From gwaldon at geneinfinity.org  Thu Mar  1 00:01:38 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Wed, 28 Feb 2007 21:01:38 -0800
Subject: [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA
Message-ID: <200703010501.l2151dk5093954@mmm1924.dulles19-verio.com>

Hi,

I have a simple problem with the genbank parser. It returns a RichSequence with a description that sometimes contains newline characters derived from the inital genbank file (keyword DEFINITION and following description, which encompasses one or several lines). This is particularly annoying when converting to other file formats. I am not familiar with the parsers; maybe someone could volonteer to correct this problem.

Thanks,
George

From mark.schreiber at novartis.com  Thu Mar  1 00:23:46 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 1 Mar 2007 13:23:46 +0800
Subject: [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA
Message-ID: <OFA44D5585.0218F7A1-ON48257291.001D6F52-48257291.001DA4A4@ah.novartis.com>

Hi George -

I think someone will fix it promptly but to make sure it gets done and 
doesn't happen again could you submit a bug report with an example 
accession. We recently made a decision that fixes to bug reports should be 
accompanied by JUnit tests that make sure that bug gets tested with every 
new build to avoid the same issues creaping back in.

Thanks,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
03/01/2007 01:01 PM
Please respond to george waldon

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA


Hi,

I have a simple problem with the genbank parser. It returns a RichSequence 
with a description that sometimes contains newline characters derived from 
the inital genbank file (keyword DEFINITION and following description, 
which encompasses one or several lines). This is particularly annoying 
when converting to other file formats. I am not familiar with the parsers; 
maybe someone could volonteer to correct this problem.

Thanks,
George
_______________________________________________
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 Mar  1 21:58:50 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 1 Mar 2007 21:58:50 -0500
Subject: [Biojava-dev] [Bug 2223] New: newline characters in RichSequence
	description
Message-ID: <bug-2223-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2223

           Summary: newline characters in RichSequence description
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


The biojavax genbank parser returns a RichSequence with a description that
sometimes contains newline characters derived from the inital genbank file
(keyword DEFINITION and following description, which encompasses one or several
lines). This is particularly annoying when converting to other file formats. It
might be the same for with embl files. This is reproduced by parsing any
genbank file containing multiple lines in the DESCRIPTION keywords with
RichSequence.IOTools.readGenbankDNA, e.g. try AAB31603.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar  2 05:12:05 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 2 Mar 2007 05:12:05 -0500
Subject: [Biojava-dev] [Bug 2223] newline characters in RichSequence
	description
In-Reply-To: <bug-2223-485@http.bugzilla.open-bio.org/>
Message-ID: <200703021012.l22AC51i013336@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2223


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-02 05:12 EST -------
This newline stuff is annoying, admittedly, but it is deliberate. There are a
number of formats out there which rely on newlines being preserved within
comment or description text, such as the Genbank-like format produced by
Vectorbase. Also, some comments or descriptions are meaningless if the newlines
are not preserved (consider a description or comment block that makes an
ordered list of points, one per line, but those points do not take up the whole
line - if the newlines were ignored and the block reformatted on output then
the points would run into each other). 

I originally had this code to drop the newlines, but there were too many
problems due to the above situations, and so I made it preserve them. Granted
this makes transfers to other formats a little messy, sometimes introducing
newlines where they are not necessary, but it preserves things much better. 

If you need the newlines taken out, a simple search-and-replace on the text
would do it:  mydesc = mydesc.replaceAll("\n","");

If you then need to update the record before formatting it you can update (or
replace) the comment object involved.


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From holland at ebi.ac.uk  Mon Mar  5 04:32:14 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 05 Mar 2007 09:32:14 +0000
Subject: [Biojava-dev] Google Summer of Code
Message-ID: <45EBE39E.9010402@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

The Phyloinformatics Hackathon group, which aims to foster collaboration
among the Bio* toolkit developers (see http://phyloinformatics.net/ ),
is preparing to apply for the Google Summer of Code program.

The page for collecting ideas etc is at

http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2007

This is mostly a stub right now but will rapidly (have to) be fleshed
out over the next couple of days (the deadline for application is March
9). Please feel free to add ideas that you have directly (wiki
registration is open), or email them to Hilmar Lapp (hlapp at duke dot
edu) who is managing the program.

If we are accepted, we'll (hopefully) have students over the summer,
some of which will possibly work on BioPerl and BioJava-related
projects. These may be newcomers to BioJava, newcomers to distributed
OSS development, or even programming newbies ... Given the helping hand
that this community has readily extended to newbies in the past, I'm
hoping that you'll help us help them overcome the initial barriers, too.
Also, this offers us a chance to get work done on BioJava and find
future contributors with the financial and logistic help of Google.

If anyone is willing to go beyond that and would be willing to help out
as a mentor (or back-up mentor), that'd be great; just send me an email.

cheers,
Richard
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From darin.london at duke.edu  Tue Mar  6 11:03:59 2007
From: darin.london at duke.edu (Darin London)
Date: Tue, 06 Mar 2007 11:03:59 -0500
Subject: [Biojava-dev] Announcing BOSC 2007
Message-ID: <45ED90EF.7030000@duke.edu>

The BOSC Organizing Committee are proud to announce BOSC 2007, occurring
in Vienna, Austria on July 19th, 20th.  The conference this year
promises to be exciting, as the BOSC developers attempt to define and
solve currently intractable problems in Bioinformatics. Please refer to
the following website for complete information, and requests for
submissions.   Thank you, and we hope to see you in Vienna.

http://open-bio.org/wiki/BOSC_2007


The BOSC organizing Committee


Please pass this email on to anyone that would be interested.

From bugzilla-daemon at portal.open-bio.org  Tue Mar 13 20:48:31 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 13 Mar 2007 20:48:31 -0400
Subject: [Biojava-dev] [Bug 2234] New: Error during "rich" conversion of
	genbank to EMBL format
Message-ID: <bug-2234-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234

           Summary: Error during "rich" conversion of genbank to EMBL format
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


An EMBL file generated by RichSequence.IOTools.writeEMBL is not read by
RichSequence.IOTools.readEMBLDNA. To reproduce, get AY847516 from NCBI (a
CTLA-4 mAb); read with RichSequence.IOTools.readGenbankDNA, write with
writeEMBL, and then read again with readEMBLDNA. An IO exception is thrown at
the first line with the message "error during parsing". The first line has a
suspect null data class (ID   AY847516; linear; mRNA; null; PRI; 362 BP). 
The problem does not appear when AY847516 is queried from EMBL, written and
read in EMBL format (ID   AY847516; linear; mRNA; STD; HUM; 362 BP).

Thanks,
George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 04:23:55 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 04:23:55 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703140823.l2E8NtJ0031964@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-14 04:23 EST -------
Thanks for pointing this out. It was due to the data class being an
EMBL-specific thing and not being populated when reading from other formats
such as Genbank. I have made EMBLFormat use a default value of STD for the data
class in these cases. This should solve the problem.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 14:12:51 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 14:12:51 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703141812.l2EICp56032597@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


gwaldon at geneinfinity.org changed:

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




------- Comment #2 from gwaldon at geneinfinity.org  2007-03-14 14:12 EST -------
Thanks Richard for the fix, but it seems that other problems were uncovered.
First doing the read/write/read operation with EMBL format only, I got "Bad ID
line found":
ID   AY847516; linear; mRNA; STD; HUM; 362 BP.

I added the version by hand:
ID   AY847516; SV 1; linear; mRNA; STD; HUM; 362 BP.
and I got "Current bioentry already has a version".

I removed the SV line, and I got "Bad date line found...",which corresponds to
the following line:
DT   01-JUN-2005 (Rel. 84 Created)

Finally, I added a coma after 84, and the file finally parsed without error.

