From Michael.Rusch at STJUDE.ORG  Wed Dec  1 13:37:00 2010
From: Michael.Rusch at STJUDE.ORG (Rusch, Michael)
Date: Wed, 1 Dec 2010 12:37:00 -0600
Subject: [Biojava-l] newbie question about gff
Message-ID: <A475AF196964604CAEE109F1CA0275AB157D014772@SJMEMXMBS10.stjude.sjcrh.local>

Newbie question:

I want to read in a GFF file and process it taking full advantage of the gene model (e.g. exons belong to a transcript).  I see that I can read the GFF into an EntrySet, and then annotate a Sequence with the EntrySet, but I don't have a sequence to start off with.  I could read in sequence from a FASTA file, but since I'm not actually using sequence, and I'm dealing with human chromosomes, it seems quite wasteful to do so.  I could also just use the EntrySet, but then I can't take advantage of the gene model.  Is there a way to get a Sequence object with no sequence, just features from a GFF file?

Thanks,
Michael

________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer


From darnells at dnastar.com  Fri Dec  3 18:35:21 2010
From: darnells at dnastar.com (Steve Darnell)
Date: Fri, 3 Dec 2010 17:35:21 -0600
Subject: [Biojava-l] PDBFileParser question using PDBID 470D
In-Reply-To: <AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
References: <A4009967D1886D4286A9B7931FD58610027E0C4B@FS1.dnastar.com>
	<AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
Message-ID: <A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>

Andreas,

I've been using biojava to gather sequence data from structure files for an internal project.  My intent was to test the limitations of my work (hence files similar to 470D), but came across this behavior in biojava.

It is not critical to obtain this particular mapping since it can be derived from the atom records.  However, I didn't understand why the SEQRES list would be empty and was looking for clarification.  Is it because the chain is RNA and the empty list prevents the unsupported alignment of RNA records?

Regards,
Steve

-----Original Message-----
From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: Monday, November 29, 2010 6:36 PM
To: Steve Darnell
Cc: biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] PDBFileParser question using PDBID 470D

Hi Steve,

as you already are saying, this is an "exotic" sequence, in the sense
that this is an RNA. The alignments of the SEQRES records for RNA
currently is not supported as of yet. Can you explain a bit more what
you are doing and why you need this mapping in this case?

Thanks,
Andreas

On Mon, Nov 29, 2010 at 12:51 PM, Steve Darnell <darnells at dnastar.com> wrote:
> Greetings,
>
> After parsing PDBID 470D with biojava-3.0-alpha5, Chain A returns an
> empty SEQRES sequence (Chain.getSeqResSequence) and empty SEQRES group
> list (Chain.getSeqResGroups) but the one-letter ATOM sequence is
> properly translated and the ATOM group list contains the appropriate
> number of groups (LoadChemCompInfo set to true).
>
> This is an exotic sequence, but my expectation is that the SEQRES group
> list would have members in it (and one-letter sequence translated if
> LoadChemCompInfo is true). ?Am I mistaken and the current behavior is
> the intended result?
>
> Best regards,
> Steve Darnell
>
> --
> SEQRES records exist in 470D:
>
> SEQRES ? 1 A ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>
> SEQRES ? 1 B ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>
>
>
> Sample println output (ln 1 record type, ln 2 get${TYPE}Sequence, ln 3
> get${TYPE}Groups):
>
> SEQRES
> ''
> []
>
> ATOM
> 'CGCGAAUUCGCG'
> [PDB: C43 1 trueatoms: 21, PDB: G48 2 trueatoms: 27, PDB: C43 3
> trueatoms: 24, ...]
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From andreas at sdsc.edu  Sat Dec  4 12:46:08 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 4 Dec 2010 09:46:08 -0800
Subject: [Biojava-l] PDBFileParser question using PDBID 470D
In-Reply-To: <A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>
References: <A4009967D1886D4286A9B7931FD58610027E0C4B@FS1.dnastar.com>
	<AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>
Message-ID: <AANLkTimSWNZOpLwCnPyqsR1RVgj_BvK4YT6pPTUESeZ9@mail.gmail.com>

Hi Steve,

> I've been using biojava to gather sequence data from structure files for an internal project. ?My intent was to test the limitations of my work (hence files similar to 470D), but came across this behavior in biojava.

ok

> It is not critical to obtain this particular mapping since it can be derived from the atom records. ?However, I didn't understand why the SEQRES list would be empty and was looking for clarification. ?Is it because the chain is RNA and the empty list prevents the unsupported alignment of RNA records?

When working with PDB files the list gets built up after the
alignment. Since RNA alignment is not supported by the parser, the
list can't get created...

In principle mmCif files contain the info how to join SEQRES and ATOM
groups correctly and no alignment is needed.  I will take a look
again, how this works in this case...

Andreas

> -----Original Message-----
> From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
> Sent: Monday, November 29, 2010 6:36 PM
> To: Steve Darnell
> Cc: biojava-l at lists.open-bio.org
> Subject: Re: [Biojava-l] PDBFileParser question using PDBID 470D
>
> Hi Steve,
>
> as you already are saying, this is an "exotic" sequence, in the sense
> that this is an RNA. The alignments of the SEQRES records for RNA
> currently is not supported as of yet. Can you explain a bit more what
> you are doing and why you need this mapping in this case?
>
> Thanks,
> Andreas
>
> On Mon, Nov 29, 2010 at 12:51 PM, Steve Darnell <darnells at dnastar.com> wrote:
>> Greetings,
>>
>> After parsing PDBID 470D with biojava-3.0-alpha5, Chain A returns an
>> empty SEQRES sequence (Chain.getSeqResSequence) and empty SEQRES group
>> list (Chain.getSeqResGroups) but the one-letter ATOM sequence is
>> properly translated and the ATOM group list contains the appropriate
>> number of groups (LoadChemCompInfo set to true).
>>
>> This is an exotic sequence, but my expectation is that the SEQRES group
>> list would have members in it (and one-letter sequence translated if
>> LoadChemCompInfo is true). ?Am I mistaken and the current behavior is
>> the intended result?
>>
>> Best regards,
>> Steve Darnell
>>
>> --
>> SEQRES records exist in 470D:
>>
>> SEQRES ? 1 A ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>>
>> SEQRES ? 1 B ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>>
>>
>>
>> Sample println output (ln 1 record type, ln 2 get${TYPE}Sequence, ln 3
>> get${TYPE}Groups):
>>
>> SEQRES
>> ''
>> []
>>
>> ATOM
>> 'CGCGAAUUCGCG'
>> [PDB: C43 1 trueatoms: 21, PDB: G48 2 trueatoms: 27, PDB: C43 3
>> trueatoms: 24, ...]
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>



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


From cfriedline at vcu.edu  Mon Dec  6 07:45:38 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 07:45:38 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
Message-ID: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>

Hello,

Found another potential error case, this time in beta2 (fresh pull
from git last evening). ?For more info, please see
http://pastie.org/1351388 for test case and stack trace. ?The JUnit
test passes simply because the pair object is not null, but fails when
trying to extract any information from the pair itself (toString(),
getIdenticals(), etc). The substitution matrix file is from
ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
pairwise alignments, which do not all fail, but most do with this same
error.

Thanks,
Chris

--
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA


From ayates at ebi.ac.uk  Mon Dec  6 08:50:20 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 13:50:20 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
Message-ID: <610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>

Hi Chris,

Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful

Andy

On 6 Dec 2010, at 12:45, Chris Friedline wrote:

> Hello,
> 
> Found another potential error case, this time in beta2 (fresh pull
> from git last evening).  For more info, please see
> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> test passes simply because the pair object is not null, but fails when
> trying to extract any information from the pair itself (toString(),
> getIdenticals(), etc). The substitution matrix file is from
> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> pairwise alignments, which do not all fail, but most do with this same
> error.
> 
> Thanks,
> Chris
> 
> --
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From ayates at ebi.ac.uk  Mon Dec  6 10:13:49 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 15:13:49 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
Message-ID: <8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>

So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.

Does anyone on list know how the AlignedSequence code encodes gaps & the alike? 

Andy

On 6 Dec 2010, at 13:50, Andy Yates wrote:

> Hi Chris,
> 
> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
> 
> Andy
> 
> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> 
>> Hello,
>> 
>> Found another potential error case, this time in beta2 (fresh pull
>> from git last evening).  For more info, please see
>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
>> test passes simply because the pair object is not null, but fails when
>> trying to extract any information from the pair itself (toString(),
>> getIdenticals(), etc). The substitution matrix file is from
>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
>> pairwise alignments, which do not all fail, but most do with this same
>> error.
>> 
>> Thanks,
>> Chris
>> 
>> --
>> PhD Candidate, Integrative Life Sciences
>> Virginia Commonwealth University
>> Richmond, VA
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From andreas at sdsc.edu  Mon Dec  6 12:22:55 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 6 Dec 2010 09:22:55 -0800
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
Message-ID: <AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>

Hi Andy,

Check out the SimpleAlignedSequence class, for how Gaps are handled...
Does that help?

Andreas

On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>
> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>
> Andy
>
> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>
>> Hi Chris,
>>
>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>
>> Andy
>>
>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>
>>> Hello,
>>>
>>> Found another potential error case, this time in beta2 (fresh pull
>>> from git last evening). ?For more info, please see
>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>> test passes simply because the pair object is not null, but fails when
>>> trying to extract any information from the pair itself (toString(),
>>> getIdenticals(), etc). The substitution matrix file is from
>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>> pairwise alignments, which do not all fail, but most do with this same
>>> error.
>>>
>>> Thanks,
>>> Chris
>>>
>>> --
>>> PhD Candidate, Integrative Life Sciences
>>> Virginia Commonwealth University
>>> Richmond, VA
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From cfriedline at vcu.edu  Mon Dec  6 13:28:37 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 13:28:37 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
Message-ID: <AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>

That does help, thanks.  However, when calling getAsList() on the
aligned sequences and printing, this is what I see.  Something seems
wrong.  It does appear as though null is being inserted where there
should be gaps

seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
null, null, null, null, null, null]
seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]

Chris

On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Andy,
>
> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> Does that help?
>
> Andreas
>
> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>
>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>
>> Andy
>>
>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>
>>> Hi Chris,
>>>
>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>
>>> Andy
>>>
>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>
>>>> Hello,
>>>>
>>>> Found another potential error case, this time in beta2 (fresh pull
>>>> from git last evening). ?For more info, please see
>>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>>> test passes simply because the pair object is not null, but fails when
>>>> trying to extract any information from the pair itself (toString(),
>>>> getIdenticals(), etc). The substitution matrix file is from
>>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>>> pairwise alignments, which do not all fail, but most do with this same
>>>> error.
>>>>
>>>> Thanks,
>>>> Chris
>>>>
>>>> --
>>>> PhD Candidate, Integrative Life Sciences
>>>> Virginia Commonwealth University
>>>> Richmond, VA
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> --
>> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
>> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>>
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA


From cfriedline at vcu.edu  Mon Dec  6 13:41:17 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 13:41:17 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
Message-ID: <AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>

OK, so here's a quick fix now that I know where to look.  In my local
source I added the following line to the constructor of DNACompoundSet
and recompiled.

addNucleotideCompound("-", "-");

Not sure if this is the correct place for it in terms of what the devs
want to do globally, but it gets me moving forward again.  Gap
characters are in AminoAcidCompoundSet so I'm wondering if this was
just a tiny oversight on the nucleotide front.

Thanks again for the help everyone,
Chris

On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
> That does help, thanks. ?However, when calling getAsList() on the
> aligned sequences and printing, this is what I see. ?Something seems
> wrong. ?It does appear as though null is being inserted where there
> should be gaps
>
> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> null, null, null, null, null, null]
> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
>
> Chris
>
> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Andy,
>>
>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
>> Does that help?
>>
>> Andreas
>>
>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>>
>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>>
>>> Andy
>>>
>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>>
>>>> Andy
>>>>
>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Found another potential error case, this time in beta2 (fresh pull
>>>>> from git last evening). ?For more info, please see
>>>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>>>> test passes simply because the pair object is not null, but fails when
>>>>> trying to extract any information from the pair itself (toString(),
>>>>> getIdenticals(), etc). The substitution matrix file is from
>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>>>> pairwise alignments, which do not all fail, but most do with this same
>>>>> error.
>>>>>
>>>>> Thanks,
>>>>> Chris
>>>>>
>>>>> --
>>>>> PhD Candidate, Integrative Life Sciences
>>>>> Virginia Commonwealth University
>>>>> Richmond, VA
>>>>>
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>> --
>>> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
>>> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA
>



-- 
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA


From ayates at ebi.ac.uk  Mon Dec  6 14:32:55 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 19:32:55 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
Message-ID: <91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>

I would say partially an oversight on my part & partially done on purpose (a gap is not a nucleotide after all). However I'm all in favour of being pragmatic here so lets add them in. If I get an okay from the relevant parties I'll commit the change in.

Andy

On 6 Dec 2010, at 18:41, Chris Friedline wrote:

> OK, so here's a quick fix now that I know where to look.  In my local
> source I added the following line to the constructor of DNACompoundSet
> and recompiled.
> 
> addNucleotideCompound("-", "-");
> 
> Not sure if this is the correct place for it in terms of what the devs
> want to do globally, but it gets me moving forward again.  Gap
> characters are in AminoAcidCompoundSet so I'm wondering if this was
> just a tiny oversight on the nucleotide front.
> 
> Thanks again for the help everyone,
> Chris
> 
> On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>> That does help, thanks.  However, when calling getAsList() on the
>> aligned sequences and printing, this is what I see.  Something seems
>> wrong.  It does appear as though null is being inserted where there
>> should be gaps
>> 
>> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
>> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
>> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
>> null, null, null, null, null, null]
>> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
>> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
>> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
>> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
>> 
>> Chris
>> 
>> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Andy,
>>> 
>>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
>>> Does that help?
>>> 
>>> Andreas
>>> 
>>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>>> 
>>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>>> 
>>>> Andy
>>>> 
>>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>>> 
>>>>> Andy
>>>>> 
>>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> Found another potential error case, this time in beta2 (fresh pull
>>>>>> from git last evening).  For more info, please see
>>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
>>>>>> test passes simply because the pair object is not null, but fails when
>>>>>> trying to extract any information from the pair itself (toString(),
>>>>>> getIdenticals(), etc). The substitution matrix file is from
>>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
>>>>>> pairwise alignments, which do not all fail, but most do with this same
>>>>>> error.
>>>>>> 
>>>>>> Thanks,
>>>>>> Chris
>>>>>> 
>>>>>> --
>>>>>> PhD Candidate, Integrative Life Sciences
>>>>>> Virginia Commonwealth University
>>>>>> Richmond, VA
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>>> --
>>>> Andrew Yates                   Ensembl Genomes Engineer
>>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> -----------------------------------------------------------------------
>>> Dr. Andreas Prlic
>>> Senior Scientist, RCSB PDB Protein Data Bank
>>> University of California, San Diego
>>> (+1) 858.246.0526
>>> -----------------------------------------------------------------------
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>> 
>> 
>> 
>> --
>> PhD Candidate, Integrative Life Sciences
>> Virginia Commonwealth University
>> Richmond, VA
>> 
> 
> 
> 
> -- 
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From willishf at ufl.edu  Mon Dec  6 15:00:18 2010
From: willishf at ufl.edu (Scooter Willis)
Date: Mon, 6 Dec 2010 15:00:18 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
	<91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
Message-ID: <AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>

It would be nice to have a cool indexing system that allowed dynamic indexes
of the data model but not worth the headache. If we are going to go big we
should use the same gap symbols that were added for protein sequences.

