bug on bugzilla (http://bugzilla.open-bio.org/)?

Best,
George

On Wed, Sep 22, 2010 at 4:10 PM, Deniz Koellhofer <deniz.koellhofer at cambia.org> wrote:

    Hi George,

    This entry is from the embl patent protein database: ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

    Have you used the RichSequence.IOTools successfully for parsing EMBL protein files before? I assume this should always fail due to the "BP" in the regex?

    Deniz

    On Thu, Sep 23, 2010 at 7:18 AM, George Waldon <gwaldon at geneinfinity.org> wrote:

        Hi Deniz:

        I have a quick question that may be obvious, but which database do you get those protein files from?

        Thank you,

        George


        On Tue, Sep 21, 2010 at 3:59 PM, Deniz Koellhofer <deniz.koellhofer at cambia.org> wrote:

           Hi,

           I'm trying to parse EMBL formatted files
           with RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID
           lines don't match.

           Looks like the parser utilises the EMBLFormat class with the following ID
           pattern:

           *protected** **static** **final** Pattern **lp** = Pattern.compile(**
           "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$"
           **);*

           The ID lines in my files (retrieved from EMBL-EBI) look like *ID   A00197;
           SV 1; linear; protein; PRT; SYN; 602 AA.*

           Looks like the pattern is specifically written for dna/rna and should more
           look like:

           *protected** **static** **final** Pattern **lp** = Pattern.compile(**
           "^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);
           **\\s+(\\d+)\\s+(BP|AA)\\.$"**);*

           Or am I using he wrong RichSequence.IOTools function?

           Cheers,

           Deniz
           --
           Deniz Koellhofer
           Cambia
           Initiative for Open Innovation (IOI)
           Cambia at QUT, G301, 2 George Street, Brisbane Qld 4000, Australia
           _______________________________________________
           biojava-dev mailing list
           biojava-dev at lists.open-bio.org
           http://lists.open-bio.org/mailman/listinfo/biojava-dev






From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 04:35:54 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 00:35:54 -0400
Subject: [Biojava-dev] [Bug 3137] New:
	RichSequence.IOTools.readEMBLProtein() fails on EMBL patent
	protein entries.
Message-ID: <bug-3137-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3137

           Summary: RichSequence.IOTools.readEMBLProtein() fails on EMBL
                    patent protein entries.
           Product: BioJava
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dkoellhofer at gmail.com


Hi,

I'm trying to parse EMBL formatted files with
RichSequence.IOTools.readEMBLProtein() - but the pattern for the ID lines don't
match.

Looks like the parser utilises the EMBLFormat class with the following ID
pattern:
protected static final Pattern lp =
Pattern.compile("^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+BP\\.$");

The ID lines in my files (retrieved from EMBL-EBI) look like ID   A00197; SV 1;
linear; protein; PRT; SYN; 602 AA.

Looks like the pattern is specifically written for dna/rna and should more look
like:

protected static final Pattern lp =
Pattern.compile("^(\\S+);\\s+SV\\s+(\\d+);\\s+(linear|circular);\\s+(\\S+\\s?\\S+?);\\s+(\\S+);\\s+(\\S+);\\s+(\\d+)\\s+(BP|AA)\\.$");

The failing protein sequences come from the embl patent protein database:
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

Cheers,

Deniz


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From biopython at maubp.freeserve.co.uk  Thu Sep 23 09:10:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 10:10:56 +0100
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <20100923042349.77746.qmail@mxw1102.verio-web.com>
References: <20100923042349.77746.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>

On Thu, Sep 23, 2010 at 5:23 AM, George Waldon <gwaldon at geneinfinity.org> wrote:
>
> Curious, this seems to be the only place to find this type of files.
> Not really an official format, a little bit like GenPept. Your fix
> should probably work. Can you fill a bug on bugzilla
> (http://bugzilla.open-bio.org/)?
>
> Best,
> George

Bug filed: http://bugzilla.open-bio.org/show_bug.cgi?id=3137

Interestingly Biopython doesn't support Protein EMBL files either
(I didn't know they existed), I wonder if BioPerl does?