In the process, I noticed that the first reference lost the last character of
the last RT line (missing 's' at the end of lymphocytes); note that the second
reference does not have RT lines.

Secondly, doing the read/write/read operation from Genbank to EMBL format, I
got similar progression; the bad date line has now a 0 instead of 84, but
adding the coma after 0 resolved the reading problem. Then I got a new error:
"Could not read sequence For input string: "GI:61815557", which is generated by
the following FT line:
FT                   /db_xref="taxon:GI:61815557"
I did not investigate further at this point.

I noticed that the above reference is now complete, but is incomplete when I do
the read/write/read operation from EMBL to Genbank. Therefore, this is probably
a read problem in the EMBL parser.


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From zbhuang2005 at hotmail.com  Wed Mar 14 15:08:03 2007
From: zbhuang2005 at hotmail.com (Huang Zhibin)
Date: Wed, 14 Mar 2007 19:08:03 +0000
Subject: [Biojava-dev] tandem repeats in biojava
Message-ID: <BAY20-F2314898223128973270EC5A5730@phx.gbl>

Hi,
 I just wonder whether biojava implements the function of exact/approximate 
tandem repeats in DNA. I thought it is a typical function of dna, but I 
could not find anything about it in biojava.
 Hope someone can give me some hints. Thanks
Best,
zbhuang

_________________________________________________________________
???????????????????????????? MSN Messenger:  http://messenger.msn.com/cn  


From joel.pitt at gmail.com  Wed Mar 14 17:13:00 2007
From: joel.pitt at gmail.com (Joel Pitt)
Date: Thu, 15 Mar 2007 10:13:00 +1300
Subject: [Biojava-dev] tandem repeats in biojava
In-Reply-To: <BAY20-F2314898223128973270EC5A5730@phx.gbl>
References: <BAY20-F2314898223128973270EC5A5730@phx.gbl>
Message-ID: <d7e54a6c0703141413i47021cf1hf2c4c070ca09cc8b@mail.gmail.com>

Hi zbhuang,

When I last checked about a couple of years ago there wasn't anything
like that as part of the core biojava. I'm the author of
http://repeatfinder.sourceforge.net/ which is an approximate
tandem/exact repeatfinder using our own searching algorithm. I was
planning to port it into biojava (as well as build a nice GUI for it),
but as is usually the case, I haven't had the time.

The RepeatFinder source code is available though, so feel free to port
it yourself ;)

Cheers,
Joel

On 3/15/07, Huang Zhibin <zbhuang2005 at hotmail.com> wrote:
> Hi,
>  I just wonder whether biojava implements the function of exact/approximate
> tandem repeats in DNA. I thought it is a typical function of dna, but I
> could not find anything about it in biojava.
>  Hope someone can give me some hints. Thanks
> Best,
> zbhuang
>
> _________________________________________________________________
> ???????????????????????????? MSN Messenger:  http://messenger.msn.com/cn
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
-Joel

"Unless you try to do something beyond what you have mastered, you
will never grow." -C.R. Lawton


From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 19:02:49 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 19:02:49 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703142302.l2EN2ngu013096@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234





------- Comment #3 from holland at ebi.ac.uk  2007-03-14 19:02 EST -------
good grief, what a can of worms.... i'll get onto it on Friday when I'm back in
the office!


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 15 06:11:58 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 15 Mar 2007 06:11:58 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703151011.l2FABw47005920@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234





------- Comment #4 from holland at ebi.ac.uk  2007-03-15 06:11 EST -------
I've identified the problem areas in the EMBLFormat code. I will fix them
tomorrow.

Note to self:

if (format.equals(EMBL_FORMAT)) {
                // accession; SV version; circular/linear; moltype; dataclass;
division; length BP.
                locusLine.append(rs.getAccession());
                locusLine.append("; ");
--- INSERT "SV versionLine;" here
                locusLine.append(rs.getCircular()?"circular; ":"linear; ");
                locusLine.append(moltype);

        // version line
--- WRAP in test - only execute if EMBL_PRE87_FORMAT
        if (versionLine!=null) StringTools.writeKeyValueLine(VERSION_TAG,
versionLine, 5, this.getLineWidth(), null, VERSION_TAG, this.getPrintStream());
        else StringTools.writeKeyValueLine(VERSION_TAG,
accession+"."+rs.getVersion(), 5, this.getLineWidth(), null, VERSION_TAG,
this.getPrintStream());
        this.getPrintStream().println(DELIMITER_TAG+"   ");


        // date line
-- INSERT commaa before space before Created
        StringTools.writeKeyValueLine(DATE_TAG, (cdat==null?udat:cdat)+" (Rel.
"+(crel==null?"0":crel)+" Created)", 5, this.getLineWidth(), null, DATE_TAG,
this.getPrintStream());

--- CHECK that leading space chomped first - does this record start in space
then "? It ends in "; on last line but does not start on same line
if (key.equals(TITLE_TAG)) {
                        if (val.length()>1) {
                            if (val.endsWith(";")) val =
val.substring(0,val.length()-1); // chomp semicolon
                            if (val.endsWith("\"")) val =
val.substring(1,val.length()-2); // chomp quotes
                            title = val;
                        } else title=null; // single semi-colon indicates no
title
                    }

            // add-in other dbxrefs where present
            for (Iterator j = f.getRankedCrossRefs().iterator(); j.hasNext(); )
{
                RankedCrossRef rcr = (RankedCrossRef)j.next();
                CrossRef cr = rcr.getCrossRef();
--- REMOVE taxon: prefix - shouldn't be there...
                StringTools.writeKeyValueLine(FEATURE_TAG,
"/db_xref=\"taxon:"+cr.getDbname()+":"+cr.getAccession()+"\"", 21,
this.getLineWidth(), null, FEATURE_TAG, this.getPrintStream());
            }




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From bugzilla-daemon at portal.open-bio.org  Fri Mar 16 05:50:27 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Mar 2007 05:50:27 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703160950.l2G9oR2a005733@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


holland at ebi.ac.uk changed:

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




------- Comment #5 from holland at ebi.ac.uk  2007-03-16 05:50 EST -------
Fixes made and committed.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 14:38:34 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 14:38:34 -0400
Subject: [Biojava-dev] [Bug 2244] New: uniprot files do not load
Message-ID: <bug-2244-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244

           Summary: uniprot files do not load
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


Exceptions are thrown when Uniprot files are tentatively read by the biojavax
parser.

Reading P01717 or P07724 with RichSequence.IOTools.readUniProt throw :
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:393)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)

P07724

(this one initially reported by Sofia Burvall)
Reading P13346 throw:
Caused by: org.biojava.bio.seq.io.ParseException: Bad date line found:
01-JAN-1990 (Rel. 13, Created)
        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:349)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 15:07:57 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 15:07:57 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703211907.l2LJ7v5u010410@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |holland at ebi.ac.uk
             Status|NEW                         |ASSIGNED




------- Comment #1 from holland at ebi.ac.uk  2007-03-21 15:07 EST -------
I don't understand what the problem is. If I download UniProt files for the 3
accessions you mention from the official UniProt website at
http://www.pir.uniprot.org/ then I get files that parse correctly.

The date lines shown in your example are not in UniProt format. They are EMBL
format date lines.

Where are you getting your UniProt files from? This sounds like a bug in the
software at the site you are getting from, not a bug with BioJava.

Please let me know where you are getting the files from and I will investigate
a bit more.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 16:15:56 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 16:15:56 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212015.l2LKFu2x014547@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #2 from gwaldon at geneinfinity.org  2007-03-21 16:15 EST -------
Hi Richard,

We must have some mixup of some sort. The bad date line was reported when I
tried to parse the file included in the email from Sofia (it was posted on
biojava-1 on March 16, 2007). Effectively, this file is different from what the
one I get at the uniprot web site. Reading Sophia email, it is possible that
the incorrect file was in fact generated by biojavax (in the same kind of
operation like read/write/read problem that was corrected recently).