Scooter

On Mon, Dec 6, 2010 at 2:32 PM, Andy Yates <ayates at ebi.ac.uk> wrote:

> I would say partially an oversight on my part & partially done on purpose
> (a gap is not a nucleotide after all). However I'm all in favour of being
> pragmatic here so lets add them in. If I get an okay from the relevant
> parties I'll commit the change in.
>
> Andy
>
> On 6 Dec 2010, at 18:41, Chris Friedline wrote:
>
> > OK, so here's a quick fix now that I know where to look.  In my local
> > source I added the following line to the constructor of DNACompoundSet
> > and recompiled.
> >
> > addNucleotideCompound("-", "-");
> >
> > Not sure if this is the correct place for it in terms of what the devs
> > want to do globally, but it gets me moving forward again.  Gap
> > characters are in AminoAcidCompoundSet so I'm wondering if this was
> > just a tiny oversight on the nucleotide front.
> >
> > Thanks again for the help everyone,
> > Chris
> >
> > On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu>
> wrote:
> >> That does help, thanks.  However, when calling getAsList() on the
> >> aligned sequences and printing, this is what I see.  Something seems
> >> wrong.  It does appear as though null is being inserted where there
> >> should be gaps
> >>
> >> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> >> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> >> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> >> null, null, null, null, null, null]
> >> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> >> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> >> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> >> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
> >>
> >> Chris
> >>
> >> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu>
> wrote:
> >>> Hi Andy,
> >>>
> >>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> >>> Does that help?
> >>>
> >>> Andreas
> >>>
> >>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> >>>> So myself & Chris have discussed this off list & we believe it's
> because of a NULL compound element in the Sequence given to the
> SequenceMixin method.
> >>>>
> >>>> Does anyone on list know how the AlignedSequence code encodes gaps &
> the alike?
> >>>>
> >>>> Andy
> >>>>
> >>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
> >>>>
> >>>>> Hi Chris,
> >>>>>
> >>>>> Well that's going into my toStringBuilder() method & that particular
> line is concerned with asking a compound for its String representation. How
> often do we get nulls in our Sequences and how to deal with them. After all
> the Sequence AGTCNULLAGTC is probably more harmful then helpful
> >>>>>
> >>>>> Andy
> >>>>>
> >>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> Found another potential error case, this time in beta2 (fresh pull
> >>>>>> from git last evening).  For more info, please see
> >>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> >>>>>> test passes simply because the pair object is not null, but fails
> when
> >>>>>> trying to extract any information from the pair itself (toString(),
> >>>>>> getIdenticals(), etc). The substitution matrix file is from
> >>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> >>>>>> pairwise alignments, which do not all fail, but most do with this
> same
> >>>>>> error.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Chris
> >>>>>>
> >>>>>> --
> >>>>>> PhD Candidate, Integrative Life Sciences
> >>>>>> Virginia Commonwealth University
> >>>>>> Richmond, VA
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>> --
> >>>> Andrew Yates                   Ensembl Genomes Engineer
> >>>> EMBL-EBI                       Tel: +44-(0)1223-492538
> >>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> >>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> -----------------------------------------------------------------------
> >>> Dr. Andreas Prlic
> >>> Senior Scientist, RCSB PDB Protein Data Bank
> >>> University of California, San Diego
> >>> (+1) 858.246.0526
> >>> -----------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>
> >>
> >>
> >> --
> >> PhD Candidate, Integrative Life Sciences
> >> Virginia Commonwealth University
> >> Richmond, VA
> >>
> >
> >
> >
> > --
> > PhD Candidate, Integrative Life Sciences
> > Virginia Commonwealth University
> > Richmond, VA
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

From ayates at ebi.ac.uk  Wed Dec  8 04:06:32 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 8 Dec 2010 09:06:32 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
	<91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
	<AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>
Message-ID: <771AA57F-8AD4-4E9E-A1F0-EA44FA2518F2@ebi.ac.uk>

I've added the gap symbol to DNA & RNA compound sets. Hopefully this error will go away. If not then we'll have to look into the alignment code & get it to use the gap symbol

Andy

On 6 Dec 2010, at 20:00, Scooter Willis wrote:

> It would be nice to have a cool indexing system that allowed dynamic indexes of the data model but not worth the headache. If we are going to go big we should use the same gap symbols that were added for protein sequences.
> 
> Scooter
> 
> On Mon, Dec 6, 2010 at 2:32 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> I would say partially an oversight on my part & partially done on purpose (a gap is not a nucleotide after all). However I'm all in favour of being pragmatic here so lets add them in. If I get an okay from the relevant parties I'll commit the change in.
> 
> Andy
> 
> On 6 Dec 2010, at 18:41, Chris Friedline wrote:
> 
> > OK, so here's a quick fix now that I know where to look.  In my local
> > source I added the following line to the constructor of DNACompoundSet
> > and recompiled.
> >
> > addNucleotideCompound("-", "-");
> >
> > Not sure if this is the correct place for it in terms of what the devs
> > want to do globally, but it gets me moving forward again.  Gap
> > characters are in AminoAcidCompoundSet so I'm wondering if this was
> > just a tiny oversight on the nucleotide front.
> >
> > Thanks again for the help everyone,
> > Chris
> >
> > On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
> >> That does help, thanks.  However, when calling getAsList() on the
> >> aligned sequences and printing, this is what I see.  Something seems
> >> wrong.  It does appear as though null is being inserted where there
> >> should be gaps
> >>
> >> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> >> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> >> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> >> null, null, null, null, null, null]
> >> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> >> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> >> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> >> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
> >>
> >> Chris
> >>
> >> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >>> Hi Andy,
> >>>
> >>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> >>> Does that help?
> >>>
> >>> Andreas
> >>>
> >>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> >>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
> >>>>
> >>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
> >>>>
> >>>> Andy
> >>>>
> >>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
> >>>>
> >>>>> Hi Chris,
> >>>>>
> >>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
> >>>>>
> >>>>> Andy
> >>>>>
> >>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> Found another potential error case, this time in beta2 (fresh pull
> >>>>>> from git last evening).  For more info, please see
> >>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> >>>>>> test passes simply because the pair object is not null, but fails when
> >>>>>> trying to extract any information from the pair itself (toString(),
> >>>>>> getIdenticals(), etc). The substitution matrix file is from
> >>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> >>>>>> pairwise alignments, which do not all fail, but most do with this same
> >>>>>> error.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Chris
> >>>>>>
> >>>>>> --
> >>>>>> PhD Candidate, Integrative Life Sciences
> >>>>>> Virginia Commonwealth University
> >>>>>> Richmond, VA
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>> --
> >>>> Andrew Yates                   Ensembl Genomes Engineer
> >>>> EMBL-EBI                       Tel: +44-(0)1223-492538
> >>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> >>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> -----------------------------------------------------------------------
> >>> Dr. Andreas Prlic
> >>> Senior Scientist, RCSB PDB Protein Data Bank
> >>> University of California, San Diego
> >>> (+1) 858.246.0526
> >>> -----------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>
> >>
> >>
> >> --
> >> PhD Candidate, Integrative Life Sciences
> >> Virginia Commonwealth University
> >> Richmond, VA
> >>
> >
> >
> >
> > --
> > PhD Candidate, Integrative Life Sciences
> > Virginia Commonwealth University
> > Richmond, VA
> 
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From jayunit100 at gmail.com  Sun Dec 12 17:42:09 2010
From: jayunit100 at gmail.com (Jay Vyas)
Date: Sun, 12 Dec 2010 17:42:09 -0500
Subject: [Biojava-l] predicting atoms from backbone
Message-ID: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>

Hi guys :

Im trying to add C, O , and N atoms to a protein structure, when I only have
a backbone trace..
That is, I have a series of CA atoms in a backbone of a protein structure,
and I want to generate other atom coordinates.

I know biojava can add hydrogents... Anybody have any ideas about how to add
and predict other atoms?

-- 
Jay Vyas
MMSB/UCHC

From andreas at sdsc.edu  Mon Dec 13 10:56:12 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 13 Dec 2010 07:56:12 -0800
Subject: [Biojava-l] predicting atoms from backbone
In-Reply-To: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>
References: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>
Message-ID: <AANLkTi=atfUTzSiriL995XS4KgSGer5LwHJ55ZL9FCiD@mail.gmail.com>

Hi Jay,

I guess you want to do something like that:
http://peds.oxfordjournals.org/content/5/2/147.abstract

Although all the tools for such calculations are available in BioJava,
there is currently no simple method call that allows to calculate such
a mainchain-model.

Before doing any coding, probably best to check out other software
like COOT, if it can do that...

Andreas

On Sun, Dec 12, 2010 at 2:42 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys :
>
> Im trying to add C, O , and N atoms to a protein structure, when I only have
> a backbone trace..
> That is, I have a series of CA atoms in a backbone of a protein structure,
> and I want to generate other atom coordinates.
>
> I know biojava can add hydrogents... Anybody have any ideas about how to add
> and predict other atoms?
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From wuuter at gmail.com  Wed Dec 15 21:45:42 2010
From: wuuter at gmail.com (Fico)
Date: Thu, 16 Dec 2010 10:45:42 +0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB file
Message-ID: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>

Hi, dear all:

I use biojava3 beta1 to parse the PDB files recently, my program is:

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(pdbDirPath);

            FileParsingParameters params = new FileParsingParameters();
            params.setLoadChemCompInfo(*false*);
            params.setHeaderOnly(*false*);
            params.setAlignSeqRes(*true*);
            params.setParseSecStruc(*false*);
            pdbreader.setFileParsingParameters(params);

            Structure structure = null;
            try {
                structure = pdbreader.getStructure(pdbDirPath + "\\" +
file);
            } catch (IOException e) {
                e.printStackTrace();
            }

when I execute this program, it will download something such as:

*creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*

but I do not want to lownload those stuff, How can I cancel it?
Thanks.

From marcelito_tony at hotmail.com  Wed Dec 15 22:59:11 2010
From: marcelito_tony at hotmail.com (marcelo rodriguez)
Date: Thu, 16 Dec 2010 03:59:11 +0000
Subject: [Biojava-l]  Is there  cvtree algorithm in biojava?
In-Reply-To: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
Message-ID: <BLU154-w7E5736538026F9298C9BAFA150@phx.gbl>


I am investigating cvtree algorithm biojava?
i need help
regards
marcelo 		 	   		  

From darnells at dnastar.com  Thu Dec 16 11:26:51 2010
From: darnells at dnastar.com (Steve Darnell)
Date: Thu, 16 Dec 2010 10:26:51 -0600
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
Message-ID: <A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>

The SeqRes to Atom record alignment forces the use of chemical
components to translate non-standard residues to their closest standard
counterpart for the sequence alignment.  I have to disable
setLoadChemCompInfo and setAlignSeqRes when I don't want to download
chemical component files from RCSB when parsing a PDB file.

Regards,
Steve

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
Sent: Wednesday, December 15, 2010 8:46 PM
To: Biojava-l at lists.open-bio.org
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
file

Hi, dear all:

I use biojava3 beta1 to parse the PDB files recently, my program is:

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(pdbDirPath);

            FileParsingParameters params = new FileParsingParameters();
            params.setLoadChemCompInfo(*false*);
            params.setHeaderOnly(*false*);
            params.setAlignSeqRes(*true*);
            params.setParseSecStruc(*false*);
            pdbreader.setFileParsingParameters(params);

            Structure structure = null;
            try {
                structure = pdbreader.getStructure(pdbDirPath + "\\" +
file);
            } catch (IOException e) {
                e.printStackTrace();
            }

when I execute this program, it will download something such as:

*creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*

but I do not want to lownload those stuff, How can I cancel it?
Thanks.
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


From andreas at sdsc.edu  Fri Dec 17 10:24:16 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 17 Dec 2010 07:24:16 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
Message-ID: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>

ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
set to true and it will not download chemical components if
loadChemComp is false. The drawback is that the data representation
will not be as precise.

Andreas



On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com> wrote:
> The SeqRes to Atom record alignment forces the use of chemical
> components to translate non-standard residues to their closest standard
> counterpart for the sequence alignment. ?I have to disable
> setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> chemical component files from RCSB when parsing a PDB file.
>
> Regards,
> Steve
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> Sent: Wednesday, December 15, 2010 8:46 PM
> To: Biojava-l at lists.open-bio.org
> Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> file
>
> Hi, dear all:
>
> I use biojava3 beta1 to parse the PDB files recently, my program is:
>
> ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
> ? ? ? ? ? ?pdbreader.setAutoFetch(false);
> ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>
> ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
> ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
> ? ? ? ? ? ?params.setHeaderOnly(*false*);
> ? ? ? ? ? ?params.setAlignSeqRes(*true*);
> ? ? ? ? ? ?params.setParseSecStruc(*false*);
> ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>
> ? ? ? ? ? ?Structure structure = null;
> ? ? ? ? ? ?try {
> ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
> file);
> ? ? ? ? ? ?} catch (IOException e) {
> ? ? ? ? ? ? ? ?e.printStackTrace();
> ? ? ? ? ? ?}
>
> when I execute this program, it will download something such as:
>
> *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>
> but I do not want to lownload those stuff, How can I cancel it?
> Thanks.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From dasarnow at gmail.com  Sat Dec 18 22:36:28 2010
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Sat, 18 Dec 2010 19:36:28 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
Message-ID: <AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>

Prior to this, did setting loadChemComp true add processing overhead if
setAlignSeqRes is also true?  I.e. what's the difference between AlignSeqRes
with and without loadChemComp?
Just want to know what the right flags are when one wants accurate SEQRES
<---> ATOM alignments but isn't otherwise using the components info...

On a related note, I ended up writing a class that loaded and discarded
Structure objects for my PDBs, to trigger all the downloads before my big
processing jobs.  Though I guess the right (non-lazy) thing to do is parse
out the combined components library to the individual files.