Peter


From biopython at maubp.freeserve.co.uk  Thu Sep 23 10:51:35 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 23 Sep 2010 11:51:35 +0100
Subject: [Biojava-dev] Parsing protein EMBL files with
	RichSequence.IOTools.readEMBLProtein
In-Reply-To: <AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>
References: <20100923042349.77746.qmail@mxw1102.verio-web.com>
	<AANLkTin=dXwDF3evBF6iKbEB-M5Kqxxc00r=_qABL_B9@mail.gmail.com>
Message-ID: <AANLkTimpPKyhfpFsXg0E2Qob6rPqeu7aByAi=H2cQ=f4@mail.gmail.com>

Hi BioJava team et al,

Thanks for the indirect alert that protein EMBL files exist, e.g.
ftp://ftp.ebi.ac.uk/pub/databases/embl/patent/epo_prt.dat.gz

I've just updated Biopython to support them.

Chris - I've CC'd you in case you want to look at this for BioPerl.

Peter

On Thu, Sep 23, 2010 at 10:10 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Sep 23, 2010 at 5:23 AM, George Waldon <gwaldon at geneinfinity.org> wrote:
>>
>> Curious, this seems to be the only place to find this type of files.
>> Not really an official format, a little bit like GenPept. Your fix
>> should probably work. Can you fill a bug on bugzilla
>> (http://bugzilla.open-bio.org/)?
>>
>> Best,
>> George
>
> Bug filed: http://bugzilla.open-bio.org/show_bug.cgi?id=3137
>
> Interestingly Biopython doesn't support Protein EMBL files either
> (I didn't know they existed), I wonder if BioPerl does?
>
> Peter


From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 22:45:44 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 18:45:44 -0400
Subject: [Biojava-dev] [Bug 3138] New: SeqRes2AtomAligner misaligns Atom
	groups at N-terminus
Message-ID: <bug-3138-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3138

           Summary: SeqRes2AtomAligner misaligns Atom groups at N-terminus
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: structure
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: darnells at dnastar.com


The SeqRes2AtomAligner misaligns the N-terminus residues for 1BKV (Collagen)
and 3NLC (VP0956).  Both structures have SEQRES residues without corresponding
ATOM residues at the N-terminus.  In the case of 3NLC, the observed mapping is
(* = no ATOM group):

SEQRES MGHHHHHHSHMIRINE
ATOM   M**********IRINE

and the correct mapping should be:

SEQRES MGHHHHHHSHMIRINE
ATOM   **********MIRINE

Activating the Chemical Component Dictionary does not help the alignment.  Is
it significant that for 1BKV and 3NLC the first SEQRES group and the first ATOM
group are the same residue (nearly the same for 1BKV, PRO ~ HYP)?  Is this a
situation that is difficult for the Needleman-Wunsch algorithm used by
SeqRes2AtomAligner?


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From bugzilla-daemon at portal.open-bio.org  Thu Sep 23 22:50:11 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 23 Sep 2010 18:50:11 -0400
Subject: [Biojava-dev] [Bug 3138] SeqRes2AtomAligner misaligns Atom groups
	at N-terminus
In-Reply-To: <bug-3138-485@http.bugzilla.open-bio.org/>
Message-ID: <201009232250.o8NMoBr0029097@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3138


ap3 at sanger.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|biojava-dev at biojava.org     |andreas at sdsc.edu




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From bugzilla-daemon at portal.open-bio.org  Fri Sep 24 05:45:17 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 24 Sep 2010 01:45:17 -0400
Subject: [Biojava-dev] [Bug 3137] RichSequence.IOTools.readEMBLProtein()
	fails on EMBL patent protein entries.
In-Reply-To: <bug-3137-485@http.bugzilla.open-bio.org/>
Message-ID: <201009240545.o8O5jHw9007788@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3137


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2010-09-24 01:45 EST -------
Committed new pattern and added a test. Note that protein sequences from KIPO
have a non-regular ID line that prevent parsing.


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From gindin at gmail.com  Sun Sep 26 23:05:50 2010
From: gindin at gmail.com (Yevgeniy Gindin)
Date: Sun, 26 Sep 2010 19:05:50 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties
Message-ID: <AANLkTikqR=hvwnQOwxbvPTvfEU+QfKLAn18QpPrhYZTd@mail.gmail.com>

There seems to be a bug in
org.biojavax.bio.alignment.blast.RemoteQBlastAlignmentProperties.setBlastProgram(String)
The method throws an exception when a valid program name is given. I
believe that this is due to the fact that two String objects are
tested with the "==" operator rather then equals().