I am going to investigate the other exception. The 2 files were from the
correct source (http://www.expasy.org/uniprot/P01717, click on "View entry in
original UniProtKB/Swiss-Prot format", etc.). I'll get back on this latter.

- George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 16:27:15 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 16:27:15 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212027.l2LKRFrc015247@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #3 from gwaldon at geneinfinity.org  2007-03-21 16:27 EST -------

Well, the 2 files are respectively from:
http://www.expasy.org/cgi-bin/get-sprot-entry?P07724
http://www.expasy.org/cgi-bin/get-sprot-entry?P01717

The ArrayIndexOutOfBoundsException are thrown for the lines:

P07724:
DR   ProDom [Domain structure / List of seq. sharing at least 1 domain ]

P01717:
DR   HOVERGEN [Family / Alignment / Tree]

Hope this helps!
- George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 17:53:26 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 17:53:26 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212153.l2LLrQ8X020150@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #4 from holland at ebi.ac.uk  2007-03-21 17:53 EST -------
Thanks for that extra info! I'll investigate further over the next couple of
days and get back to you when I've got a solution.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 22 08:19:20 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Mar 2007 08:19:20 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703221219.l2MCJKIM028661@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #5 from holland at ebi.ac.uk  2007-03-22 08:19 EST -------
I have investigated the two problem DR lines and found that they do not match
the current UniProt file format specifications as defined at
http://www.expasy.org/sprot/userman.html#DR_line .

There is no indication in the UniProt file format specification as to what a DR
line in this format might actually mean.

As these files came from UniProt themselves, I think the best thing to do is
for you to contact UniProt and raise a bug report with them directly indicating
that their website is producing files that do not conform to their own file
format standards.

BJX can only parse files which follow the official format definition. There's
only so much flexibility we can build in! :)

I'll leave this bug as ASSIGNED for now so that you can add any comments
regarding what UniProt say about their bug.


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From bugzilla-daemon at portal.open-bio.org  Mon Mar 26 04:23:09 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 26 Mar 2007 04:23:09 -0400
Subject: [Biojava-dev] [Bug 2250] New: Genbank format error
Message-ID: <bug-2250-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2250

           Summary: Genbank format error
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


I think that the following error was caused by the last fix to GenbankFormat

Format_object=org.biojavax.bio.seq.io.GenbankFormat
Accession=null
Id=null
Comments=Bad locus line
Parse_block=LOCUS   NM_182008               1629 bp    mRNA    linear   INV
23-MAR-2007
Stack trace follows ....


        at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 2 more


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From bugzilla-daemon at portal.open-bio.org  Mon Mar 26 10:41:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 26 Mar 2007 10:41:40 -0400
Subject: [Biojava-dev] [Bug 2250] Genbank format error
In-Reply-To: <bug-2250-485@http.bugzilla.open-bio.org/>
Message-ID: <200703261441.l2QEfent022095@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2250


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-26 10:41 EST -------
Fixed. Now testing before commit.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 00:47:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 00:47:10 -0400
Subject: [Biojava-dev] [Bug 2253] New: NullPointerException in
	MultiSourceCompoundRichLocation
Message-ID: <bug-2253-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253

           Summary: NullPointerException in MultiSourceCompoundRichLocation
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


More exactly in the blockIterator method taken from CompoundRichLocation where
the "sortedMembers" variable is null. This set is actually never instantiated,
see constructor. Well, I don't understand the function of the "sortedMembers"
list; why not sorting the "members" list instead from the start?
- George


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 01:27:41 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 01:27:41 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703290527.l2T5Rfu3010839@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #6 from gwaldon at geneinfinity.org  2007-03-29 01:27 EST -------
The problem is limited to the Expasy server. I am trying to get in touch with
someone overthere.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 04:54:26 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 04:54:26 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703290854.l2T8sQkH019389@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-29 04:54 EST -------
The only way that sortedMembers can be null is if the object is loaded in via
Hibernate. This is a bug which I have now fixed in CVS.

PS. In order to reproduce output files that are largely the same as the input
files these locations are read from, whilst simultaneously providing a sensible
iterator for the user, it is important to maintain two separate orders. If the
user ever calls sort() on the location, the two orders become the same.

PPS. There is NO test in BJX for this bug as it is Hibernate-related and
therefore almost impossible to write a test case for!


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 12:08:42 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 12:08:42 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703291608.l2TG8gWo008372@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |VERIFIED




------- Comment #2 from gwaldon at geneinfinity.org  2007-03-29 12:08 EST -------
The problem was in MultiSourceCompoundRichLocation and not its parent class.
This resulted in the second set to be null from both public constructors.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 13:13:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 13:13:40 -0400
Subject: [Biojava-dev] [Bug 2255] New: Problems with read and write of EMBL
	files
Message-ID: <bug-2255-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2255

           Summary: Problems with read and write of EMBL files
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


I just noticed two problems with EMBL files. During read operations, the first
keyword (KW line) is not parsed. Also during write operations, the sequence
line (SQ) is missing the word "Sequence" in the output.
- George


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From gwaldon at geneinfinity.org  Fri Mar 30 01:28:51 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Thu, 29 Mar 2007 22:28:51 -0700
Subject: [Biojava-dev] Exception in MassCalc.getMass
Message-ID: <20070330052851.16176.qmail@mmm1924.dulles19-verio.com>

I got a NullPointerException in MassCalc.getMass that I traced to the presence of an ambiguity symbol X in the peptide sequence. 
The origin lies in SimpleSymbolPropertyTable.getDoubleValue.  The ambiguity symbol is first validated (through its matches in AbstractAlphabet) and the exception is thrown when we try to find a value associated with a null key in the property map.
First I think we should redirect this exception to the checked IllegalSymbolException to tell the user that something is going wrong.
Concerning calculating masses, I see two needs: need to estimate the mass of polypeptides containing ambiguity symbols and need to obtain an exact mass or an IllegalSymbolException when ambiguity occurs.
I propose to add a new method MassCalc.getEstimatedMass to do the first part and to modify the existing method so that  an IllegalSymbolException is thrown whenever a non-atomic symbol is encounter. Mass values for ambiguity symbols would be added to the ResidueProperty.xml file and taken as simple average of the atomic match values.

- George

From mark.schreiber at novartis.com  Fri Mar 30 01:43:05 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 30 Mar 2007 13:43:05 +0800
Subject: [Biojava-dev] Exception in MassCalc.getMass
Message-ID: <OFD6A9167E.6BCEF3E4-ON482572AE.001F02B8-482572AE.001F6937@ah.novartis.com>

Hi George -

Sounds like a good idea. Can you check it in? And add a JUnit test???

You probably don't need to add ambiguity weights to the XML as you can 
decompose a basis symbol into it's components, look up each and get the 
average. Infact there are so many possible amino acid ambiguities it would 
be a very bad idea to list them all in the XML file. Although IUPAC only 
has about 3 amino acid ambiguities BioJava's BasisSymbols can infact 
represent any and every possible combination of ambiguity (although there 
is no obvious way to tokenize them to text) so you would need to allow for 
this in your getEstimated mass method. 