-da

On Fri, Dec 17, 2010 at 07:24, Andreas Prlic <andreas at sdsc.edu> wrote:

> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
> set to true and it will not download chemical components if
> loadChemComp is false. The drawback is that the data representation
> will not be as precise.
>
> Andreas
>
>
>
> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > The SeqRes to Atom record alignment forces the use of chemical
> > components to translate non-standard residues to their closest standard
> > counterpart for the sequence alignment.  I have to disable
> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> > chemical component files from RCSB when parsing a PDB file.
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org
> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> > Sent: Wednesday, December 15, 2010 8:46 PM
> > To: Biojava-l at lists.open-bio.org
> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> > file
> >
> > Hi, dear all:
> >
> > I use biojava3 beta1 to parse the PDB files recently, my program is:
> >
> >            PDBFileReader pdbreader = new PDBFileReader();
> >            pdbreader.setAutoFetch(false);
> >            pdbreader.setPath(pdbDirPath);
> >
> >            FileParsingParameters params = new FileParsingParameters();
> >            params.setLoadChemCompInfo(*false*);
> >            params.setHeaderOnly(*false*);
> >            params.setAlignSeqRes(*true*);
> >            params.setParseSecStruc(*false*);
> >            pdbreader.setFileParsingParameters(params);
> >
> >            Structure structure = null;
> >            try {
> >                structure = pdbreader.getStructure(pdbDirPath + "\\" +
> > file);
> >            } catch (IOException e) {
> >                e.printStackTrace();
> >            }
> >
> > when I execute this program, it will download something such as:
> >
> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
> >
> > but I do not want to lownload those stuff, How can I cancel it?
> > Thanks.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From dasarnow at gmail.com  Sat Dec 18 22:47:27 2010
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Sat, 18 Dec 2010 19:47:27 -0800
Subject: [Biojava-l] Thread safety of the AtomCache
Message-ID: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>

Is AtomCache expected to be thread-safe?  It would be nice to have multiple
threads work off the same AtomCache, when those threads might each ask for
some of the same PDB IDs.

Best,

-da

From andreas at sdsc.edu  Sun Dec 19 03:19:40 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 00:19:40 -0800
Subject: [Biojava-l] Thread safety of the AtomCache
In-Reply-To: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>
References: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>
Message-ID: <AANLkTimmOrOr=aTppWiBKNawQOGL1by_Lo518wEwnQ_2@mail.gmail.com>

Hi Daniel,

Yes, the AtomCache is thread-safe. Caching across multiple threads was
one of the ideas behind this class...

Andreas


On Sat, Dec 18, 2010 at 7:47 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Is AtomCache expected to be thread-safe? ?It would be nice to have multiple
> threads work off the same AtomCache, when those threads might each ask for
> some of the same PDB IDs.
>
> Best,
>
> -da
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From andreas at sdsc.edu  Sun Dec 19 03:38:08 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 00:38:08 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
	<AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>
Message-ID: <AANLkTim+K8S1XQCNevLiWkmGEwA4q8ZnW8QYi_K658Xh@mail.gmail.com>

Hi Daniel,

The chemical components provide the chemically correct definition of
the various groups. There are quite a few chemically modified amino
acids in PDB files which can be represented as amino acids, rather
than Hetatom groups, based on these definitions. This has an impact on
the sequence alignment that is done during the alignSeqRes process.
Without the correct representations, those groups would be flagged as
"X", or might be missing. Will set up a wiki page which explains all
the parsing options in detail.

About your 2nd comment. There is now a new ChemCompProvider interface.
Perhaps there should be a new implementation of this, which is
downloading the file that contains all chemcomps bundled and provide
the data from there...

Andreas





On Sat, Dec 18, 2010 at 7:36 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Prior to this, did setting loadChemComp true add processing overhead if
> setAlignSeqRes is also true? ?I.e. what's the difference between AlignSeqRes
> with and without loadChemComp?
> Just want to know what the right flags are when one wants accurate SEQRES
> <---> ATOM alignments but isn't otherwise using the components info...
> On a related note, I ended up writing a class that loaded and discarded
> Structure objects for my PDBs, to trigger all the downloads before my big
> processing jobs. ?Though I guess the right (non-lazy) thing to do is parse
> out the combined components library to the individual files.
> -da
>
> On Fri, Dec 17, 2010 at 07:24, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
>> set to true and it will not download chemical components if
>> loadChemComp is false. The drawback is that the data representation
>> will not be as precise.
>>
>> Andreas
>>
>>
>>
>> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>> > The SeqRes to Atom record alignment forces the use of chemical
>> > components to translate non-standard residues to their closest standard
>> > counterpart for the sequence alignment. ?I have to disable
>> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
>> > chemical component files from RCSB when parsing a PDB file.
>> >
>> > Regards,
>> > Steve
>> >
>> > -----Original Message-----
>> > From: biojava-l-bounces at lists.open-bio.org
>> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
>> > Sent: Wednesday, December 15, 2010 8:46 PM
>> > To: Biojava-l at lists.open-bio.org
>> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
>> > file
>> >
>> > Hi, dear all:
>> >
>> > I use biojava3 beta1 to parse the PDB files recently, my program is:
>> >
>> > ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
>> > ? ? ? ? ? ?pdbreader.setAutoFetch(false);
>> > ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>> >
>> > ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
>> > ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
>> > ? ? ? ? ? ?params.setHeaderOnly(*false*);
>> > ? ? ? ? ? ?params.setAlignSeqRes(*true*);
>> > ? ? ? ? ? ?params.setParseSecStruc(*false*);
>> > ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>> >
>> > ? ? ? ? ? ?Structure structure = null;
>> > ? ? ? ? ? ?try {
>> > ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
>> > file);
>> > ? ? ? ? ? ?} catch (IOException e) {
>> > ? ? ? ? ? ? ? ?e.printStackTrace();
>> > ? ? ? ? ? ?}
>> >
>> > when I execute this program, it will download something such as:
>> >
>> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
>> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
>> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>> >
>> > but I do not want to lownload those stuff, How can I cancel it?
>> > Thanks.
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
>>
>>
>> --


From andreas at sdsc.edu  Sun Dec 19 09:29:13 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 06:29:13 -0800
Subject: [Biojava-l] biojava3.0-beta4
Message-ID: <AANLkTikN0dN+1jePh5+QJhWTixPxxZGq3wRT0cA+xy74@mail.gmail.com>

The fourth beta version for BioJava 3.0  has been released in our
Maven repository http://biojava.org/download/maven/

New things:

- tons of javadoc improvements
- a patch in the protmod module
- bug fix regarding automated download of chemcomp files in the structure module

A new set of javadoc files is available from:
http://www.biojava.org/docs/api_latest/

Andreas

From wuuter at gmail.com  Mon Dec 20 00:31:24 2010
From: wuuter at gmail.com (Fico)
Date: Mon, 20 Dec 2010 13:31:24 +0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
Message-ID: <AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>

now the question of ChemComp download is OK, but I found a new question when
I test bioJava3-Beta4, my program fragment:

        FileParsingParameters params = new FileParsingParameters();
        params.setLoadChemCompInfo(false);
        params.setHeaderOnly(false);
        // params.setParseCAOnly(true);
        params.setAlignSeqRes(true);
        params.setParseSecStruc(false);

        // loop file
        for (String file : getPdbFiles()) {

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(getPdbDir());

            pdbreader.setFileParsingParameters(params);

            // pdbreader.setLoadChemCompInfo(true);
            Structure struc = null;
            try {
                struc = pdbreader.getStructure(getPdbDir() + "\\" + file);
            } catch (IOException e) {
                e.printStackTrace();
            }

            String pdbid = struc.getPDBCode();

            for (int i = 0; i < struc.nrModels(); i++) {

                // loop chain
                for (Chain ch : struc.getModel(i)) {
                    System.out.println(pdbid + ">>>" + ch.getChainID() +
">>>"
                            + ch.getAtomSequence());
                    System.out.println(pdbid + ">>>" + ch.getChainID() +
">>>"
                            + ch.getSeqResSequence());
                    // Test the getAtomGroups() and getSeqResGroups() method
                    // List<Group> group = ch.getAtomGroups();
                    List<Group> group = ch.getSeqResGroups();
                    for (Group gp : group) {
                        System.out.println(gp.getResidueNumber() + ":"
                                + gp.getPDBName());
                    }
                }
            }
        }

my test PDB file is 1O1G.pdb, there are 45 modified residues in chain A,
when I use .getAtomGroups() I can get all residues' atom information, such
as ResidueNumber and PDBName:
797:PHE
798:LEU
799:MET
800:ARG
801:VAL
802:GLU
......
840:PRO
841:LEU
842:LEU
843:LYS

but use .getSeqResGroups(), the last 45 residues will miss some information,
such as ResidueNumber and atom coordinate, the output of the program is:
797:PHE
798:LEU
null:MET
null:ARG
null:VAL
null:GLU
......
null:PRO
null:LEU
null:LEU
null:LYS

In biojava3-Beta1 the two method produce same result just as
.getAtomGroups() in Beta4. so is it a bug?

P.S.
    Could we add new method to get all amino acid sequence with modifed
residues directly? now both getAtomSequence() and getSeqResSequence() can't
do this, if I want get the amino acid sequence with modifed residues, I had
to use .getAtomGroups() or .getSeqResGroups() first and then loop each
residue to get one letter amino acid sequence.





2010/12/17 Andreas Prlic <andreas at sdsc.edu>

> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
> set to true and it will not download chemical components if
> loadChemComp is false. The drawback is that the data representation
> will not be as precise.
>
> Andreas
>
>
>
> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > The SeqRes to Atom record alignment forces the use of chemical
> > components to translate non-standard residues to their closest standard
> > counterpart for the sequence alignment.  I have to disable
> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> > chemical component files from RCSB when parsing a PDB file.
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org
> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> > Sent: Wednesday, December 15, 2010 8:46 PM
> > To: Biojava-l at lists.open-bio.org
> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> > file
> >
> > Hi, dear all:
> >
> > I use biojava3 beta1 to parse the PDB files recently, my program is:
> >
> >            PDBFileReader pdbreader = new PDBFileReader();
> >            pdbreader.setAutoFetch(false);
> >            pdbreader.setPath(pdbDirPath);
> >
> >            FileParsingParameters params = new FileParsingParameters();
> >            params.setLoadChemCompInfo(*false*);
> >            params.setHeaderOnly(*false*);
> >            params.setAlignSeqRes(*true*);
> >            params.setParseSecStruc(*false*);
> >            pdbreader.setFileParsingParameters(params);
> >
> >            Structure structure = null;
> >            try {
> >                structure = pdbreader.getStructure(pdbDirPath + "\\" +
> > file);
> >            } catch (IOException e) {
> >                e.printStackTrace();
> >            }
> >
> > when I execute this program, it will download something such as:
> >
> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
> >
> > but I do not want to lownload those stuff, How can I cancel it?
> > Thanks.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>

From andreas at sdsc.edu  Tue Dec 21 18:55:39 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 21 Dec 2010 15:55:39 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
	<AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>
Message-ID: <AANLkTin0sazkTCa6u3WVagN+xVmSxWY_ViTt0wKOkuak@mail.gmail.com>

Hi Fico,

- you are right, this was a bug (some index was off). I committed a
patch for this to SVN.
- I also added new behaviour for downloading chem comp files: The
default chem comp provider will fetch the components.cif.gz file and
extract all definitions into small files, which will be used from then
on.
- not sure about your last question. That is kind of already possible
I believe. You can use the getChemComp method to get the exact
definition for a group.

Andreas

On Sun, Dec 19, 2010 at 9:31 PM, Fico <wuuter at gmail.com> wrote:
> now the question of ChemComp download is OK, but I found a new question when
> I test bioJava3-Beta4, my program fragment:
>
> ??????? FileParsingParameters params = new FileParsingParameters();
> ??? ??? params.setLoadChemCompInfo(false);
> ??? ??? params.setHeaderOnly(false);
> ??? ??? // params.setParseCAOnly(true);
> ??? ??? params.setAlignSeqRes(true);
> ??? ??? params.setParseSecStruc(false);
>
> ??? ??? // loop file
> ??? ??? for (String file : getPdbFiles()) {
>
> ??? ??? ??? PDBFileReader pdbreader = new PDBFileReader();
> ??? ??? ??? pdbreader.setAutoFetch(false);
> ??? ??? ??? pdbreader.setPath(getPdbDir());
>
> ??? ??? ??? pdbreader.setFileParsingParameters(params);
>
> ??? ??? ??? // pdbreader.setLoadChemCompInfo(true);
> ??? ??? ??? Structure struc = null;
> ??? ??? ??? try {
> ??? ??? ??? ??? struc = pdbreader.getStructure(getPdbDir() + "\\" + file);
> ??? ??? ??? } catch (IOException e) {
> ??? ??? ??? ??? e.printStackTrace();
> ??? ??? ??? }
>
> ??? ??? ??? String pdbid = struc.getPDBCode();
>
> ??? ??? ??? for (int i = 0; i < struc.nrModels(); i++) {
>
> ??? ??? ??? ??? // loop chain
> ??? ??? ??? ??? for (Chain ch : struc.getModel(i)) {
> ??? ??? ??? ??? ??? System.out.println(pdbid + ">>>" + ch.getChainID() +
> ">>>"
> ??? ??? ??? ??? ??? ??? ??? + ch.getAtomSequence());
> ??? ??? ??? ??? ??? System.out.println(pdbid + ">>>" + ch.getChainID() +
> ">>>"
> ??? ??? ??? ??? ??? ??? ??? + ch.getSeqResSequence());
> ??? ??? ??? ??? ??? // Test the getAtomGroups() and getSeqResGroups() method
> ??????????????????? // List<Group> group = ch.getAtomGroups();
> ??? ??? ??? ??? ??? List<Group> group = ch.getSeqResGroups();
> ??? ??? ??? ??? ??? for (Group gp : group) {
> ??? ??? ??? ??? ??? ??? System.out.println(gp.getResidueNumber() + ":"
> ??? ??? ??? ??? ??? ??? ??? ??? + gp.getPDBName());
> ??? ??? ??? ??? ??? }
> ??? ??? ??? ??? }
> ??? ??? ??? }
> ??? ??? }
>
> my test PDB file is 1O1G.pdb, there are 45 modified residues in chain A,
> when I use .getAtomGroups() I can get all residues' atom information, such
> as ResidueNumber and PDBName:
> 797:PHE
> 798:LEU
> 799:MET
> 800:ARG
> 801:VAL
> 802:GLU
> ......
> 840:PRO
> 841:LEU
> 842:LEU
> 843:LYS
>
> but use .getSeqResGroups(), the last 45 residues will miss some information,
> such as ResidueNumber and atom coordinate, the output of the program is:
> 797:PHE
> 798:LEU
> null:MET
> null:ARG
> null:VAL
> null:GLU
> ......
> null:PRO
> null:LEU
> null:LEU
> null:LYS
>
> In biojava3-Beta1 the two method produce same result just as
> .getAtomGroups() in Beta4. so is it a bug?
>
> P.S.
> ??? Could we add new method to get all amino acid sequence with modifed
> residues directly? now both getAtomSequence() and getSeqResSequence() can't
> do this, if I want get the amino acid sequence with modifed residues, I had
> to use .getAtomGroups() or .getSeqResGroups() first and then loop each
> residue to get one letter amino acid sequence.
>
>
>
>
>
> 2010/12/17 Andreas Prlic <andreas at sdsc.edu>
>>
>> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
>> set to true and it will not download chemical components if
>> loadChemComp is false. The drawback is that the data representation
>> will not be as precise.
>>
>> Andreas
>>
>>
>>
>> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>> > The SeqRes to Atom record alignment forces the use of chemical
>> > components to translate non-standard residues to their closest standard
>> > counterpart for the sequence alignment. ?I have to disable
>> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
>> > chemical component files from RCSB when parsing a PDB file.
>> >
>> > Regards,
>> > Steve
>> >
>> > -----Original Message-----
>> > From: biojava-l-bounces at lists.open-bio.org
>> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
>> > Sent: Wednesday, December 15, 2010 8:46 PM
>> > To: Biojava-l at lists.open-bio.org
>> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
>> > file
>> >
>> > Hi, dear all:
>> >
>> > I use biojava3 beta1 to parse the PDB files recently, my program is:
>> >
>> > ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
>> > ? ? ? ? ? ?pdbreader.setAutoFetch(false);
>> > ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>> >
>> > ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
>> > ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
>> > ? ? ? ? ? ?params.setHeaderOnly(*false*);
>> > ? ? ? ? ? ?params.setAlignSeqRes(*true*);
>> > ? ? ? ? ? ?params.setParseSecStruc(*false*);
>> > ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>> >
>> > ? ? ? ? ? ?Structure structure = null;
>> > ? ? ? ? ? ?try {
>> > ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
>> > file);
>> > ? ? ? ? ? ?} catch (IOException e) {
>> > ? ? ? ? ? ? ? ?e.printStackTrace();
>> > ? ? ? ? ? ?}
>> >
>> > when I execute this program, it will download something such as:
>> >
>> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
>> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
>> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>> >
>> > but I do not want to lownload those stuff, How can I cancel it?
>> > Thanks.
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>
>