To illustrate:
String a = new String ("a");
String b = new String ("a");
System.out.println (a == b);

The above will return false.

--
Yevgeniy


From pedros at berkeley.edu  Mon Sep 27 19:55:05 2010
From: pedros at berkeley.edu (Pedro Silva)
Date: Mon, 27 Sep 2010 12:55:05 -0700
Subject: [Biojava-dev] BioJava 3 current status
Message-ID: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>

On 30 Jun 2010, at 12:18, Andreas Prlic wrote:

> About BioJava 3: This has made great progress over the last weeks and
> a lot of new functionality has been committed to SVN. To make this
> release ready there are now two new tools:
> 
> * There is now a BioJava Maven repository, which is hosting SNAPSHOT
> builds from the current SVN.

Hi Andreas,

A couple questions about Biojava 3, with which I'm trying to interoperate from Clojure:

1. You mention SVN above, but I also see an active git repository at github. 
   Is that only a mirror, and active development occurs at biojava.org's svn repo?
2. Are all non biojava3-prefixed modules in the Maven repository not suitable to use with Biojava 3?
   Eg., biosql, das, etc.
3. Will the Maven repository eventually also host releases, not just snapshots?
   How far along would a release be?

To provide some context, I've started coding on 'Bioclojure', and my strategy is to position my efforts downstream from Biojava (3).
To that end, I'm trying to figure out the best way to pull development snapshots and stable releases from you guys, as well as
your current state of affairs in the porting of biojava1/biojavax to biojava3.

Thanks for your help. 

Pedro
-- 
Pedro Silva <pedros at berkeley.edu>
UC Berkeley - PMB



From andreas at sdsc.edu  Mon Sep 27 20:40:30 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 27 Sep 2010 13:40:30 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
Message-ID: <AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>

Hi Pedro,


> 1. You mention SVN above, but I also see an active git repository at github.
> ? Is that only a mirror, and active development occurs at biojava.org's svn repo?

Yes, git is only a mirror. The main development happens in an ssh
protected SVN, which is replicated onto the anonymous SVN and git
servers (within one hour after a commit).

> 2. Are all non biojava3-prefixed modules in the Maven repository not suitable to use with Biojava 3?
> ? Eg., biosql, das, etc.

In an ideal world we would have a clear separation of biojava 3 and
biojava 1.  However the way things are at the present there is some
mix and  there is still legacy code in SVN. e.g. the module "core" is
essentially a lot of biojava1.7. It is up to the module maintainers to
upgrade their code. We will need to take a decision soon if we want to
drop all legacy code from SVN and only support biojava3 based code
from that point on. ( need to do a dependency analysis how many
modules are still depending on the old core).

> 3. Will the Maven repository eventually also host releases, not just snapshots?

yes

> ? How far along would a release be?

We have not set a date at the present.  I will write a proposal about
the next steps to the mailing list soon and then this is up for
discussion. Having said this, several people are using the current SVN
checkouts in production environments and what seems mostly missing is
lots of documentation...

> To provide some context, I've started coding on 'Bioclojure', and my strategy is to position my efforts downstream from Biojava (3).

Excellent! Are you planning to add additional functionality or is it
mainly a wrapper for biojava?

> To that end, I'm trying to figure out the best way to pull development snapshots and stable releases from you guys, as well as
> your current state of affairs in the porting of biojava1/biojavax to biojava3.

The automated build system pushes any successful build to

http://www.biojava.org/download/maven/

This means all libraries that are available from there are guaranteed
to pass the junit tests and compile correctly.

Andreas



From pedros at berkeley.edu  Mon Sep 27 23:13:17 2010
From: pedros at berkeley.edu (Pedro Silva)
Date: Mon, 27 Sep 2010 16:13:17 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
	<AANLkTim0bGchAmypN+iZXsj8G4zz367yOWX24RWgm-A2@mail.gmail.com>
Message-ID: <1285629197.25539.38.camel@dev.dzlab.pmb.berkeley.edu>

On Mon, 2010-09-27 at 13:40 -0700, Andreas Prlic wrote:

> Excellent! Are you planning to add additional functionality or is it
> mainly a wrapper for biojava?

Well, it started as native Clojure all the way, then I figured it would
be a wrapper around Biojava, *then* I figured, Clojure-Java
interoperability is so good, I don't need any wrapper at all.