Thanks for spotting this,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
03/30/2007 01:28 PM
Please respond to george waldon

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Exception in MassCalc.getMass


I got a NullPointerException in MassCalc.getMass that I traced to the 
presence of an ambiguity symbol X in the peptide sequence. 
The origin lies in SimpleSymbolPropertyTable.getDoubleValue.  The 
ambiguity symbol is first validated (through its matches in 
AbstractAlphabet) and the exception is thrown when we try to find a value 
associated with a null key in the property map.
First I think we should redirect this exception to the checked 
IllegalSymbolException to tell the user that something is going wrong.
Concerning calculating masses, I see two needs: need to estimate the mass 
of polypeptides containing ambiguity symbols and need to obtain an exact 
mass or an IllegalSymbolException when ambiguity occurs.
I propose to add a new method MassCalc.getEstimatedMass to do the first 
part and to modify the existing method so that  an IllegalSymbolException 
is thrown whenever a non-atomic symbol is encounter. Mass values for 
ambiguity symbols would be added to the ResidueProperty.xml file and taken 
as simple average of the atomic match values.

- George
_______________________________________________
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  Fri Mar 30 04:51:20 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 04:51:20 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703300851.l2U8pKbZ016735@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #3 from holland at ebi.ac.uk  2007-03-30 04:51 EST -------
Indeed you're right. I just checked again and the bugfix I applied should have
fixed this too. Could you confirm that?


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From holland at ebi.ac.uk  Fri Mar 30 04:53:02 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 30 Mar 2007 09:53:02 +0100
Subject: [Biojava-dev] ParseExceptions
Message-ID: <460CCFEE.4030609@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi all. Can the person who recently modified the BJX EMBLFormat to throw
ParseExceptions using the ParseException.newMessage() method please
check all their code to make sure that it is correct. I have noticed
that every occurrence of this in EMBLFormat was implemented incorrectly
and never threw the generated message. I have fixed it there, but have
no idea how many other places this might have happened.

I have replaced all occurrences with two lines similar to this:

String message = ParseException.newMessage(....);
throw new ParseException(message);

cheers,
Richard
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGDM/u4C5LeMEKA/QRAkf3AJ4opHh8SDa+jUIoNnKTc3XgdJzLAACfcci5
LyA41NgjkULPvdy4AeALOhw=
=PXKG
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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 06:29:41 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 06:29:41 -0400
Subject: [Biojava-dev] [Bug 2255] Problems with read and write of EMBL files
In-Reply-To: <bug-2255-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301029.l2UATf4w020994@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2255


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-30 06:29 EST -------
Fixed in CVS.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 11:39:11 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:39:11 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301539.l2UFdB29001755@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #4 from gwaldon at geneinfinity.org  2007-03-30 11:39 EST -------
Yes, it is fixed. I'll try to get the time to write a test on equality of
MultiSourceCompoundRichLocation - this is how the bug was revealed.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 11:45:38 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:45:38 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301545.l2UFjcY8002022@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


gwaldon at geneinfinity.org changed:

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




------- Comment #7 from gwaldon at geneinfinity.org  2007-03-30 11:45 EST -------
Following is the comment of Severine Duvaud from Expasy. The links she
mentionned are found on niceprot View; here is a link exemple:
http://www.expasy.org/cgi-bin/niceprot.pl?P01717

======================================================================

When clicking on "View entry in original UniProtKB/Swiss-Prot format",
you get an "enhanced" view of the original entry (compared to the "raw"
entry view as pointed out by the other link), notably with implicit
links. The standard entry, in (hopefully) regular Swiss-Prot format can
be found when clicking on "View entry in raw text format (no link)" or
by downloading uniprot_sprot.dat on our FTP server.
Sorry for the confusion.
Best regards,

Severine

-- 
**************************************
Severine Duvaud, Swiss-Prot Group

Swiss Institute of Bioinformatics
CMU, 1 rue Michel Servet
CH - 1211 Geneva 4
Switzerland

Tel. (+41) 22 379 58 25
Fax (+41) 22 379 58 58

Severine.Duvaud at isb-sib.ch
http://www.expasy.org
************************************** 


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 11:46:09 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:46:09 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301546.l2UFk96q002090@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #5 from holland at ebi.ac.uk  2007-03-30 11:46 EST -------
Great. If you get time to come up with a test, can you add a note to this bug
and then close the bug! I'll leave it as verified/fixed in the meantime.

Tests should go in an appropriate package under the tests/ folder in
biojava-live - you'll get the picture I'm sure just by looking around there to
see where other tests have gone (e.g. org.biojavax.bio.seq.io for all BJX
sequence i/o related tests). Please do create a new test package if you can't
find one that seems appropriate. 


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 11:49:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:49:40 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301549.l2UFnekY002285@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |CLOSED




------- Comment #8 from holland at ebi.ac.uk  2007-03-30 11:49 EST -------
Thanks for that. I'm glad I'm not going mad! :)

So it seems that Expasy is providing slightly confusing links, and the best
route to get files from them for programmatic parsing is to get raw text files
wherever possible rather then cutting-and-pasting their
enhanced-with-HTML-links versions that they show by default when browsing their
database.


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From amit.p at ocimumbio.com  Tue Mar 13 02:38:52 2007
From: amit.p at ocimumbio.com (Amit Dattatreya Parhar)
Date: Tue, 13 Mar 2007 06:38:52 -0000
Subject: [Biojava-dev] ESD megabace trace file parser
Message-ID: <004a01c76537$adca6e40$fc01a8c0@ocimumbio.net>

Hi,
         I need a .esd file parser. can anybody help me out? atleast information on how to parse this type of trace file.

thanks in advance
Amit
Bioinformatics Analyst
amit.p at ocimumbio.com

Ocimum Biosolutions
   ...enabling R&D
6th Floor, Reliance Classic, Road No.1, Banjara Hills, Hyderabad - 500 034, A.P, India
Business Phone: 04055627203,ext-132  | Fax: 04055627205
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From renauxc.isat at gmail.com  Mon Mar 26 09:18:08 2007
From: renauxc.isat at gmail.com (Caroline Renaux)
Date: Mon, 26 Mar 2007 15:18:08 +0200
Subject: [Biojava-dev] org.biojava.bio.symbol.UkkonenSuffixTree.class BUG
Message-ID: <401c5fc20703260618t3f38eb86yd7d66043399ba69e@mail.gmail.com>

Bonjour,

j'ai r?cemment utilis? le Package org.biojava.bio.symbol et plus
particuli?rement la classe UkkonenSuffixTree. Cependant lorsque que je veux
ajouter un ensemble de s?quences ? l'arbre et que je les s?pares par le
caract?re de s?paration '$' cel? ne fonctionne pas. Lorsqu'il traite la
seconde s?quence j'obtiens une erreur "NullPointerException" dans la m?thode
jumpTo ? la ligne :

arrivedAt=(SuffixNode)currentNode.children.get(*new* Character(source.charAt
(from)));

Je ne comprend pas ce que j'aurai pu faire de travers.

D'avance merci de votre r?ponse.

RENAUX C.

--------------------------------
Hello,

I used for a java application the org.biojava.bio.symbol package and
particularly the UkkonenSuffixTree class. When i want to add a set of
sequences to the tree, i add a '$' between the sequences but it doesn't
work. I have a NullPointerException when the system add the second sequence
int the method jumTo at the line :

arrivedAt=(SuffixNode)currentNode.children.get(*new* Character(source.charAt
(from)));

I don't understand why it doesn't work.

Thank you in advance.

RENAUX C.


From gwaldon at geneinfinity.org  Thu Mar  1 05:01:38 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Wed, 28 Feb 2007 21:01:38 -0800
Subject: [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA
Message-ID: <200703010501.l2151dk5093954@mmm1924.dulles19-verio.com>

Hi,

I have a simple problem with the genbank parser. It returns a RichSequence with a description that sometimes contains newline characters derived from the inital genbank file (keyword DEFINITION and following description, which encompasses one or several lines). This is particularly annoying when converting to other file formats. I am not familiar with the parsers; maybe someone could volonteer to correct this problem.