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


From andreas at sdsc.edu  Tue Dec 28 16:22:57 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 28 Dec 2010 13:22:57 -0800
Subject: [Biojava-l] BioJava 3.0 released
Message-ID: <AANLkTimQ-OC7upHhZe11EPP8F+=A-bS1q6uLvfYYXX0O@mail.gmail.com>

BioJava 3.0 has been released and is available from
http://biojava.org/wiki/BioJava:Download .

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

Over the last year BioJava has undergone a major re-write. It has been
modularized into small, re-usable components and a number of new
features have been added. The new approach, modeled after the apache
commons, minimizes dependencies and allows for easier contribution of
new components.

At the present the main modules are:

biojava3-core: The core module offers the basic tools required for
working with biological sequences of various types (DNA, RNA,
protein). Besides file parsers for popular file formats it provides
efficient data structures for sequence manipulation and serialization.

biojava3-genome: The genome module provides support for reading and
writing of gtf, gff2, gff3 file formats

biojava3-alignment: This module provides implementations for pairwise
and multiple sequence alignments (MSA). The implementation for MSA
provides a flexible and multi-threaded framework that works in linear
space and that, as an option, allows the users to define anchors that
are used in the build up of the multiple alignment.

biojava3-structure: The 3D protein structure module provides parsers
and a data model for working PDB and mmCif files. New features in this
release are the implementation of the CE and FATCAT structural
alignment algorithms and the support of chemical component definition
files, for a chemically and biologically correct representation of
modified residues and ligands.

biojava3-protmod: The protein modification module can detect more than
200 protein modifications and crosslinks in 3D protein structures. It
comes with an XML file and Java data structures to store information
about different types of protein modifications collected from PDB,
RESID, and PSI-MOD.

Not every feature of the BioJava 1.X code base was migrated over to
BioJava 3.0. A modularized version of the 1.X sources is available as
a new "biojava-legacy" project.

Thanks to all contributors for making this release possible.

Happy Biojava-ing,

Andreas

From science.translator at gmail.com  Tue Dec 28 18:24:49 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Tue, 28 Dec 2010 15:24:49 -0800
Subject: [Biojava-l] QBlast in BioJava3
Message-ID: <AANLkTim2-yODH2tZ2=eL74nZ4=kro_=E48zqOXgL-PDx@mail.gmail.com>

Hello BioJava community,

I'm a biologist/Java newbie, I'm trying to write a program that automates
BLAST requests using very short peptide sequences. I downloaded the new
BioJava 3 jars, and attempted to write the program, but I quickly ran into a
problem.

Here's the code I have so far:
package com.multiBLAST.model;

import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
import org.biojava3.core.sequence.*;

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastAlignmentProperties alignmentProperties;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";

        try {
            blaster = new NCBIQBlastService();
            alignmentProperties = new NCBIQBlastAlignmentProperties();
            alignmentProperties.setBlastProgram("blastp");
            alignmentProperties.setBlastDatabase("nr");

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

        }

    }

}

Eclipse is telling me that last line of code causes a compiler error: "The
type org.biojavax.bio.seq.RichSequence cannot be resolved. It is indirectly
referenced from required .class files"

I'm not sure exactly what this means, it seems to me that perhaps when this
method was updated from biojavax to biojava3, it somewhere still references
the RichSequence from biojavax. I can't find a RichSequence class anywhere
in the new BioJava3 API, and I can't find the biojavax jars on the legacy
download page, so I'm not sure how to proceed.

If someone could please provide some assistance, that would be great.

Thank you very much,

Matthew Busse, PhD

From sylvain.foisy at diploide.net  Wed Dec 29 12:22:52 2010
From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.)
Date: Wed, 29 Dec 2010 12:22:52 -0500
Subject: [Biojava-l] QBlast in BioJava3
Message-ID: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>

Hi,

I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.

Best regards

Sylvain




From andreas at sdsc.edu  Wed Dec 29 12:58:43 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 29 Dec 2010 09:58:43 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
Message-ID: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>

Thanks Sylvain,

Matthew, a workaround until we have a fix for this is to add the
http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
from the biojava-legacy project to your classpath. This should allow
your example to work...

Andreas


On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
<sylvain.foisy at diploide.net> wrote:
> Hi,
>
> I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.
>
> Best regards
>
> Sylvain
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From science.translator at gmail.com  Wed Dec 29 14:52:13 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Wed, 29 Dec 2010 11:52:13 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
Message-ID: <AANLkTin6AYfZ56TzqfYHiwx67i7MFu0R7KsU45naKves@mail.gmail.com>

Thank you everyone for your prompt responses. Adding the core-1.8.jar to the
build path took care of the problem.

Cheers!
Matthew

On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Sylvain,
>
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
>
> Andreas
>
>
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the
> problem that you found ASAP to remove the dependency on the old BJ
> architecture about representing Sequence objects. I'll work on this early
> next week, as soon as I'll have finish with my grading... I am more of a
> teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>

From science.translator at gmail.com  Wed Dec 29 16:01:33 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Wed, 29 Dec 2010 13:01:33 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
Message-ID: <AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>

Hello Sylvain, et al.,

I think I may have found another similar issue.

Here's my program:

package com.multiBLAST.model;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Set;

import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputFormat;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastOutputProperties outputProperties;
        InputStream is;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";
        String rid = new String();

        try {
            blaster = new NCBIQBlastService();
            NCBIQBlastAlignmentProperties alignmentProperties = new
NCBIQBlastAlignmentProperties();
            alignmentProperties.setBlastProgram("blastp");
            alignmentProperties.setBlastDatabase("nr");

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

            System.out.println("Trying to get BLAST results for RID " +
rid);

            boolean wasBlasted = false;

            while (!wasBlasted) {
                wasBlasted = blaster.isReady(rid,
System.currentTimeMillis());
            }

            outputProperties = new NCBIQBlastOutputProperties();
            outputProperties.setOutputFormat(NCBIQBlastOutputFormat.TEXT);

outputProperties.setAlignmentOutputFormat(NCBIQBlastOutputFormat.PAIRWISE);
            outputProperties.setDescriptionNumber(10);
            outputProperties.setAlignmentNumber(10);

            //to show that output options were followed

            Set<String> test = outputProperties.getOutputOptions();

            for(String str : test) {
                System.out.println(str);
            }

            is = blaster.getAlignmentResults(request, outputProperties);

            BufferedReader br = new BufferedReader(new
InputStreamReader(is));

            String line = null;

            while ((line = br.readLine()) != null)    {
                System.out.println(line);
            }

        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}

When I run it, it throws an exception:
java.lang.Exception: The key named PROGRAM is not set in this
RemoteQBlastOutputProperties object
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties.getAlignmentOption(NCBIQBlastAlignmentProperties.java:173)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendActualAlignementRequest(NCBIQBlastService.java:132)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendAlignmentRequest(NCBIQBlastService.java:210)
    at com.multiBLAST.model.BLASTExample.main(BLASTExample.java:30)

Because RemoteQBlastOutputProperties is the terminology used in the pre-BJ3
APIs, I'm guessing this is another conversion problem? Or am I missing
something else?

Many thanks for all your help.

Best,
Matthew

On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Sylvain,
>
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
>
> Andreas
>
>
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the
> problem that you found ASAP to remove the dependency on the old BJ
> architecture about representing Sequence objects. I'll work on this early
> next week, as soon as I'll have finish with my grading... I am more of a
> teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>

From sylvain.foisy at diploide.net  Wed Dec 29 16:15:57 2010
From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.)
Date: Wed, 29 Dec 2010 16:15:57 -0500
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
	<AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>
Message-ID: <DA1E2D38-A8E4-4971-9056-863E6347E3CC@diploide.net>

Hi Matthew,

Let me dive in this code again and I'll find the bug. Any rush on this? I am planning to do this early next week/year ;-) You are actually the first reported user of this module beside me! I mostly tested it with nucleotide sequences on the old architecture. Not much work done wince moving to the new code base...

Back to you ASAP

Best regards

Sylvain

On 2010-12-29, at 4:01 PM, Matthew Busse wrote:

> Hello Sylvain, et al., 
> 
> I think I may have found another similar issue. 
> 
> Here's my program:
> 
> package com.multiBLAST.model;
> 
> import java.io.BufferedReader;
> import java.io.InputStream;
> import java.io.InputStreamReader;
> import java.util.Set;
> 
> import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputFormat;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
> 
> public class BLASTExample {
>     
>     public static void main(String [] args) {
>         
>         NCBIQBlastService blaster;
>         NCBIQBlastOutputProperties outputProperties;
>         InputStream is;
>         String request = "";
>         final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";
>         String rid = new String();
>         
>         try {
>             blaster = new NCBIQBlastService();
>             NCBIQBlastAlignmentProperties alignmentProperties = new NCBIQBlastAlignmentProperties();
>             alignmentProperties.setBlastProgram("blastp");
>             alignmentProperties.setBlastDatabase("nr");
>             
>             request = blaster.sendAlignmentRequest(TESTSEQUENCE, alignmentProperties);
>             
>             System.out.println("Trying to get BLAST results for RID " + rid);
>             
>             boolean wasBlasted = false;
>             
>             while (!wasBlasted) {
>                 wasBlasted = blaster.isReady(rid, System.currentTimeMillis());
>             }
>             
>             outputProperties = new NCBIQBlastOutputProperties();
>             outputProperties.setOutputFormat(NCBIQBlastOutputFormat.TEXT);
>             outputProperties.setAlignmentOutputFormat(NCBIQBlastOutputFormat.PAIRWISE);
>             outputProperties.setDescriptionNumber(10);
>             outputProperties.setAlignmentNumber(10);
>             
>             //to show that output options were followed
>             
>             Set<String> test = outputProperties.getOutputOptions();
>             
>             for(String str : test) {
>                 System.out.println(str);
>             }
>             
>             is = blaster.getAlignmentResults(request, outputProperties);
>             
>             BufferedReader br = new BufferedReader(new InputStreamReader(is));
>             
>             String line = null;
>             
>             while ((line = br.readLine()) != null)    {
>                 System.out.println(line);
>             }
>             
>         } catch (Exception ex) {
>             ex.printStackTrace();
>         } 
>     }
> }
> 
> When I run it, it throws an exception:
> java.lang.Exception: The key named PROGRAM is not set in this RemoteQBlastOutputProperties object
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties.getAlignmentOption(NCBIQBlastAlignmentProperties.java:173)
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendActualAlignementRequest(NCBIQBlastService.java:132)
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendAlignmentRequest(NCBIQBlastService.java:210)
>     at com.multiBLAST.model.BLASTExample.main(BLASTExample.java:30)
> 
> Because RemoteQBlastOutputProperties is the terminology used in the pre-BJ3 APIs, I'm guessing this is another conversion problem? Or am I missing something else?
> 
> Many thanks for all your help.
> 
> Best,
> Matthew
> 
> On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Thanks Sylvain,
> 
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
> 
> Andreas
> 
> 
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> 



From andreas.prlic at gmail.com  Thu Dec 30 13:27:09 2010
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 30 Dec 2010 10:27:09 -0800
Subject: [Biojava-l] BioJava3 - Structure - Bug
In-Reply-To: <AANLkTi=Em4QBXkfuKf=ot-YfEPA5kCKWuG9ACuzd-zLi@mail.gmail.com>
References: <AANLkTi=Em4QBXkfuKf=ot-YfEPA5kCKWuG9ACuzd-zLi@mail.gmail.com>
Message-ID: <AANLkTi=6-if=E-yprYEcwhFkAD0EQsD7N4Zf+8Mnci04@mail.gmail.com>

Hi Jose,

Thanks for spotting this. I disabled the get/setPDBline a while ago
since it essentially doubles memory usage. It would be better to have
an Atom.toPDB or a FileConvert.toPDB(Atom) class that builds up the
String output dynamically.. I will flag the method calls as
deprecated.