That leaves adding additional functionality, plus wrapping the more
verbose and/or common Biojava idioms.

Thanks for your answers again. I appreciate it.

Pedro
-- 
Pedro Silva <pedros at berkeley.edu>
UC Berkeley - PMB



From gwaldon at geneinfinity.org  Tue Sep 28 03:34:01 2010
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 27 Sep 2010 23:34:01 -0400
Subject: [Biojava-dev] BioJava 3 current status
Message-ID: <20100928033401.79626.qmail@mxw1102.verio-web.com>

On Mon, Sep 27, 2010 at 1:40 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

>In an ideal world we would have a clear separation of biojava 3 and
>biojava 1.  However the way things are at the present there is some
>mix and  there is still legacy code in SVN. e.g. the module "core" is
>essentially a lot of biojava1.7. It is up to the module maintainers to
>upgrade their code. We will need to take a decision soon if we want to
>drop all legacy code from SVN and only support biojava3 based code
>from that point on. ( need to do a dependency analysis how many
>modules are still depending on the old core).

I see a few (rather lonely) BioException in the biojava3-ws module and a "biojava1-core" dependency in org.biojava3.core.sequence.transcription.DefaultRNAProteinTranscription in the sequence-core module. I also see that many of the classes of the sequence-core module are duplicated in the biojava3-core module. Is-there a meaning for this duplication?

George



From andreas at sdsc.edu  Tue Sep 28 17:17:37 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 28 Sep 2010 10:17:37 -0700
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <20100928033401.79626.qmail@mxw1102.verio-web.com>
References: <20100928033401.79626.qmail@mxw1102.verio-web.com>
Message-ID: <AANLkTikFqh-Uz4sLj86aOHt2kQFgCq8xuDqrgBXJ7W9m@mail.gmail.com>

>
> I see a few (rather lonely) BioException in the biojava3-ws module and a "biojava1-core" dependency in org.biojava3.core.sequence.transcription.DefaultRNAProteinTranscription in the sequence-core module. I also see that many of the classes of the sequence-core module are duplicated in the biojava3-core module. Is-there a meaning for this duplication?

Andy, Scooter, is this a leftover from the initial days? Can I delete
the sequence module? Is this all biojava3-core now?

On a related matter, is anybody working on genebank and embl file
parsing for biojava3? There were some feature requests for this and
would be nice if this could be done in biojava3 as well...

Andreas



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From sylvain.foisy at inflammgen.org  Tue Sep 28 13:54:43 2010
From: sylvain.foisy at inflammgen.org (Sylvain Foisy)
Date: Tue, 28 Sep 2010 09:54:43 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy
	Gindin)
Message-ID: <C8C76BE3.7499%sylvain.foisy@inflammgen.org>

Hi,

Ok, it should be fixed in SVN. I actually replaced the == by a call to the
Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
the array obsolete.

Thanks for pointing it ;-)

Best regards

Sylvain





From HWillis at scripps.edu  Tue Sep 28 17:30:50 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 28 Sep 2010 13:30:50 -0400
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties
	(Yevgeniy	Gindin)
Message-ID: <BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>

Andreas

Yes you can delete the sequence modules. I will add the parsers to the list and will use that to make sure core sequence module properly models the data elements.

Thanks

Scooter

----- Reply message -----
From: "Sylvain Foisy" <sylvain.foisy at inflammgen.org>
Date: Tue, Sep 28, 2010 1:18 pm
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy Gindin)
To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>

Hi,

Ok, it should be fixed in SVN. I actually replaced the == by a call to the
Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
the array obsolete.

Thanks for pointing it ;-)

Best regards

Sylvain



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biojava-dev mailing list
biojava-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-dev



From bugzilla-daemon at portal.open-bio.org  Wed Sep 29 04:48:46 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 29 Sep 2010 00:48:46 -0400
Subject: [Biojava-dev] [Bug 3140] New: Required Correction in
	GenbankLocationParser class
Message-ID: <bug-3140-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=3140

           Summary: Required Correction in GenbankLocationParser class
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


Reported on behalf of Deepak Sheoran:

Their is problem with GenbankLocationParser class, this class don't process
genbank record with    Accession: M32882. LocationParser class fails at
following line in genbank record:

    gene  </nuccore/150738?itemid=33&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
    mRNA  </nuccore/150738?itemid=15&report=gbwithparts>            
join((8298.8300)..10206,1..855)
                    /gene="bcn"
                    /note="alternative transcript"


Exception stack trace is as follows:

       Could not understand position: 10206,1..855
       org.biojava.bio.seq.io.ParseException: Could not understand position:
10206,1..855
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:285)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:277)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:244)
       at
org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:131)

I did some investigation in following matter, and found the defect in regular
expression named as "gp" in GenbankLocationParser class.