Thanks,
George


From mark.schreiber at novartis.com  Thu Mar  1 05:23:46 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Thu, 1 Mar 2007 13:23:46 +0800
Subject: [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA
Message-ID: <OFA44D5585.0218F7A1-ON48257291.001D6F52-48257291.001DA4A4@ah.novartis.com>

Hi George -

I think someone will fix it promptly but to make sure it gets done and 
doesn't happen again could you submit a bug report with an example 
accession. We recently made a decision that fixes to bug reports should be 
accompanied by JUnit tests that make sure that bug gets tested with every 
new build to avoid the same issues creaping back in.

Thanks,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
03/01/2007 01:01 PM
Please respond to george waldon

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Problem with RichSequence.IOTools.readGenbankDNA


Hi,

I have a simple problem with the genbank parser. It returns a RichSequence 
with a description that sometimes contains newline characters derived from 
the inital genbank file (keyword DEFINITION and following description, 
which encompasses one or several lines). This is particularly annoying 
when converting to other file formats. I am not familiar with the parsers; 
maybe someone could volonteer to correct this problem.

Thanks,
George
_______________________________________________
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  Fri Mar  2 02:58:50 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 1 Mar 2007 21:58:50 -0500
Subject: [Biojava-dev] [Bug 2223] New: newline characters in RichSequence
	description
Message-ID: <bug-2223-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2223

           Summary: newline characters in RichSequence description
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


The biojavax genbank parser returns a RichSequence with a description that
sometimes contains newline characters derived from the inital genbank file
(keyword DEFINITION and following description, which encompasses one or several
lines). This is particularly annoying when converting to other file formats. It
might be the same for with embl files. This is reproduced by parsing any
genbank file containing multiple lines in the DESCRIPTION keywords with
RichSequence.IOTools.readGenbankDNA, e.g. try AAB31603.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar  2 10:12:05 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 2 Mar 2007 05:12:05 -0500
Subject: [Biojava-dev] [Bug 2223] newline characters in RichSequence
	description
In-Reply-To: <bug-2223-485@http.bugzilla.open-bio.org/>
Message-ID: <200703021012.l22AC51i013336@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2223


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-02 05:12 EST -------
This newline stuff is annoying, admittedly, but it is deliberate. There are a
number of formats out there which rely on newlines being preserved within
comment or description text, such as the Genbank-like format produced by
Vectorbase. Also, some comments or descriptions are meaningless if the newlines
are not preserved (consider a description or comment block that makes an
ordered list of points, one per line, but those points do not take up the whole
line - if the newlines were ignored and the block reformatted on output then
the points would run into each other). 

I originally had this code to drop the newlines, but there were too many
problems due to the above situations, and so I made it preserve them. Granted
this makes transfers to other formats a little messy, sometimes introducing
newlines where they are not necessary, but it preserves things much better. 

If you need the newlines taken out, a simple search-and-replace on the text
would do it:  mydesc = mydesc.replaceAll("\n","");

If you then need to update the record before formatting it you can update (or
replace) the comment object involved.


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From holland at ebi.ac.uk  Mon Mar  5 09:32:14 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Mon, 05 Mar 2007 09:32:14 +0000
Subject: [Biojava-dev] Google Summer of Code
Message-ID: <45EBE39E.9010402@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

The Phyloinformatics Hackathon group, which aims to foster collaboration
among the Bio* toolkit developers (see http://phyloinformatics.net/ ),
is preparing to apply for the Google Summer of Code program.

The page for collecting ideas etc is at

http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2007

This is mostly a stub right now but will rapidly (have to) be fleshed
out over the next couple of days (the deadline for application is March
9). Please feel free to add ideas that you have directly (wiki
registration is open), or email them to Hilmar Lapp (hlapp at duke dot
edu) who is managing the program.

If we are accepted, we'll (hopefully) have students over the summer,
some of which will possibly work on BioPerl and BioJava-related
projects. These may be newcomers to BioJava, newcomers to distributed
OSS development, or even programming newbies ... Given the helping hand
that this community has readily extended to newbies in the past, I'm
hoping that you'll help us help them overcome the initial barriers, too.
Also, this offers us a chance to get work done on BioJava and find
future contributors with the financial and logistic help of Google.

If anyone is willing to go beyond that and would be willing to help out
as a mentor (or back-up mentor), that'd be great; just send me an email.

cheers,
Richard
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From darin.london at duke.edu  Tue Mar  6 16:03:59 2007
From: darin.london at duke.edu (Darin London)
Date: Tue, 06 Mar 2007 11:03:59 -0500
Subject: [Biojava-dev] Announcing BOSC 2007
Message-ID: <45ED90EF.7030000@duke.edu>

The BOSC Organizing Committee are proud to announce BOSC 2007, occurring
in Vienna, Austria on July 19th, 20th.  The conference this year
promises to be exciting, as the BOSC developers attempt to define and
solve currently intractable problems in Bioinformatics. Please refer to
the following website for complete information, and requests for
submissions.   Thank you, and we hope to see you in Vienna.

http://open-bio.org/wiki/BOSC_2007


The BOSC organizing Committee


Please pass this email on to anyone that would be interested.


From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 00:48:31 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Tue, 13 Mar 2007 20:48:31 -0400
Subject: [Biojava-dev] [Bug 2234] New: Error during "rich" conversion of
	genbank to EMBL format
Message-ID: <bug-2234-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234

           Summary: Error during "rich" conversion of genbank to EMBL format
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


An EMBL file generated by RichSequence.IOTools.writeEMBL is not read by
RichSequence.IOTools.readEMBLDNA. To reproduce, get AY847516 from NCBI (a
CTLA-4 mAb); read with RichSequence.IOTools.readGenbankDNA, write with
writeEMBL, and then read again with readEMBLDNA. An IO exception is thrown at
the first line with the message "error during parsing". The first line has a
suspect null data class (ID   AY847516; linear; mRNA; null; PRI; 362 BP). 
The problem does not appear when AY847516 is queried from EMBL, written and
read in EMBL format (ID   AY847516; linear; mRNA; STD; HUM; 362 BP).

Thanks,
George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 08:23:55 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 04:23:55 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703140823.l2E8NtJ0031964@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-14 04:23 EST -------
Thanks for pointing this out. It was due to the data class being an
EMBL-specific thing and not being populated when reading from other formats
such as Genbank. I have made EMBLFormat use a default value of STD for the data
class in these cases. This should solve the problem.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 18:12:51 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 14:12:51 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703141812.l2EICp56032597@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


gwaldon at geneinfinity.org changed:

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




------- Comment #2 from gwaldon at geneinfinity.org  2007-03-14 14:12 EST -------
Thanks Richard for the fix, but it seems that other problems were uncovered.
First doing the read/write/read operation with EMBL format only, I got "Bad ID
line found":
ID   AY847516; linear; mRNA; STD; HUM; 362 BP.

I added the version by hand:
ID   AY847516; SV 1; linear; mRNA; STD; HUM; 362 BP.
and I got "Current bioentry already has a version".

I removed the SV line, and I got "Bad date line found...",which corresponds to
the following line:
DT   01-JUN-2005 (Rel. 84 Created)

Finally, I added a coma after 84, and the file finally parsed without error.

In the process, I noticed that the first reference lost the last character of
the last RT line (missing 's' at the end of lymphocytes); note that the second
reference does not have RT lines.

Secondly, doing the read/write/read operation from Genbank to EMBL format, I
got similar progression; the bad date line has now a 0 instead of 84, but
adding the coma after 0 resolved the reading problem. Then I got a new error:
"Could not read sequence For input string: "GI:61815557", which is generated by
the following FT line:
FT                   /db_xref="taxon:GI:61815557"
I did not investigate further at this point.

I noticed that the above reference is now complete, but is incomplete when I do
the read/write/read operation from EMBL to Genbank. Therefore, this is probably
a read problem in the EMBL parser.