Andreas


2010/12/30 Jos? Augusto Salim <jose.asalim at gmail.com>:
> Hi Andreas,
>
> I have used BioJava3 and I find some kind of bug on it. When I try to use
> the function getPBDline from Atom interface it return a blank string, it
> because in PDBFileParser when a new AtomImpl is created no pdbLine is set.
> So, I change the code for it works, just but the line:
>
> atom.setPDBline(line.trim());
>
> in PDBFileParser.java
>
> I'm sending the file for you.
>
> thanks for BioJava3 it has been very useful for my work.
>
> best regardless,
>
> ===
> Jos? Augusto Salim
> Computer Engineer
> -------------------------------
> http://www.thezeitgeistmovement.com
> http://www.zeitgeistmovie.com
>
>


From philipp.comans at mytum.de  Fri Dec 31 12:07:46 2010
From: philipp.comans at mytum.de (Philipp Comans)
Date: Fri, 31 Dec 2010 18:07:46 +0100
Subject: [Biojava-l] Error parsing GFF3 file
Message-ID: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>

Hello everyone,

I am trying to parse the file available here: ftp://ftp.jgi-psf.org/pub/JGI_data/Amphimedon_queenslandica/annotation/Aqu1.gff3.gz
with the following commands:

import java.util.Iterator;

import org.biojava3.genome.parsers.gff.FeatureI;
import org.biojava3.genome.parsers.gff.FeatureList;
import org.biojava3.genome.parsers.gff.GFF3Reader;

public class GFFReader3 {

	public static void main(String[] args) throws Exception {
		
		FeatureList features = (FeatureList) GFF3Reader.read("/Users/philipp/Dropbox/IDP/JGI_data/annotation/Smiles.gff3");
		Iterator<FeatureI> featureIterator = features.iterator();
		
		FeatureI currentFeature = null;
		
		while (featureIterator.hasNext()) {
			currentFeature = featureIterator.next();
			System.out.println(currentFeature);
		}

	}

}

The error I get is:
31.12.2010 18:05:10 org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading /Users/philipp/Dropbox/IDP/JGI_data/annotation/Aqu1.gff3
Exception in thread "main" java.lang.IllegalArgumentException: Improper location parameters: (-1864985,746)
	at org.biojava3.genome.parsers.gff.Location.<init>(Location.java:75)
	at org.biojava3.genome.parsers.gff.Location.union(Location.java:258)
	at org.biojava3.genome.parsers.gff.FeatureList.add(FeatureList.java:49)
	at org.biojava3.genome.parsers.gff.GFF3Reader.read(GFF3Reader.java:59)
	at GFFReader3.main(GFFReader3.java:11)

I find this very strange because the file is a valid GFF document according to
http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Is this a bug or am I doing something wrong?
Thanks for your help, I wish you a happy New Year!

Philipp

From willishf at ufl.edu  Fri Dec 31 13:21:48 2010
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 31 Dec 2010 13:21:48 -0500
Subject: [Biojava-l] Error parsing GFF3 file
In-Reply-To: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>
References: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>
Message-ID: <AANLkTi=DZi1ue=8FkCGmLGW0Gs8=Pz5q6wwkckDJtp-0@mail.gmail.com>

Phillip

I think it is complaining about the negative location (-1864985,746). Is
this a circular genome? That seems to be a rather large sequence segment and
I think it is correct to complain about the negative location. We tried to
plan ahead on circular genomes and genes that cross the boundary begin/end
boundary and at the same time not have the programmer brain explode trying
to handle all the combinations that exist.  It gets really fun when you have
a negative strand.

One of the challenges of a valid gff3 file is that you can make sure
ontology is correct and the file format is correct but when you try and
bring it all together to do something with the data(turn it into a protein)
you need to check harder.

If this is a valid location can you send me the gff3 segment and the DNA
sequence that describes the features and I will see what I can do to make it
work without previous reference to head exploding. Let me know what the end
goal is on parsing gff3 file and what is missing when you try and map to a
GeneSequence/ProteinSequence.

Thanks

Scooter

On Fri, Dec 31, 2010 at 12:07 PM, Philipp Comans <philipp.comans at mytum.de>wrote:

> Hello everyone,
>
> I am trying to parse the file available here:
> ftp://ftp.jgi-psf.org/pub/JGI_data/Amphimedon_queenslandica/annotation/Aqu1.gff3.gz
> with the following commands:
>
> import java.util.Iterator;
>
> import org.biojava3.genome.parsers.gff.FeatureI;
> import org.biojava3.genome.parsers.gff.FeatureList;
> import org.biojava3.genome.parsers.gff.GFF3Reader;
>
> public class GFFReader3 {
>
>        public static void main(String[] args) throws Exception {
>
>                FeatureList features = (FeatureList)
> GFF3Reader.read("/Users/philipp/Dropbox/IDP/JGI_data/annotation/Smiles.gff3");
>                Iterator<FeatureI> featureIterator = features.iterator();
>
>                FeatureI currentFeature = null;
>
>                while (featureIterator.hasNext()) {
>                        currentFeature = featureIterator.next();
>                        System.out.println(currentFeature);
>                }
>
>        }
>
> }
>
> The error I get is:
> 31.12.2010 18:05:10 org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/philipp/Dropbox/IDP/JGI_data/annotation/Aqu1.gff3
> Exception in thread "main" java.lang.IllegalArgumentException: Improper
> location parameters: (-1864985,746)
>        at org.biojava3.genome.parsers.gff.Location.<init>(Location.java:75)
>        at org.biojava3.genome.parsers.gff.Location.union(Location.java:258)
>        at
> org.biojava3.genome.parsers.gff.FeatureList.add(FeatureList.java:49)
>        at
> org.biojava3.genome.parsers.gff.GFF3Reader.read(GFF3Reader.java:59)
>        at GFFReader3.main(GFFReader3.java:11)
>
> I find this very strange because the file is a valid GFF document according
> to
> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>
> Is this a bug or am I doing something wrong?
> Thanks for your help, I wish you a happy New Year!
>
> Philipp
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

From Michael.Rusch at STJUDE.ORG  Wed Dec  1 18:37:00 2010
From: Michael.Rusch at STJUDE.ORG (Rusch, Michael)
Date: Wed, 1 Dec 2010 12:37:00 -0600
Subject: [Biojava-l] newbie question about gff
Message-ID: <A475AF196964604CAEE109F1CA0275AB157D014772@SJMEMXMBS10.stjude.sjcrh.local>

Newbie question:

I want to read in a GFF file and process it taking full advantage of the gene model (e.g. exons belong to a transcript).  I see that I can read the GFF into an EntrySet, and then annotate a Sequence with the EntrySet, but I don't have a sequence to start off with.  I could read in sequence from a FASTA file, but since I'm not actually using sequence, and I'm dealing with human chromosomes, it seems quite wasteful to do so.  I could also just use the EntrySet, but then I can't take advantage of the gene model.  Is there a way to get a Sequence object with no sequence, just features from a GFF file?

Thanks,
Michael

________________________________
Email Disclaimer: www.stjude.org/emaildisclaimer



From darnells at dnastar.com  Fri Dec  3 23:35:21 2010
From: darnells at dnastar.com (Steve Darnell)
Date: Fri, 3 Dec 2010 17:35:21 -0600
Subject: [Biojava-l] PDBFileParser question using PDBID 470D
In-Reply-To: <AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
References: <A4009967D1886D4286A9B7931FD58610027E0C4B@FS1.dnastar.com>
	<AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
Message-ID: <A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>

Andreas,

I've been using biojava to gather sequence data from structure files for an internal project.  My intent was to test the limitations of my work (hence files similar to 470D), but came across this behavior in biojava.

It is not critical to obtain this particular mapping since it can be derived from the atom records.  However, I didn't understand why the SEQRES list would be empty and was looking for clarification.  Is it because the chain is RNA and the empty list prevents the unsupported alignment of RNA records?

Regards,
Steve

-----Original Message-----
From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: Monday, November 29, 2010 6:36 PM
To: Steve Darnell
Cc: biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] PDBFileParser question using PDBID 470D

Hi Steve,

as you already are saying, this is an "exotic" sequence, in the sense
that this is an RNA. The alignments of the SEQRES records for RNA
currently is not supported as of yet. Can you explain a bit more what
you are doing and why you need this mapping in this case?

Thanks,
Andreas

On Mon, Nov 29, 2010 at 12:51 PM, Steve Darnell <darnells at dnastar.com> wrote:
> Greetings,
>
> After parsing PDBID 470D with biojava-3.0-alpha5, Chain A returns an
> empty SEQRES sequence (Chain.getSeqResSequence) and empty SEQRES group
> list (Chain.getSeqResGroups) but the one-letter ATOM sequence is
> properly translated and the ATOM group list contains the appropriate
> number of groups (LoadChemCompInfo set to true).
>
> This is an exotic sequence, but my expectation is that the SEQRES group
> list would have members in it (and one-letter sequence translated if
> LoadChemCompInfo is true). ?Am I mistaken and the current behavior is
> the intended result?
>
> Best regards,
> Steve Darnell
>
> --
> SEQRES records exist in 470D:
>
> SEQRES ? 1 A ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>
> SEQRES ? 1 B ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>
>
>
> Sample println output (ln 1 record type, ln 2 get${TYPE}Sequence, ln 3
> get${TYPE}Groups):
>
> SEQRES
> ''
> []
>
> ATOM
> 'CGCGAAUUCGCG'
> [PDB: C43 1 trueatoms: 21, PDB: G48 2 trueatoms: 27, PDB: C43 3
> trueatoms: 24, ...]
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From andreas at sdsc.edu  Sat Dec  4 17:46:08 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sat, 4 Dec 2010 09:46:08 -0800
Subject: [Biojava-l] PDBFileParser question using PDBID 470D
In-Reply-To: <A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>
References: <A4009967D1886D4286A9B7931FD58610027E0C4B@FS1.dnastar.com>
	<AANLkTinvARNuVHwkjVn0gsuy+r00OJAv_r482JqU3OP8@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD58610027E139C@FS1.dnastar.com>
Message-ID: <AANLkTimSWNZOpLwCnPyqsR1RVgj_BvK4YT6pPTUESeZ9@mail.gmail.com>

Hi Steve,

> I've been using biojava to gather sequence data from structure files for an internal project. ?My intent was to test the limitations of my work (hence files similar to 470D), but came across this behavior in biojava.

ok

> It is not critical to obtain this particular mapping since it can be derived from the atom records. ?However, I didn't understand why the SEQRES list would be empty and was looking for clarification. ?Is it because the chain is RNA and the empty list prevents the unsupported alignment of RNA records?

When working with PDB files the list gets built up after the
alignment. Since RNA alignment is not supported by the parser, the
list can't get created...

In principle mmCif files contain the info how to join SEQRES and ATOM
groups correctly and no alignment is needed.  I will take a look
again, how this works in this case...

Andreas

> -----Original Message-----
> From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
> Sent: Monday, November 29, 2010 6:36 PM
> To: Steve Darnell
> Cc: biojava-l at lists.open-bio.org
> Subject: Re: [Biojava-l] PDBFileParser question using PDBID 470D
>
> Hi Steve,
>
> as you already are saying, this is an "exotic" sequence, in the sense
> that this is an RNA. The alignments of the SEQRES records for RNA
> currently is not supported as of yet. Can you explain a bit more what
> you are doing and why you need this mapping in this case?
>
> Thanks,
> Andreas
>
> On Mon, Nov 29, 2010 at 12:51 PM, Steve Darnell <darnells at dnastar.com> wrote:
>> Greetings,
>>
>> After parsing PDBID 470D with biojava-3.0-alpha5, Chain A returns an
>> empty SEQRES sequence (Chain.getSeqResSequence) and empty SEQRES group
>> list (Chain.getSeqResGroups) but the one-letter ATOM sequence is
>> properly translated and the ATOM group list contains the appropriate
>> number of groups (LoadChemCompInfo set to true).
>>
>> This is an exotic sequence, but my expectation is that the SEQRES group
>> list would have members in it (and one-letter sequence translated if
>> LoadChemCompInfo is true). ?Am I mistaken and the current behavior is
>> the intended result?
>>
>> Best regards,
>> Steve Darnell
>>
>> --
>> SEQRES records exist in 470D:
>>
>> SEQRES ? 1 A ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>>
>> SEQRES ? 1 B ? 12 ?C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48
>>
>>
>>
>> Sample println output (ln 1 record type, ln 2 get${TYPE}Sequence, ln 3
>> get${TYPE}Groups):
>>
>> SEQRES
>> ''
>> []
>>
>> ATOM
>> 'CGCGAAUUCGCG'
>> [PDB: C43 1 trueatoms: 21, PDB: G48 2 trueatoms: 27, PDB: C43 3
>> trueatoms: 24, ...]
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>



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



From cfriedline at vcu.edu  Mon Dec  6 12:45:38 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 07:45:38 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
Message-ID: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>

Hello,

Found another potential error case, this time in beta2 (fresh pull
from git last evening). ?For more info, please see
http://pastie.org/1351388 for test case and stack trace. ?The JUnit
test passes simply because the pair object is not null, but fails when
trying to extract any information from the pair itself (toString(),
getIdenticals(), etc). The substitution matrix file is from
ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
pairwise alignments, which do not all fail, but most do with this same
error.

Thanks,
Chris

--
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA



From ayates at ebi.ac.uk  Mon Dec  6 13:50:20 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 13:50:20 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
Message-ID: <610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>

Hi Chris,

Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful

Andy

On 6 Dec 2010, at 12:45, Chris Friedline wrote:

> Hello,
> 
> Found another potential error case, this time in beta2 (fresh pull
> from git last evening).  For more info, please see
> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> test passes simply because the pair object is not null, but fails when
> trying to extract any information from the pair itself (toString(),
> getIdenticals(), etc). The substitution matrix file is from
> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> pairwise alignments, which do not all fail, but most do with this same
> error.
> 
> Thanks,
> Chris
> 
> --
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l




From ayates at ebi.ac.uk  Mon Dec  6 15:13:49 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 15:13:49 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
Message-ID: <8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>

So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.

Does anyone on list know how the AlignedSequence code encodes gaps & the alike? 

Andy

On 6 Dec 2010, at 13:50, Andy Yates wrote:

> Hi Chris,
> 
> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
> 
> Andy
> 
> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> 
>> Hello,
>> 
>> Found another potential error case, this time in beta2 (fresh pull
>> from git last evening).  For more info, please see
>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
>> test passes simply because the pair object is not null, but fails when
>> trying to extract any information from the pair itself (toString(),
>> getIdenticals(), etc). The substitution matrix file is from
>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
>> pairwise alignments, which do not all fail, but most do with this same
>> error.
>> 
>> Thanks,
>> Chris
>> 
>> --
>> PhD Candidate, Integrative Life Sciences
>> Virginia Commonwealth University
>> Richmond, VA
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From andreas at sdsc.edu  Mon Dec  6 17:22:55 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 6 Dec 2010 09:22:55 -0800
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
Message-ID: <AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>

Hi Andy,

Check out the SimpleAlignedSequence class, for how Gaps are handled...
Does that help?