This error can be fixed by applying attached patch. And then for testing I have
created a method which proves that it can now understand all the possible
combination of location. This test class is also attached so that you can test
my patch before and after its application.


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From bugzilla-daemon at portal.open-bio.org  Wed Sep 29 04:52:33 2010
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 29 Sep 2010 00:52:33 -0400
Subject: [Biojava-dev] [Bug 3140] Required Correction in
	GenbankLocationParser class
In-Reply-To: <bug-3140-485@http.bugzilla.open-bio.org/>
Message-ID: <201009290452.o8T4qXkg023352@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=3140


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from gwaldon at geneinfinity.org  2010-09-29 00:52 EST -------
Applied proposed patch and test case. 

Index: GenbankLocationParser.java
===================================================================
--- GenbankLocationParser.java  (revision 8212)
+++ GenbankLocationParser.java  (working copy)
@@ -133,7 +133,7 @@

     // O beautiful regex, we worship you. (:-)
     // this matches grouped locations
-    private static Pattern gp =
Pattern.compile("^([^\\(\\):]*?:)?(complement|join|order)?\\(*{0,1}(.*?)\\)*{0,1}$");
+    private static Pattern gp =
Pattern.compile("^([^\\(\\):]*?:)?(complement|join|order)?\\({0,1}(.*?\\)*{0,1})$");
     // this matches range locations
     private static Pattern rp =
Pattern.compile("^\\(*(.*?)\\)*(\\.\\.\\(*(.*)\\)*)?$");
     // this matches accession/version pairs


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From chapmanb at 50mail.com  Wed Sep 29 11:49:24 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Wed, 29 Sep 2010 07:49:24 -0400
Subject: [Biojava-dev] BioJava 3 current status
In-Reply-To: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
References: <1285617305.25539.15.camel@dev.dzlab.pmb.berkeley.edu>
Message-ID: <20100929114924.GC8837@sobchak.mgh.harvard.edu>

Pedro;

> To provide some context, I've started coding on 'Bioclojure', and my
> strategy is to position my efforts downstream from Biojava (3).

That's awesome. I've been teaching myself Clojure to be able to
interoperate with Biojava and the GATK/Picard toolkits. Great to
hear you are tackling this.

Have you also seen Jan Aerts work?

http://github.com/jandot/bioclojure

Brad


From andreas at sdsc.edu  Thu Sep 30 02:17:45 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 29 Sep 2010 19:17:45 -0700
Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy
	Gindin)
In-Reply-To: <BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>
References: <ActfFLPB8id2wMsHEd+Nfci8yIq+ogAHjHPf>
	<BC8BB15C-C3A2-42E9-83DC-01E693D61727@scripps.edu>
Message-ID: <AANLkTimvxFXHOuVM_cRdmWGJrABxkMqB4K-okqDA-7sr@mail.gmail.com>

Hi Scooter,

I just deleted the sequence modules in SVN. If it later turns out that
there is some code that was forgotten to be moved to biojava3-core,
there is still a tag in svn to show the status before it got
deleted...

Andreas

On Tue, Sep 28, 2010 at 10:30 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> Andreas
>
> Yes you can delete the sequence modules. I will add the parsers to the list and will use that to make sure core sequence module properly models the data elements.
>
> Thanks
>
> Scooter
>
> ----- Reply message -----
> From: "Sylvain Foisy" <sylvain.foisy at inflammgen.org>
> Date: Tue, Sep 28, 2010 1:18 pm
> Subject: [Biojava-dev] Bug in RemoteQBlastAlignmentProperties (Yevgeniy Gindin)
> To: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org>
>
> Hi,
>
> Ok, it should be fixed in SVN. I actually replaced the == by a call to the
> Arrays.binarySearch(Object[] obj, Object obj) method, which makes traversing
> the array obsolete.
>
> Thanks for pointing it ;-)
>
> Best regards
>
> Sylvain
>
>
>
> _______________________________________________
> 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
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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