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From zbhuang2005 at hotmail.com  Wed Mar 14 19:08:03 2007
From: zbhuang2005 at hotmail.com (Huang Zhibin)
Date: Wed, 14 Mar 2007 19:08:03 +0000
Subject: [Biojava-dev] tandem repeats in biojava
Message-ID: <BAY20-F2314898223128973270EC5A5730@phx.gbl>

Hi,
 I just wonder whether biojava implements the function of exact/approximate 
tandem repeats in DNA. I thought it is a typical function of dna, but I 
could not find anything about it in biojava.
 Hope someone can give me some hints. Thanks
Best,
zbhuang

_________________________________________________________________
?????????????? MSN Messenger:  http://messenger.msn.com/cn  



From joel.pitt at gmail.com  Wed Mar 14 21:13:00 2007
From: joel.pitt at gmail.com (Joel Pitt)
Date: Thu, 15 Mar 2007 10:13:00 +1300
Subject: [Biojava-dev] tandem repeats in biojava
In-Reply-To: <BAY20-F2314898223128973270EC5A5730@phx.gbl>
References: <BAY20-F2314898223128973270EC5A5730@phx.gbl>
Message-ID: <d7e54a6c0703141413i47021cf1hf2c4c070ca09cc8b@mail.gmail.com>

Hi zbhuang,

When I last checked about a couple of years ago there wasn't anything
like that as part of the core biojava. I'm the author of
http://repeatfinder.sourceforge.net/ which is an approximate
tandem/exact repeatfinder using our own searching algorithm. I was
planning to port it into biojava (as well as build a nice GUI for it),
but as is usually the case, I haven't had the time.

The RepeatFinder source code is available though, so feel free to port
it yourself ;)

Cheers,
Joel

On 3/15/07, Huang Zhibin <zbhuang2005 at hotmail.com> wrote:
> Hi,
>  I just wonder whether biojava implements the function of exact/approximate
> tandem repeats in DNA. I thought it is a typical function of dna, but I
> could not find anything about it in biojava.
>  Hope someone can give me some hints. Thanks
> Best,
> zbhuang
>
> _________________________________________________________________
> ?????????????? MSN Messenger:  http://messenger.msn.com/cn
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
-Joel

"Unless you try to do something beyond what you have mastered, you
will never grow." -C.R. Lawton



From bugzilla-daemon at portal.open-bio.org  Wed Mar 14 23:02:49 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 14 Mar 2007 19:02:49 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703142302.l2EN2ngu013096@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234





------- Comment #3 from holland at ebi.ac.uk  2007-03-14 19:02 EST -------
good grief, what a can of worms.... i'll get onto it on Friday when I'm back in
the office!


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 15 10:11:58 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 15 Mar 2007 06:11:58 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703151011.l2FABw47005920@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234





------- Comment #4 from holland at ebi.ac.uk  2007-03-15 06:11 EST -------
I've identified the problem areas in the EMBLFormat code. I will fix them
tomorrow.

Note to self:

if (format.equals(EMBL_FORMAT)) {
                // accession; SV version; circular/linear; moltype; dataclass;
division; length BP.
                locusLine.append(rs.getAccession());
                locusLine.append("; ");
--- INSERT "SV versionLine;" here
                locusLine.append(rs.getCircular()?"circular; ":"linear; ");
                locusLine.append(moltype);

        // version line
--- WRAP in test - only execute if EMBL_PRE87_FORMAT
        if (versionLine!=null) StringTools.writeKeyValueLine(VERSION_TAG,
versionLine, 5, this.getLineWidth(), null, VERSION_TAG, this.getPrintStream());
        else StringTools.writeKeyValueLine(VERSION_TAG,
accession+"."+rs.getVersion(), 5, this.getLineWidth(), null, VERSION_TAG,
this.getPrintStream());
        this.getPrintStream().println(DELIMITER_TAG+"   ");


        // date line
-- INSERT commaa before space before Created
        StringTools.writeKeyValueLine(DATE_TAG, (cdat==null?udat:cdat)+" (Rel.
"+(crel==null?"0":crel)+" Created)", 5, this.getLineWidth(), null, DATE_TAG,
this.getPrintStream());

--- CHECK that leading space chomped first - does this record start in space
then "? It ends in "; on last line but does not start on same line
if (key.equals(TITLE_TAG)) {
                        if (val.length()>1) {
                            if (val.endsWith(";")) val =
val.substring(0,val.length()-1); // chomp semicolon
                            if (val.endsWith("\"")) val =
val.substring(1,val.length()-2); // chomp quotes
                            title = val;
                        } else title=null; // single semi-colon indicates no
title
                    }

            // add-in other dbxrefs where present
            for (Iterator j = f.getRankedCrossRefs().iterator(); j.hasNext(); )
{
                RankedCrossRef rcr = (RankedCrossRef)j.next();
                CrossRef cr = rcr.getCrossRef();
--- REMOVE taxon: prefix - shouldn't be there...
                StringTools.writeKeyValueLine(FEATURE_TAG,
"/db_xref=\"taxon:"+cr.getDbname()+":"+cr.getAccession()+"\"", 21,
this.getLineWidth(), null, FEATURE_TAG, this.getPrintStream());
            }




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From bugzilla-daemon at portal.open-bio.org  Fri Mar 16 09:50:27 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 16 Mar 2007 05:50:27 -0400
Subject: [Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank
	to EMBL format
In-Reply-To: <bug-2234-485@http.bugzilla.open-bio.org/>
Message-ID: <200703160950.l2G9oR2a005733@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2234


holland at ebi.ac.uk changed:

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




------- Comment #5 from holland at ebi.ac.uk  2007-03-16 05:50 EST -------
Fixes made and committed.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 18:38:34 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 14:38:34 -0400
Subject: [Biojava-dev] [Bug 2244] New: uniprot files do not load
Message-ID: <bug-2244-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244

           Summary: uniprot files do not load
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


Exceptions are thrown when Uniprot files are tentatively read by the biojavax
parser.

Reading P01717 or P07724 with RichSequence.IOTools.readUniProt throw :
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:393)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)

P07724

(this one initially reported by Sofia Burvall)
Reading P13346 throw:
Caused by: org.biojava.bio.seq.io.ParseException: Bad date line found:
01-JAN-1990 (Rel. 13, Created)
        at
org.biojavax.bio.seq.io.UniProtFormat.readRichSequence(UniProtFormat.java:349)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 19:07:57 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 15:07:57 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703211907.l2LJ7v5u010410@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |holland at ebi.ac.uk
             Status|NEW                         |ASSIGNED




------- Comment #1 from holland at ebi.ac.uk  2007-03-21 15:07 EST -------
I don't understand what the problem is. If I download UniProt files for the 3
accessions you mention from the official UniProt website at
http://www.pir.uniprot.org/ then I get files that parse correctly.

The date lines shown in your example are not in UniProt format. They are EMBL
format date lines.

Where are you getting your UniProt files from? This sounds like a bug in the
software at the site you are getting from, not a bug with BioJava.

Please let me know where you are getting the files from and I will investigate
a bit more.


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 20:15:56 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 16:15:56 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212015.l2LKFu2x014547@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #2 from gwaldon at geneinfinity.org  2007-03-21 16:15 EST -------
Hi Richard,

We must have some mixup of some sort. The bad date line was reported when I
tried to parse the file included in the email from Sofia (it was posted on
biojava-1 on March 16, 2007). Effectively, this file is different from what the
one I get at the uniprot web site. Reading Sophia email, it is possible that
the incorrect file was in fact generated by biojavax (in the same kind of
operation like read/write/read problem that was corrected recently).

I am going to investigate the other exception. The 2 files were from the
correct source (http://www.expasy.org/uniprot/P01717, click on "View entry in
original UniProtKB/Swiss-Prot format", etc.). I'll get back on this latter.