Andreas

On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>
> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>
> Andy
>
> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>
>> Hi Chris,
>>
>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>
>> Andy
>>
>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>
>>> Hello,
>>>
>>> Found another potential error case, this time in beta2 (fresh pull
>>> from git last evening). ?For more info, please see
>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>> test passes simply because the pair object is not null, but fails when
>>> trying to extract any information from the pair itself (toString(),
>>> getIdenticals(), etc). The substitution matrix file is from
>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>> pairwise alignments, which do not all fail, but most do with this same
>>> error.
>>>
>>> Thanks,
>>> Chris
>>>
>>> --
>>> PhD Candidate, Integrative Life Sciences
>>> Virginia Commonwealth University
>>> Richmond, VA
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From cfriedline at vcu.edu  Mon Dec  6 18:28:37 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 13:28:37 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
Message-ID: <AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>

That does help, thanks.  However, when calling getAsList() on the
aligned sequences and printing, this is what I see.  Something seems
wrong.  It does appear as though null is being inserted where there
should be gaps

seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
null, null, null, null, null, null]
seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]

Chris

On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Andy,
>
> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> Does that help?
>
> Andreas
>
> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>
>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>
>> Andy
>>
>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>
>>> Hi Chris,
>>>
>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>
>>> Andy
>>>
>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>
>>>> Hello,
>>>>
>>>> Found another potential error case, this time in beta2 (fresh pull
>>>> from git last evening). ?For more info, please see
>>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>>> test passes simply because the pair object is not null, but fails when
>>>> trying to extract any information from the pair itself (toString(),
>>>> getIdenticals(), etc). The substitution matrix file is from
>>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>>> pairwise alignments, which do not all fail, but most do with this same
>>>> error.
>>>>
>>>> Thanks,
>>>> Chris
>>>>
>>>> --
>>>> PhD Candidate, Integrative Life Sciences
>>>> Virginia Commonwealth University
>>>> Richmond, VA
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> --
>> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
>> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>>
>>
>>
>>
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA



From cfriedline at vcu.edu  Mon Dec  6 18:41:17 2010
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 6 Dec 2010 13:41:17 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
Message-ID: <AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>

OK, so here's a quick fix now that I know where to look.  In my local
source I added the following line to the constructor of DNACompoundSet
and recompiled.

addNucleotideCompound("-", "-");

Not sure if this is the correct place for it in terms of what the devs
want to do globally, but it gets me moving forward again.  Gap
characters are in AminoAcidCompoundSet so I'm wondering if this was
just a tiny oversight on the nucleotide front.

Thanks again for the help everyone,
Chris

On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
> That does help, thanks. ?However, when calling getAsList() on the
> aligned sequences and printing, this is what I see. ?Something seems
> wrong. ?It does appear as though null is being inserted where there
> should be gaps
>
> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> null, null, null, null, null, null]
> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
>
> Chris
>
> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> Hi Andy,
>>
>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
>> Does that help?
>>
>> Andreas
>>
>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>>
>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>>
>>> Andy
>>>
>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>>
>>>> Andy
>>>>
>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Found another potential error case, this time in beta2 (fresh pull
>>>>> from git last evening). ?For more info, please see
>>>>> http://pastie.org/1351388 for test case and stack trace. ?The JUnit
>>>>> test passes simply because the pair object is not null, but fails when
>>>>> trying to extract any information from the pair itself (toString(),
>>>>> getIdenticals(), etc). The substitution matrix file is from
>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices. ?I'm doing large numbers of
>>>>> pairwise alignments, which do not all fail, but most do with this same
>>>>> error.
>>>>>
>>>>> Thanks,
>>>>> Chris
>>>>>
>>>>> --
>>>>> PhD Candidate, Integrative Life Sciences
>>>>> Virginia Commonwealth University
>>>>> Richmond, VA
>>>>>
>>>>> _______________________________________________
>>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
>>>>
>>>> _______________________________________________
>>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>> --
>>> Andrew Yates ? ? ? ? ? ? ? ? ? Ensembl Genomes Engineer
>>> EMBL-EBI ? ? ? ? ? ? ? ? ? ? ? Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus ? Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK ? ? ? ? http://www.ensemblgenomes.org/
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
> --
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA
>



-- 
PhD Candidate, Integrative Life Sciences
Virginia Commonwealth University
Richmond, VA



From ayates at ebi.ac.uk  Mon Dec  6 19:32:55 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 6 Dec 2010 19:32:55 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
Message-ID: <91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>

I would say partially an oversight on my part & partially done on purpose (a gap is not a nucleotide after all). However I'm all in favour of being pragmatic here so lets add them in. If I get an okay from the relevant parties I'll commit the change in.

Andy

On 6 Dec 2010, at 18:41, Chris Friedline wrote:

> OK, so here's a quick fix now that I know where to look.  In my local
> source I added the following line to the constructor of DNACompoundSet
> and recompiled.
> 
> addNucleotideCompound("-", "-");
> 
> Not sure if this is the correct place for it in terms of what the devs
> want to do globally, but it gets me moving forward again.  Gap
> characters are in AminoAcidCompoundSet so I'm wondering if this was
> just a tiny oversight on the nucleotide front.
> 
> Thanks again for the help everyone,
> Chris
> 
> On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>> That does help, thanks.  However, when calling getAsList() on the
>> aligned sequences and printing, this is what I see.  Something seems
>> wrong.  It does appear as though null is being inserted where there
>> should be gaps
>> 
>> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
>> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
>> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
>> null, null, null, null, null, null]
>> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
>> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
>> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
>> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
>> 
>> Chris
>> 
>> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Hi Andy,
>>> 
>>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
>>> Does that help?
>>> 
>>> Andreas
>>> 
>>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
>>>> 
>>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
>>>> 
>>>> Andy
>>>> 
>>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
>>>> 
>>>>> Hi Chris,
>>>>> 
>>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
>>>>> 
>>>>> Andy
>>>>> 
>>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> Found another potential error case, this time in beta2 (fresh pull
>>>>>> from git last evening).  For more info, please see
>>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
>>>>>> test passes simply because the pair object is not null, but fails when
>>>>>> trying to extract any information from the pair itself (toString(),
>>>>>> getIdenticals(), etc). The substitution matrix file is from
>>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
>>>>>> pairwise alignments, which do not all fail, but most do with this same
>>>>>> error.
>>>>>> 
>>>>>> Thanks,
>>>>>> Chris
>>>>>> 
>>>>>> --
>>>>>> PhD Candidate, Integrative Life Sciences
>>>>>> Virginia Commonwealth University
>>>>>> Richmond, VA
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>>> --
>>>> Andrew Yates                   Ensembl Genomes Engineer
>>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> -----------------------------------------------------------------------
>>> Dr. Andreas Prlic
>>> Senior Scientist, RCSB PDB Protein Data Bank
>>> University of California, San Diego
>>> (+1) 858.246.0526
>>> -----------------------------------------------------------------------
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>> 
>> 
>> 
>> --
>> PhD Candidate, Integrative Life Sciences
>> Virginia Commonwealth University
>> Richmond, VA
>> 
> 
> 
> 
> -- 
> PhD Candidate, Integrative Life Sciences
> Virginia Commonwealth University
> Richmond, VA

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From willishf at ufl.edu  Mon Dec  6 20:00:18 2010
From: willishf at ufl.edu (Scooter Willis)
Date: Mon, 6 Dec 2010 15:00:18 -0500
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
	<91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
Message-ID: <AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>

It would be nice to have a cool indexing system that allowed dynamic indexes
of the data model but not worth the headache. If we are going to go big we
should use the same gap symbols that were added for protein sequences.

Scooter

On Mon, Dec 6, 2010 at 2:32 PM, Andy Yates <ayates at ebi.ac.uk> wrote:

> I would say partially an oversight on my part & partially done on purpose
> (a gap is not a nucleotide after all). However I'm all in favour of being
> pragmatic here so lets add them in. If I get an okay from the relevant
> parties I'll commit the change in.
>
> Andy
>
> On 6 Dec 2010, at 18:41, Chris Friedline wrote:
>
> > OK, so here's a quick fix now that I know where to look.  In my local
> > source I added the following line to the constructor of DNACompoundSet
> > and recompiled.
> >
> > addNucleotideCompound("-", "-");
> >
> > Not sure if this is the correct place for it in terms of what the devs
> > want to do globally, but it gets me moving forward again.  Gap
> > characters are in AminoAcidCompoundSet so I'm wondering if this was
> > just a tiny oversight on the nucleotide front.
> >
> > Thanks again for the help everyone,
> > Chris
> >
> > On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu>
> wrote:
> >> That does help, thanks.  However, when calling getAsList() on the
> >> aligned sequences and printing, this is what I see.  Something seems
> >> wrong.  It does appear as though null is being inserted where there
> >> should be gaps
> >>
> >> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> >> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> >> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> >> null, null, null, null, null, null]
> >> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> >> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> >> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> >> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
> >>
> >> Chris
> >>
> >> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu>
> wrote:
> >>> Hi Andy,
> >>>
> >>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> >>> Does that help?
> >>>
> >>> Andreas
> >>>
> >>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> >>>> So myself & Chris have discussed this off list & we believe it's
> because of a NULL compound element in the Sequence given to the
> SequenceMixin method.
> >>>>
> >>>> Does anyone on list know how the AlignedSequence code encodes gaps &
> the alike?
> >>>>
> >>>> Andy
> >>>>
> >>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
> >>>>
> >>>>> Hi Chris,
> >>>>>
> >>>>> Well that's going into my toStringBuilder() method & that particular
> line is concerned with asking a compound for its String representation. How
> often do we get nulls in our Sequences and how to deal with them. After all
> the Sequence AGTCNULLAGTC is probably more harmful then helpful
> >>>>>
> >>>>> Andy
> >>>>>
> >>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> Found another potential error case, this time in beta2 (fresh pull
> >>>>>> from git last evening).  For more info, please see
> >>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> >>>>>> test passes simply because the pair object is not null, but fails
> when
> >>>>>> trying to extract any information from the pair itself (toString(),
> >>>>>> getIdenticals(), etc). The substitution matrix file is from
> >>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> >>>>>> pairwise alignments, which do not all fail, but most do with this
> same
> >>>>>> error.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Chris
> >>>>>>
> >>>>>> --
> >>>>>> PhD Candidate, Integrative Life Sciences
> >>>>>> Virginia Commonwealth University
> >>>>>> Richmond, VA
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>> --
> >>>> Andrew Yates                   Ensembl Genomes Engineer
> >>>> EMBL-EBI                       Tel: +44-(0)1223-492538
> >>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> >>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> -----------------------------------------------------------------------
> >>> Dr. Andreas Prlic
> >>> Senior Scientist, RCSB PDB Protein Data Bank
> >>> University of California, San Diego
> >>> (+1) 858.246.0526
> >>> -----------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>
> >>
> >>
> >> --
> >> PhD Candidate, Integrative Life Sciences
> >> Virginia Commonwealth University
> >> Richmond, VA
> >>
> >
> >
> >
> > --
> > PhD Candidate, Integrative Life Sciences
> > Virginia Commonwealth University
> > Richmond, VA
>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From ayates at ebi.ac.uk  Wed Dec  8 09:06:32 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 8 Dec 2010 09:06:32 +0000
Subject: [Biojava-l] SequenceMixin Error in BioJava3 Alignment
In-Reply-To: <AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>
References: <AANLkTi=tcvXNJajQ6LXFy_JTh_P=hbZn6uA+N4B=rW_z@mail.gmail.com>
	<610B0600-699D-4249-A6F6-27EBEAEAD585@ebi.ac.uk>
	<8C833CB3-C110-496B-9285-1A3FE150ED01@ebi.ac.uk>
	<AANLkTing0UOmQG1UYvg_EkFQ64XpV8KUjmG=Oo2vBdei@mail.gmail.com>
	<AANLkTikv6dQEGrPqvsnMVj1OL8p_g7oTajkCyhNa8Cm9@mail.gmail.com>
	<AANLkTimagPcUeReu+maTZk9MNRBLab0kN79OFA9mSqkH@mail.gmail.com>
	<91FB5471-89AD-463F-AB1F-9D93F5EA46C7@ebi.ac.uk>
	<AANLkTikYh5cE+fZBRS_cJraFzHMcPJRCqx4ApeT2MpG=@mail.gmail.com>
Message-ID: <771AA57F-8AD4-4E9E-A1F0-EA44FA2518F2@ebi.ac.uk>

I've added the gap symbol to DNA & RNA compound sets. Hopefully this error will go away. If not then we'll have to look into the alignment code & get it to use the gap symbol

Andy

On 6 Dec 2010, at 20:00, Scooter Willis wrote:

> It would be nice to have a cool indexing system that allowed dynamic indexes of the data model but not worth the headache. If we are going to go big we should use the same gap symbols that were added for protein sequences.
> 
> Scooter
> 
> On Mon, Dec 6, 2010 at 2:32 PM, Andy Yates <ayates at ebi.ac.uk> wrote:
> I would say partially an oversight on my part & partially done on purpose (a gap is not a nucleotide after all). However I'm all in favour of being pragmatic here so lets add them in. If I get an okay from the relevant parties I'll commit the change in.
> 
> Andy
> 
> On 6 Dec 2010, at 18:41, Chris Friedline wrote:
> 
> > OK, so here's a quick fix now that I know where to look.  In my local
> > source I added the following line to the constructor of DNACompoundSet
> > and recompiled.
> >
> > addNucleotideCompound("-", "-");
> >
> > Not sure if this is the correct place for it in terms of what the devs
> > want to do globally, but it gets me moving forward again.  Gap
> > characters are in AminoAcidCompoundSet so I'm wondering if this was
> > just a tiny oversight on the nucleotide front.
> >
> > Thanks again for the help everyone,
> > Chris
> >
> > On Mon, Dec 6, 2010 at 1:28 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
> >> That does help, thanks.  However, when calling getAsList() on the
> >> aligned sequences and printing, this is what I see.  Something seems
> >> wrong.  It does appear as though null is being inserted where there
> >> should be gaps
> >>
> >> seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C,
> >> G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T,
> >> T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C,
> >> null, null, null, null, null, null]
> >> seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T,
> >> G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G,
> >> null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null,
> >> null, null, null, A, G, A, C, A, C, T, G, G, G, A, T]
> >>
> >> Chris
> >>
> >> On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> >>> Hi Andy,
> >>>
> >>> Check out the SimpleAlignedSequence class, for how Gaps are handled...
> >>> Does that help?
> >>>
> >>> Andreas
> >>>
> >>> On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> >>>> So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
> >>>>
> >>>> Does anyone on list know how the AlignedSequence code encodes gaps & the alike?
> >>>>
> >>>> Andy
> >>>>
> >>>> On 6 Dec 2010, at 13:50, Andy Yates wrote:
> >>>>
> >>>>> Hi Chris,
> >>>>>
> >>>>> Well that's going into my toStringBuilder() method & that particular line is concerned with asking a compound for its String representation. How often do we get nulls in our Sequences and how to deal with them. After all the Sequence AGTCNULLAGTC is probably more harmful then helpful
> >>>>>
> >>>>> Andy
> >>>>>
> >>>>> On 6 Dec 2010, at 12:45, Chris Friedline wrote:
> >>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> Found another potential error case, this time in beta2 (fresh pull
> >>>>>> from git last evening).  For more info, please see
> >>>>>> http://pastie.org/1351388 for test case and stack trace.  The JUnit
> >>>>>> test passes simply because the pair object is not null, but fails when
> >>>>>> trying to extract any information from the pair itself (toString(),
> >>>>>> getIdenticals(), etc). The substitution matrix file is from
> >>>>>> ftp://ftp.ncbi.nih.gov/blast/matrices.  I'm doing large numbers of
> >>>>>> pairwise alignments, which do not all fail, but most do with this same
> >>>>>> error.
> >>>>>>
> >>>>>> Thanks,
> >>>>>> Chris
> >>>>>>
> >>>>>> --
> >>>>>> PhD Candidate, Integrative Life Sciences
> >>>>>> Virginia Commonwealth University
> >>>>>> Richmond, VA
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>> --
> >>>> Andrew Yates                   Ensembl Genomes Engineer
> >>>> EMBL-EBI                       Tel: +44-(0)1223-492538
> >>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> >>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> -----------------------------------------------------------------------
> >>> Dr. Andreas Prlic
> >>> Senior Scientist, RCSB PDB Protein Data Bank
> >>> University of California, San Diego
> >>> (+1) 858.246.0526
> >>> -----------------------------------------------------------------------
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>>
> >>
> >>
> >>
> >> --
> >> PhD Candidate, Integrative Life Sciences
> >> Virginia Commonwealth University
> >> Richmond, VA
> >>
> >
> >
> >
> > --
> > PhD Candidate, Integrative Life Sciences
> > Virginia Commonwealth University
> > Richmond, VA
> 
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From jayunit100 at gmail.com  Sun Dec 12 22:42:09 2010
From: jayunit100 at gmail.com (Jay Vyas)
Date: Sun, 12 Dec 2010 17:42:09 -0500
Subject: [Biojava-l] predicting atoms from backbone
Message-ID: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>

Hi guys :

Im trying to add C, O , and N atoms to a protein structure, when I only have
a backbone trace..
That is, I have a series of CA atoms in a backbone of a protein structure,
and I want to generate other atom coordinates.