- George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 20:27:15 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 16:27:15 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212027.l2LKRFrc015247@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #3 from gwaldon at geneinfinity.org  2007-03-21 16:27 EST -------

Well, the 2 files are respectively from:
http://www.expasy.org/cgi-bin/get-sprot-entry?P07724
http://www.expasy.org/cgi-bin/get-sprot-entry?P01717

The ArrayIndexOutOfBoundsException are thrown for the lines:

P07724:
DR   ProDom [Domain structure / List of seq. sharing at least 1 domain ]

P01717:
DR   HOVERGEN [Family / Alignment / Tree]

Hope this helps!
- George


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From bugzilla-daemon at portal.open-bio.org  Wed Mar 21 21:53:26 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 21 Mar 2007 17:53:26 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703212153.l2LLrQ8X020150@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #4 from holland at ebi.ac.uk  2007-03-21 17:53 EST -------
Thanks for that extra info! I'll investigate further over the next couple of
days and get back to you when I've got a solution.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 22 12:19:20 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 22 Mar 2007 08:19:20 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703221219.l2MCJKIM028661@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #5 from holland at ebi.ac.uk  2007-03-22 08:19 EST -------
I have investigated the two problem DR lines and found that they do not match
the current UniProt file format specifications as defined at
http://www.expasy.org/sprot/userman.html#DR_line .

There is no indication in the UniProt file format specification as to what a DR
line in this format might actually mean.

As these files came from UniProt themselves, I think the best thing to do is
for you to contact UniProt and raise a bug report with them directly indicating
that their website is producing files that do not conform to their own file
format standards.

BJX can only parse files which follow the official format definition. There's
only so much flexibility we can build in! :)

I'll leave this bug as ASSIGNED for now so that you can add any comments
regarding what UniProt say about their bug.


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From bugzilla-daemon at portal.open-bio.org  Mon Mar 26 08:23:09 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 26 Mar 2007 04:23:09 -0400
Subject: [Biojava-dev] [Bug 2250] New: Genbank format error
Message-ID: <bug-2250-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2250

           Summary: Genbank format error
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: mark.schreiber at novartis.com


I think that the following error was caused by the last fix to GenbankFormat

Format_object=org.biojavax.bio.seq.io.GenbankFormat
Accession=null
Id=null
Comments=Bad locus line
Parse_block=LOCUS   NM_182008               1629 bp    mRNA    linear   INV
23-MAR-2007
Stack trace follows ....


        at
org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323)
        at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 2 more


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From bugzilla-daemon at portal.open-bio.org  Mon Mar 26 14:41:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 26 Mar 2007 10:41:40 -0400
Subject: [Biojava-dev] [Bug 2250] Genbank format error
In-Reply-To: <bug-2250-485@http.bugzilla.open-bio.org/>
Message-ID: <200703261441.l2QEfent022095@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2250


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-26 10:41 EST -------
Fixed. Now testing before commit.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 04:47:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 00:47:10 -0400
Subject: [Biojava-dev] [Bug 2253] New: NullPointerException in
	MultiSourceCompoundRichLocation
Message-ID: <bug-2253-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253

           Summary: NullPointerException in MultiSourceCompoundRichLocation
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


More exactly in the blockIterator method taken from CompoundRichLocation where
the "sortedMembers" variable is null. This set is actually never instantiated,
see constructor. Well, I don't understand the function of the "sortedMembers"
list; why not sorting the "members" list instead from the start?
- George


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 05:27:41 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 01:27:41 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703290527.l2T5Rfu3010839@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244





------- Comment #6 from gwaldon at geneinfinity.org  2007-03-29 01:27 EST -------
The problem is limited to the Expasy server. I am trying to get in touch with
someone overthere.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 08:54:26 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 04:54:26 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703290854.l2T8sQkH019389@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-29 04:54 EST -------
The only way that sortedMembers can be null is if the object is loaded in via
Hibernate. This is a bug which I have now fixed in CVS.

PS. In order to reproduce output files that are largely the same as the input
files these locations are read from, whilst simultaneously providing a sensible
iterator for the user, it is important to maintain two separate orders. If the
user ever calls sort() on the location, the two orders become the same.

PPS. There is NO test in BJX for this bug as it is Hibernate-related and
therefore almost impossible to write a test case for!


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 16:08:42 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 12:08:42 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703291608.l2TG8gWo008372@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253


gwaldon at geneinfinity.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |VERIFIED




------- Comment #2 from gwaldon at geneinfinity.org  2007-03-29 12:08 EST -------
The problem was in MultiSourceCompoundRichLocation and not its parent class.
This resulted in the second set to be null from both public constructors.


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From bugzilla-daemon at portal.open-bio.org  Thu Mar 29 17:13:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Thu, 29 Mar 2007 13:13:40 -0400
Subject: [Biojava-dev] [Bug 2255] New: Problems with read and write of EMBL
	files
Message-ID: <bug-2255-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2255

           Summary: Problems with read and write of EMBL files
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: seq.io
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: gwaldon at geneinfinity.org


I just noticed two problems with EMBL files. During read operations, the first
keyword (KW line) is not parsed. Also during write operations, the sequence
line (SQ) is missing the word "Sequence" in the output.
- George


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From gwaldon at geneinfinity.org  Fri Mar 30 05:28:51 2007
From: gwaldon at geneinfinity.org (george waldon)
Date: Thu, 29 Mar 2007 22:28:51 -0700
Subject: [Biojava-dev] Exception in MassCalc.getMass
Message-ID: <20070330052851.16176.qmail@mmm1924.dulles19-verio.com>

I got a NullPointerException in MassCalc.getMass that I traced to the presence of an ambiguity symbol X in the peptide sequence. 
The origin lies in SimpleSymbolPropertyTable.getDoubleValue.  The ambiguity symbol is first validated (through its matches in AbstractAlphabet) and the exception is thrown when we try to find a value associated with a null key in the property map.
First I think we should redirect this exception to the checked IllegalSymbolException to tell the user that something is going wrong.
Concerning calculating masses, I see two needs: need to estimate the mass of polypeptides containing ambiguity symbols and need to obtain an exact mass or an IllegalSymbolException when ambiguity occurs.
I propose to add a new method MassCalc.getEstimatedMass to do the first part and to modify the existing method so that  an IllegalSymbolException is thrown whenever a non-atomic symbol is encounter. Mass values for ambiguity symbols would be added to the ResidueProperty.xml file and taken as simple average of the atomic match values.

- George


From mark.schreiber at novartis.com  Fri Mar 30 05:43:05 2007
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Fri, 30 Mar 2007 13:43:05 +0800
Subject: [Biojava-dev] Exception in MassCalc.getMass
Message-ID: <OFD6A9167E.6BCEF3E4-ON482572AE.001F02B8-482572AE.001F6937@ah.novartis.com>

Hi George -

Sounds like a good idea. Can you check it in? And add a JUnit test???

You probably don't need to add ambiguity weights to the XML as you can 
decompose a basis symbol into it's components, look up each and get the 
average. Infact there are so many possible amino acid ambiguities it would 
be a very bad idea to list them all in the XML file. Although IUPAC only 
has about 3 amino acid ambiguities BioJava's BasisSymbols can infact 
represent any and every possible combination of ambiguity (although there 
is no obvious way to tokenize them to text) so you would need to allow for 
this in your getEstimated mass method. 

Thanks for spotting this,

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

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

phone +65 6722 2973
fax  +65 6722 2910





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
03/30/2007 01:28 PM
Please respond to george waldon

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Exception in MassCalc.getMass


I got a NullPointerException in MassCalc.getMass that I traced to the 
presence of an ambiguity symbol X in the peptide sequence. 
The origin lies in SimpleSymbolPropertyTable.getDoubleValue.  The 
ambiguity symbol is first validated (through its matches in 
AbstractAlphabet) and the exception is thrown when we try to find a value 
associated with a null key in the property map.
First I think we should redirect this exception to the checked 
IllegalSymbolException to tell the user that something is going wrong.
Concerning calculating masses, I see two needs: need to estimate the mass 
of polypeptides containing ambiguity symbols and need to obtain an exact 
mass or an IllegalSymbolException when ambiguity occurs.
I propose to add a new method MassCalc.getEstimatedMass to do the first 
part and to modify the existing method so that  an IllegalSymbolException 
is thrown whenever a non-atomic symbol is encounter. Mass values for 
ambiguity symbols would be added to the ResidueProperty.xml file and taken 
as simple average of the atomic match values.

- George
_______________________________________________
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  Fri Mar 30 08:51:20 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 04:51:20 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703300851.l2U8pKbZ016735@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #3 from holland at ebi.ac.uk  2007-03-30 04:51 EST -------
Indeed you're right. I just checked again and the bugfix I applied should have
fixed this too. Could you confirm that?


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From holland at ebi.ac.uk  Fri Mar 30 08:53:02 2007
From: holland at ebi.ac.uk (Richard Holland)
Date: Fri, 30 Mar 2007 09:53:02 +0100
Subject: [Biojava-dev] ParseExceptions
Message-ID: <460CCFEE.4030609@ebi.ac.uk>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi all. Can the person who recently modified the BJX EMBLFormat to throw
ParseExceptions using the ParseException.newMessage() method please
check all their code to make sure that it is correct. I have noticed
that every occurrence of this in EMBLFormat was implemented incorrectly
and never threw the generated message. I have fixed it there, but have
no idea how many other places this might have happened.

I have replaced all occurrences with two lines similar to this:

String message = ParseException.newMessage(....);
throw new ParseException(message);

cheers,
Richard
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGDM/u4C5LeMEKA/QRAkf3AJ4opHh8SDa+jUIoNnKTc3XgdJzLAACfcci5
LyA41NgjkULPvdy4AeALOhw=
=PXKG
-----END PGP SIGNATURE-----


From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 10:29:41 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 06:29:41 -0400
Subject: [Biojava-dev] [Bug 2255] Problems with read and write of EMBL files
In-Reply-To: <bug-2255-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301029.l2UATf4w020994@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2255


holland at ebi.ac.uk changed:

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




------- Comment #1 from holland at ebi.ac.uk  2007-03-30 06:29 EST -------
Fixed in CVS.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 15:39:11 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:39:11 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301539.l2UFdB29001755@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #4 from gwaldon at geneinfinity.org  2007-03-30 11:39 EST -------
Yes, it is fixed. I'll try to get the time to write a test on equality of
MultiSourceCompoundRichLocation - this is how the bug was revealed.


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 15:45:38 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:45:38 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301545.l2UFjcY8002022@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


gwaldon at geneinfinity.org changed:

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




------- Comment #7 from gwaldon at geneinfinity.org  2007-03-30 11:45 EST -------
Following is the comment of Severine Duvaud from Expasy. The links she
mentionned are found on niceprot View; here is a link exemple:
http://www.expasy.org/cgi-bin/niceprot.pl?P01717

======================================================================

When clicking on "View entry in original UniProtKB/Swiss-Prot format",
you get an "enhanced" view of the original entry (compared to the "raw"
entry view as pointed out by the other link), notably with implicit
links. The standard entry, in (hopefully) regular Swiss-Prot format can
be found when clicking on "View entry in raw text format (no link)" or
by downloading uniprot_sprot.dat on our FTP server.
Sorry for the confusion.
Best regards,

Severine

-- 
**************************************
Severine Duvaud, Swiss-Prot Group

Swiss Institute of Bioinformatics
CMU, 1 rue Michel Servet
CH - 1211 Geneva 4
Switzerland

Tel. (+41) 22 379 58 25
Fax (+41) 22 379 58 58

Severine.Duvaud at isb-sib.ch
http://www.expasy.org
************************************** 


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 15:46:09 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:46:09 -0400
Subject: [Biojava-dev] [Bug 2253] NullPointerException in
	MultiSourceCompoundRichLocation
In-Reply-To: <bug-2253-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301546.l2UFk96q002090@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2253





------- Comment #5 from holland at ebi.ac.uk  2007-03-30 11:46 EST -------
Great. If you get time to come up with a test, can you add a note to this bug
and then close the bug! I'll leave it as verified/fixed in the meantime.

Tests should go in an appropriate package under the tests/ folder in
biojava-live - you'll get the picture I'm sure just by looking around there to
see where other tests have gone (e.g. org.biojavax.bio.seq.io for all BJX
sequence i/o related tests). Please do create a new test package if you can't
find one that seems appropriate. 


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From bugzilla-daemon at portal.open-bio.org  Fri Mar 30 15:49:40 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 30 Mar 2007 11:49:40 -0400
Subject: [Biojava-dev] [Bug 2244] uniprot files do not load
In-Reply-To: <bug-2244-485@http.bugzilla.open-bio.org/>
Message-ID: <200703301549.l2UFnekY002285@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2244


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |CLOSED




------- Comment #8 from holland at ebi.ac.uk  2007-03-30 11:49 EST -------
Thanks for that. I'm glad I'm not going mad! :)

So it seems that Expasy is providing slightly confusing links, and the best
route to get files from them for programmatic parsing is to get raw text files
wherever possible rather then cutting-and-pasting their
enhanced-with-HTML-links versions that they show by default when browsing their
database.


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From amit.p at ocimumbio.com  Tue Mar 13 06:38:52 2007
From: amit.p at ocimumbio.com (Amit Dattatreya Parhar)
Date: Tue, 13 Mar 2007 06:38:52 -0000
Subject: [Biojava-dev] ESD megabace trace file parser
Message-ID: <004a01c76537$adca6e40$fc01a8c0@ocimumbio.net>

Hi,
         I need a .esd file parser. can anybody help me out? atleast information on how to parse this type of trace file.

thanks in advance
Amit
Bioinformatics Analyst
amit.p at ocimumbio.com

Ocimum Biosolutions
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From renauxc.isat at gmail.com  Mon Mar 26 13:18:08 2007
From: renauxc.isat at gmail.com (Caroline Renaux)
Date: Mon, 26 Mar 2007 15:18:08 +0200
Subject: [Biojava-dev] org.biojava.bio.symbol.UkkonenSuffixTree.class BUG
Message-ID: <401c5fc20703260618t3f38eb86yd7d66043399ba69e@mail.gmail.com>

Bonjour,

j'ai r?cemment utilis? le Package org.biojava.bio.symbol et plus
particuli?rement la classe UkkonenSuffixTree. Cependant lorsque que je veux
ajouter un ensemble de s?quences ? l'arbre et que je les s?pares par le
caract?re de s?paration '$' cel? ne fonctionne pas. Lorsqu'il traite la
seconde s?quence j'obtiens une erreur "NullPointerException" dans la m?thode
jumpTo ? la ligne :

arrivedAt=(SuffixNode)currentNode.children.get(*new* Character(source.charAt
(from)));

Je ne comprend pas ce que j'aurai pu faire de travers.

D'avance merci de votre r?ponse.

RENAUX C.

--------------------------------
Hello,

I used for a java application the org.biojava.bio.symbol package and
particularly the UkkonenSuffixTree class. When i want to add a set of
sequences to the tree, i add a '$' between the sequences but it doesn't
work. I have a NullPointerException when the system add the second sequence
int the method jumTo at the line :

arrivedAt=(SuffixNode)currentNode.children.get(*new* Character(source.charAt
(from)));

I don't understand why it doesn't work.

Thank you in advance.

RENAUX C.