I know biojava can add hydrogents... Anybody have any ideas about how to add
and predict other atoms?

-- 
Jay Vyas
MMSB/UCHC


From andreas at sdsc.edu  Mon Dec 13 15:56:12 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 13 Dec 2010 07:56:12 -0800
Subject: [Biojava-l] predicting atoms from backbone
In-Reply-To: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>
References: <AANLkTimJf+J3mcoL4vT8Yazmm-8JV3hmiBcTxj+5aGRH@mail.gmail.com>
Message-ID: <AANLkTi=atfUTzSiriL995XS4KgSGer5LwHJ55ZL9FCiD@mail.gmail.com>

Hi Jay,

I guess you want to do something like that:
http://peds.oxfordjournals.org/content/5/2/147.abstract

Although all the tools for such calculations are available in BioJava,
there is currently no simple method call that allows to calculate such
a mainchain-model.

Before doing any coding, probably best to check out other software
like COOT, if it can do that...

Andreas

On Sun, Dec 12, 2010 at 2:42 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys :
>
> Im trying to add C, O , and N atoms to a protein structure, when I only have
> a backbone trace..
> That is, I have a series of CA atoms in a backbone of a protein structure,
> and I want to generate other atom coordinates.
>
> I know biojava can add hydrogents... Anybody have any ideas about how to add
> and predict other atoms?
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From wuuter at gmail.com  Thu Dec 16 02:45:42 2010
From: wuuter at gmail.com (Fico)
Date: Thu, 16 Dec 2010 10:45:42 +0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB file
Message-ID: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>

Hi, dear all:

I use biojava3 beta1 to parse the PDB files recently, my program is:

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(pdbDirPath);

            FileParsingParameters params = new FileParsingParameters();
            params.setLoadChemCompInfo(*false*);
            params.setHeaderOnly(*false*);
            params.setAlignSeqRes(*true*);
            params.setParseSecStruc(*false*);
            pdbreader.setFileParsingParameters(params);

            Structure structure = null;
            try {
                structure = pdbreader.getStructure(pdbDirPath + "\\" +
file);
            } catch (IOException e) {
                e.printStackTrace();
            }

when I execute this program, it will download something such as:

*creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*

but I do not want to lownload those stuff, How can I cancel it?
Thanks.


From marcelito_tony at hotmail.com  Thu Dec 16 03:59:11 2010
From: marcelito_tony at hotmail.com (marcelo rodriguez)
Date: Thu, 16 Dec 2010 03:59:11 +0000
Subject: [Biojava-l]  Is there  cvtree algorithm in biojava?
In-Reply-To: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
Message-ID: <BLU154-w7E5736538026F9298C9BAFA150@phx.gbl>


I am investigating cvtree algorithm biojava?
i need help
regards
marcelo 		 	   		  


From darnells at dnastar.com  Thu Dec 16 16:26:51 2010
From: darnells at dnastar.com (Steve Darnell)
Date: Thu, 16 Dec 2010 10:26:51 -0600
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
Message-ID: <A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>

The SeqRes to Atom record alignment forces the use of chemical
components to translate non-standard residues to their closest standard
counterpart for the sequence alignment.  I have to disable
setLoadChemCompInfo and setAlignSeqRes when I don't want to download
chemical component files from RCSB when parsing a PDB file.

Regards,
Steve

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
Sent: Wednesday, December 15, 2010 8:46 PM
To: Biojava-l at lists.open-bio.org
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
file

Hi, dear all:

I use biojava3 beta1 to parse the PDB files recently, my program is:

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(pdbDirPath);

            FileParsingParameters params = new FileParsingParameters();
            params.setLoadChemCompInfo(*false*);
            params.setHeaderOnly(*false*);
            params.setAlignSeqRes(*true*);
            params.setParseSecStruc(*false*);
            pdbreader.setFileParsingParameters(params);

            Structure structure = null;
            try {
                structure = pdbreader.getStructure(pdbDirPath + "\\" +
file);
            } catch (IOException e) {
                e.printStackTrace();
            }

when I execute this program, it will download something such as:

*creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*

but I do not want to lownload those stuff, How can I cancel it?
Thanks.
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l



From andreas at sdsc.edu  Fri Dec 17 15:24:16 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 17 Dec 2010 07:24:16 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
Message-ID: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>

ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
set to true and it will not download chemical components if
loadChemComp is false. The drawback is that the data representation
will not be as precise.

Andreas



On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com> wrote:
> The SeqRes to Atom record alignment forces the use of chemical
> components to translate non-standard residues to their closest standard
> counterpart for the sequence alignment. ?I have to disable
> setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> chemical component files from RCSB when parsing a PDB file.
>
> Regards,
> Steve
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> Sent: Wednesday, December 15, 2010 8:46 PM
> To: Biojava-l at lists.open-bio.org
> Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> file
>
> Hi, dear all:
>
> I use biojava3 beta1 to parse the PDB files recently, my program is:
>
> ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
> ? ? ? ? ? ?pdbreader.setAutoFetch(false);
> ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>
> ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
> ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
> ? ? ? ? ? ?params.setHeaderOnly(*false*);
> ? ? ? ? ? ?params.setAlignSeqRes(*true*);
> ? ? ? ? ? ?params.setParseSecStruc(*false*);
> ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>
> ? ? ? ? ? ?Structure structure = null;
> ? ? ? ? ? ?try {
> ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
> file);
> ? ? ? ? ? ?} catch (IOException e) {
> ? ? ? ? ? ? ? ?e.printStackTrace();
> ? ? ? ? ? ?}
>
> when I execute this program, it will download something such as:
>
> *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>
> but I do not want to lownload those stuff, How can I cancel it?
> Thanks.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From dasarnow at gmail.com  Sun Dec 19 03:36:28 2010
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Sat, 18 Dec 2010 19:36:28 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
Message-ID: <AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>

Prior to this, did setting loadChemComp true add processing overhead if
setAlignSeqRes is also true?  I.e. what's the difference between AlignSeqRes
with and without loadChemComp?
Just want to know what the right flags are when one wants accurate SEQRES
<---> ATOM alignments but isn't otherwise using the components info...

On a related note, I ended up writing a class that loaded and discarded
Structure objects for my PDBs, to trigger all the downloads before my big
processing jobs.  Though I guess the right (non-lazy) thing to do is parse
out the combined components library to the individual files.

-da

On Fri, Dec 17, 2010 at 07:24, Andreas Prlic <andreas at sdsc.edu> wrote:

> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
> set to true and it will not download chemical components if
> loadChemComp is false. The drawback is that the data representation
> will not be as precise.
>
> Andreas
>
>
>
> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > The SeqRes to Atom record alignment forces the use of chemical
> > components to translate non-standard residues to their closest standard
> > counterpart for the sequence alignment.  I have to disable
> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> > chemical component files from RCSB when parsing a PDB file.
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org
> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> > Sent: Wednesday, December 15, 2010 8:46 PM
> > To: Biojava-l at lists.open-bio.org
> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> > file
> >
> > Hi, dear all:
> >
> > I use biojava3 beta1 to parse the PDB files recently, my program is:
> >
> >            PDBFileReader pdbreader = new PDBFileReader();
> >            pdbreader.setAutoFetch(false);
> >            pdbreader.setPath(pdbDirPath);
> >
> >            FileParsingParameters params = new FileParsingParameters();
> >            params.setLoadChemCompInfo(*false*);
> >            params.setHeaderOnly(*false*);
> >            params.setAlignSeqRes(*true*);
> >            params.setParseSecStruc(*false*);
> >            pdbreader.setFileParsingParameters(params);
> >
> >            Structure structure = null;
> >            try {
> >                structure = pdbreader.getStructure(pdbDirPath + "\\" +
> > file);
> >            } catch (IOException e) {
> >                e.printStackTrace();
> >            }
> >
> > when I execute this program, it will download something such as:
> >
> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
> >
> > but I do not want to lownload those stuff, How can I cancel it?
> > Thanks.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From dasarnow at gmail.com  Sun Dec 19 03:47:27 2010
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Sat, 18 Dec 2010 19:47:27 -0800
Subject: [Biojava-l] Thread safety of the AtomCache
Message-ID: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>

Is AtomCache expected to be thread-safe?  It would be nice to have multiple
threads work off the same AtomCache, when those threads might each ask for
some of the same PDB IDs.

Best,

-da


From andreas at sdsc.edu  Sun Dec 19 08:19:40 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 00:19:40 -0800
Subject: [Biojava-l] Thread safety of the AtomCache
In-Reply-To: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>
References: <AANLkTimbjKc7DRGiQTofj3CX0gujJZjV9GFSb7zdRSdo@mail.gmail.com>
Message-ID: <AANLkTimmOrOr=aTppWiBKNawQOGL1by_Lo518wEwnQ_2@mail.gmail.com>

Hi Daniel,

Yes, the AtomCache is thread-safe. Caching across multiple threads was
one of the ideas behind this class...

Andreas


On Sat, Dec 18, 2010 at 7:47 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Is AtomCache expected to be thread-safe? ?It would be nice to have multiple
> threads work off the same AtomCache, when those threads might each ask for
> some of the same PDB IDs.
>
> Best,
>
> -da
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From andreas at sdsc.edu  Sun Dec 19 08:38:08 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 00:38:08 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
	<AANLkTin+oPNrKsRXMFNDb5y=icwztRAT9AFcNq21Orvc@mail.gmail.com>
Message-ID: <AANLkTim+K8S1XQCNevLiWkmGEwA4q8ZnW8QYi_K658Xh@mail.gmail.com>

Hi Daniel,

The chemical components provide the chemically correct definition of
the various groups. There are quite a few chemically modified amino
acids in PDB files which can be represented as amino acids, rather
than Hetatom groups, based on these definitions. This has an impact on
the sequence alignment that is done during the alignSeqRes process.
Without the correct representations, those groups would be flagged as
"X", or might be missing. Will set up a wiki page which explains all
the parsing options in detail.

About your 2nd comment. There is now a new ChemCompProvider interface.
Perhaps there should be a new implementation of this, which is
downloading the file that contains all chemcomps bundled and provide
the data from there...

Andreas





On Sat, Dec 18, 2010 at 7:36 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Prior to this, did setting loadChemComp true add processing overhead if
> setAlignSeqRes is also true? ?I.e. what's the difference between AlignSeqRes
> with and without loadChemComp?
> Just want to know what the right flags are when one wants accurate SEQRES
> <---> ATOM alignments but isn't otherwise using the components info...
> On a related note, I ended up writing a class that loaded and discarded
> Structure objects for my PDBs, to trigger all the downloads before my big
> processing jobs. ?Though I guess the right (non-lazy) thing to do is parse
> out the combined components library to the individual files.
> -da
>
> On Fri, Dec 17, 2010 at 07:24, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
>> set to true and it will not download chemical components if
>> loadChemComp is false. The drawback is that the data representation
>> will not be as precise.
>>
>> Andreas
>>
>>
>>
>> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>> > The SeqRes to Atom record alignment forces the use of chemical
>> > components to translate non-standard residues to their closest standard
>> > counterpart for the sequence alignment. ?I have to disable
>> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
>> > chemical component files from RCSB when parsing a PDB file.
>> >
>> > Regards,
>> > Steve
>> >
>> > -----Original Message-----
>> > From: biojava-l-bounces at lists.open-bio.org
>> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
>> > Sent: Wednesday, December 15, 2010 8:46 PM
>> > To: Biojava-l at lists.open-bio.org
>> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
>> > file
>> >
>> > Hi, dear all:
>> >
>> > I use biojava3 beta1 to parse the PDB files recently, my program is:
>> >
>> > ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
>> > ? ? ? ? ? ?pdbreader.setAutoFetch(false);
>> > ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>> >
>> > ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
>> > ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
>> > ? ? ? ? ? ?params.setHeaderOnly(*false*);
>> > ? ? ? ? ? ?params.setAlignSeqRes(*true*);
>> > ? ? ? ? ? ?params.setParseSecStruc(*false*);
>> > ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>> >
>> > ? ? ? ? ? ?Structure structure = null;
>> > ? ? ? ? ? ?try {
>> > ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
>> > file);
>> > ? ? ? ? ? ?} catch (IOException e) {
>> > ? ? ? ? ? ? ? ?e.printStackTrace();
>> > ? ? ? ? ? ?}
>> >
>> > when I execute this program, it will download something such as:
>> >
>> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
>> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
>> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>> >
>> > but I do not want to lownload those stuff, How can I cancel it?
>> > Thanks.
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
>>
>>
>> --



From andreas at sdsc.edu  Sun Dec 19 14:29:13 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Sun, 19 Dec 2010 06:29:13 -0800
Subject: [Biojava-l] biojava3.0-beta4
Message-ID: <AANLkTikN0dN+1jePh5+QJhWTixPxxZGq3wRT0cA+xy74@mail.gmail.com>

The fourth beta version for BioJava 3.0  has been released in our
Maven repository http://biojava.org/download/maven/

New things:

- tons of javadoc improvements
- a patch in the protmod module
- bug fix regarding automated download of chemcomp files in the structure module

A new set of javadoc files is available from:
http://www.biojava.org/docs/api_latest/

Andreas


From wuuter at gmail.com  Mon Dec 20 05:31:24 2010
From: wuuter at gmail.com (Fico)
Date: Mon, 20 Dec 2010 13:31:24 +0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
Message-ID: <AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>

now the question of ChemComp download is OK, but I found a new question when
I test bioJava3-Beta4, my program fragment:

        FileParsingParameters params = new FileParsingParameters();
        params.setLoadChemCompInfo(false);
        params.setHeaderOnly(false);
        // params.setParseCAOnly(true);
        params.setAlignSeqRes(true);
        params.setParseSecStruc(false);

        // loop file
        for (String file : getPdbFiles()) {

            PDBFileReader pdbreader = new PDBFileReader();
            pdbreader.setAutoFetch(false);
            pdbreader.setPath(getPdbDir());

            pdbreader.setFileParsingParameters(params);

            // pdbreader.setLoadChemCompInfo(true);
            Structure struc = null;
            try {
                struc = pdbreader.getStructure(getPdbDir() + "\\" + file);
            } catch (IOException e) {
                e.printStackTrace();
            }

            String pdbid = struc.getPDBCode();

            for (int i = 0; i < struc.nrModels(); i++) {

                // loop chain
                for (Chain ch : struc.getModel(i)) {
                    System.out.println(pdbid + ">>>" + ch.getChainID() +
">>>"
                            + ch.getAtomSequence());
                    System.out.println(pdbid + ">>>" + ch.getChainID() +
">>>"
                            + ch.getSeqResSequence());
                    // Test the getAtomGroups() and getSeqResGroups() method
                    // List<Group> group = ch.getAtomGroups();
                    List<Group> group = ch.getSeqResGroups();
                    for (Group gp : group) {
                        System.out.println(gp.getResidueNumber() + ":"
                                + gp.getPDBName());
                    }
                }
            }
        }

my test PDB file is 1O1G.pdb, there are 45 modified residues in chain A,
when I use .getAtomGroups() I can get all residues' atom information, such
as ResidueNumber and PDBName:
797:PHE
798:LEU
799:MET
800:ARG
801:VAL
802:GLU
......
840:PRO
841:LEU
842:LEU
843:LYS

but use .getSeqResGroups(), the last 45 residues will miss some information,
such as ResidueNumber and atom coordinate, the output of the program is:
797:PHE
798:LEU
null:MET
null:ARG
null:VAL
null:GLU
......
null:PRO
null:LEU
null:LEU
null:LYS

In biojava3-Beta1 the two method produce same result just as
.getAtomGroups() in Beta4. so is it a bug?

P.S.
    Could we add new method to get all amino acid sequence with modifed
residues directly? now both getAtomSequence() and getSeqResSequence() can't
do this, if I want get the amino acid sequence with modifed residues, I had
to use .getAtomGroups() or .getSeqResGroups() first and then loop each
residue to get one letter amino acid sequence.





2010/12/17 Andreas Prlic <andreas at sdsc.edu>

> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
> set to true and it will not download chemical components if
> loadChemComp is false. The drawback is that the data representation
> will not be as precise.
>
> Andreas
>
>
>
> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
> wrote:
> > The SeqRes to Atom record alignment forces the use of chemical
> > components to translate non-standard residues to their closest standard
> > counterpart for the sequence alignment.  I have to disable
> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> > chemical component files from RCSB when parsing a PDB file.
> >
> > Regards,
> > Steve
> >
> > -----Original Message-----
> > From: biojava-l-bounces at lists.open-bio.org
> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> > Sent: Wednesday, December 15, 2010 8:46 PM
> > To: Biojava-l at lists.open-bio.org
> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> > file
> >
> > Hi, dear all:
> >
> > I use biojava3 beta1 to parse the PDB files recently, my program is:
> >
> >            PDBFileReader pdbreader = new PDBFileReader();
> >            pdbreader.setAutoFetch(false);
> >            pdbreader.setPath(pdbDirPath);
> >
> >            FileParsingParameters params = new FileParsingParameters();
> >            params.setLoadChemCompInfo(*false*);
> >            params.setHeaderOnly(*false*);
> >            params.setAlignSeqRes(*true*);
> >            params.setParseSecStruc(*false*);
> >            pdbreader.setFileParsingParameters(params);
> >
> >            Structure structure = null;
> >            try {
> >                structure = pdbreader.getStructure(pdbDirPath + "\\" +
> > file);
> >            } catch (IOException e) {
> >                e.printStackTrace();
> >            }
> >
> > when I execute this program, it will download something such as:
> >
> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
> >
> > but I do not want to lownload those stuff, How can I cancel it?
> > Thanks.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>


From andreas at sdsc.edu  Tue Dec 21 23:55:39 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 21 Dec 2010 15:55:39 -0800
Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
	file
In-Reply-To: <AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>
References: <AANLkTi=V=VZ1-OMfaLom-hrr_gZNt6jbZmU=i8W40UHn@mail.gmail.com>
	<A4009967D1886D4286A9B7931FD586100282D22E@FS1.dnastar.com>
	<AANLkTi=_hTQq-BT0TmupQj1fBB-T_sF7sg3Unwb57pTc@mail.gmail.com>
	<AANLkTinBE_2t7UB6O3jRG+Q-zZ2Ab2wtOG8H4evxxw-a@mail.gmail.com>
Message-ID: <AANLkTin0sazkTCa6u3WVagN+xVmSxWY_ViTt0wKOkuak@mail.gmail.com>

Hi Fico,

- you are right, this was a bug (some index was off). I committed a
patch for this to SVN.
- I also added new behaviour for downloading chem comp files: The
default chem comp provider will fetch the components.cif.gz file and
extract all definitions into small files, which will be used from then
on.
- not sure about your last question. That is kind of already possible
I believe. You can use the getChemComp method to get the exact
definition for a group.

Andreas

On Sun, Dec 19, 2010 at 9:31 PM, Fico <wuuter at gmail.com> wrote:
> now the question of ChemComp download is OK, but I found a new question when
> I test bioJava3-Beta4, my program fragment:
>
> ??????? FileParsingParameters params = new FileParsingParameters();
> ??? ??? params.setLoadChemCompInfo(false);
> ??? ??? params.setHeaderOnly(false);
> ??? ??? // params.setParseCAOnly(true);
> ??? ??? params.setAlignSeqRes(true);
> ??? ??? params.setParseSecStruc(false);
>
> ??? ??? // loop file
> ??? ??? for (String file : getPdbFiles()) {
>
> ??? ??? ??? PDBFileReader pdbreader = new PDBFileReader();
> ??? ??? ??? pdbreader.setAutoFetch(false);
> ??? ??? ??? pdbreader.setPath(getPdbDir());
>
> ??? ??? ??? pdbreader.setFileParsingParameters(params);
>
> ??? ??? ??? // pdbreader.setLoadChemCompInfo(true);
> ??? ??? ??? Structure struc = null;
> ??? ??? ??? try {
> ??? ??? ??? ??? struc = pdbreader.getStructure(getPdbDir() + "\\" + file);
> ??? ??? ??? } catch (IOException e) {
> ??? ??? ??? ??? e.printStackTrace();
> ??? ??? ??? }
>
> ??? ??? ??? String pdbid = struc.getPDBCode();
>
> ??? ??? ??? for (int i = 0; i < struc.nrModels(); i++) {
>
> ??? ??? ??? ??? // loop chain
> ??? ??? ??? ??? for (Chain ch : struc.getModel(i)) {
> ??? ??? ??? ??? ??? System.out.println(pdbid + ">>>" + ch.getChainID() +
> ">>>"
> ??? ??? ??? ??? ??? ??? ??? + ch.getAtomSequence());
> ??? ??? ??? ??? ??? System.out.println(pdbid + ">>>" + ch.getChainID() +
> ">>>"
> ??? ??? ??? ??? ??? ??? ??? + ch.getSeqResSequence());
> ??? ??? ??? ??? ??? // Test the getAtomGroups() and getSeqResGroups() method
> ??????????????????? // List<Group> group = ch.getAtomGroups();
> ??? ??? ??? ??? ??? List<Group> group = ch.getSeqResGroups();
> ??? ??? ??? ??? ??? for (Group gp : group) {
> ??? ??? ??? ??? ??? ??? System.out.println(gp.getResidueNumber() + ":"
> ??? ??? ??? ??? ??? ??? ??? ??? + gp.getPDBName());
> ??? ??? ??? ??? ??? }
> ??? ??? ??? ??? }
> ??? ??? ??? }
> ??? ??? }
>
> my test PDB file is 1O1G.pdb, there are 45 modified residues in chain A,
> when I use .getAtomGroups() I can get all residues' atom information, such
> as ResidueNumber and PDBName:
> 797:PHE
> 798:LEU
> 799:MET
> 800:ARG
> 801:VAL
> 802:GLU
> ......
> 840:PRO
> 841:LEU
> 842:LEU
> 843:LYS
>
> but use .getSeqResGroups(), the last 45 residues will miss some information,
> such as ResidueNumber and atom coordinate, the output of the program is:
> 797:PHE
> 798:LEU
> null:MET
> null:ARG
> null:VAL
> null:GLU
> ......
> null:PRO
> null:LEU
> null:LEU
> null:LYS
>
> In biojava3-Beta1 the two method produce same result just as
> .getAtomGroups() in Beta4. so is it a bug?
>
> P.S.
> ??? Could we add new method to get all amino acid sequence with modifed
> residues directly? now both getAtomSequence() and getSeqResSequence() can't
> do this, if I want get the amino acid sequence with modifed residues, I had
> to use .getAtomGroups() or .getSeqResGroups() first and then loop each
> residue to get one letter amino acid sequence.
>
>
>
>
>
> 2010/12/17 Andreas Prlic <andreas at sdsc.edu>
>>
>> ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
>> set to true and it will not download chemical components if
>> loadChemComp is false. The drawback is that the data representation
>> will not be as precise.
>>
>> Andreas
>>
>>
>>
>> On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>> > The SeqRes to Atom record alignment forces the use of chemical
>> > components to translate non-standard residues to their closest standard
>> > counterpart for the sequence alignment. ?I have to disable
>> > setLoadChemCompInfo and setAlignSeqRes when I don't want to download
>> > chemical component files from RCSB when parsing a PDB file.
>> >
>> > Regards,
>> > Steve
>> >
>> > -----Original Message-----
>> > From: biojava-l-bounces at lists.open-bio.org
>> > [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
>> > Sent: Wednesday, December 15, 2010 8:46 PM
>> > To: Biojava-l at lists.open-bio.org
>> > Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
>> > file
>> >
>> > Hi, dear all:
>> >
>> > I use biojava3 beta1 to parse the PDB files recently, my program is:
>> >
>> > ? ? ? ? ? ?PDBFileReader pdbreader = new PDBFileReader();
>> > ? ? ? ? ? ?pdbreader.setAutoFetch(false);
>> > ? ? ? ? ? ?pdbreader.setPath(pdbDirPath);
>> >
>> > ? ? ? ? ? ?FileParsingParameters params = new FileParsingParameters();
>> > ? ? ? ? ? ?params.setLoadChemCompInfo(*false*);
>> > ? ? ? ? ? ?params.setHeaderOnly(*false*);
>> > ? ? ? ? ? ?params.setAlignSeqRes(*true*);
>> > ? ? ? ? ? ?params.setParseSecStruc(*false*);
>> > ? ? ? ? ? ?pdbreader.setFileParsingParameters(params);
>> >
>> > ? ? ? ? ? ?Structure structure = null;
>> > ? ? ? ? ? ?try {
>> > ? ? ? ? ? ? ? ?structure = pdbreader.getStructure(pdbDirPath + "\\" +
>> > file);
>> > ? ? ? ? ? ?} catch (IOException e) {
>> > ? ? ? ? ? ? ? ?e.printStackTrace();
>> > ? ? ? ? ? ?}
>> >
>> > when I execute this program, it will download something such as:
>> >
>> > *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
>> > downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
>> > downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>> >
>> > but I do not want to lownload those stuff, How can I cancel it?
>> > Thanks.
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> > _______________________________________________
>> > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>
>



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



From andreas at sdsc.edu  Tue Dec 28 21:22:57 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 28 Dec 2010 13:22:57 -0800
Subject: [Biojava-l] BioJava 3.0 released
Message-ID: <AANLkTimQ-OC7upHhZe11EPP8F+=A-bS1q6uLvfYYXX0O@mail.gmail.com>

BioJava 3.0 has been released and is available from
http://biojava.org/wiki/BioJava:Download .

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

Over the last year BioJava has undergone a major re-write. It has been
modularized into small, re-usable components and a number of new
features have been added. The new approach, modeled after the apache
commons, minimizes dependencies and allows for easier contribution of
new components.

At the present the main modules are:

biojava3-core: The core module offers the basic tools required for
working with biological sequences of various types (DNA, RNA,
protein). Besides file parsers for popular file formats it provides
efficient data structures for sequence manipulation and serialization.

biojava3-genome: The genome module provides support for reading and
writing of gtf, gff2, gff3 file formats

biojava3-alignment: This module provides implementations for pairwise
and multiple sequence alignments (MSA). The implementation for MSA
provides a flexible and multi-threaded framework that works in linear
space and that, as an option, allows the users to define anchors that
are used in the build up of the multiple alignment.

biojava3-structure: The 3D protein structure module provides parsers
and a data model for working PDB and mmCif files. New features in this
release are the implementation of the CE and FATCAT structural
alignment algorithms and the support of chemical component definition
files, for a chemically and biologically correct representation of
modified residues and ligands.

biojava3-protmod: The protein modification module can detect more than
200 protein modifications and crosslinks in 3D protein structures. It
comes with an XML file and Java data structures to store information
about different types of protein modifications collected from PDB,
RESID, and PSI-MOD.

Not every feature of the BioJava 1.X code base was migrated over to
BioJava 3.0. A modularized version of the 1.X sources is available as
a new "biojava-legacy" project.

Thanks to all contributors for making this release possible.

Happy Biojava-ing,

Andreas


From science.translator at gmail.com  Tue Dec 28 23:24:49 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Tue, 28 Dec 2010 15:24:49 -0800
Subject: [Biojava-l] QBlast in BioJava3
Message-ID: <AANLkTim2-yODH2tZ2=eL74nZ4=kro_=E48zqOXgL-PDx@mail.gmail.com>

Hello BioJava community,

I'm a biologist/Java newbie, I'm trying to write a program that automates
BLAST requests using very short peptide sequences. I downloaded the new
BioJava 3 jars, and attempted to write the program, but I quickly ran into a
problem.

Here's the code I have so far:
package com.multiBLAST.model;

import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
import org.biojava3.core.sequence.*;

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastAlignmentProperties alignmentProperties;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";

        try {
            blaster = new NCBIQBlastService();
            alignmentProperties = new NCBIQBlastAlignmentProperties();
            alignmentProperties.setBlastProgram("blastp");
            alignmentProperties.setBlastDatabase("nr");

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

        }

    }

}

Eclipse is telling me that last line of code causes a compiler error: "The
type org.biojavax.bio.seq.RichSequence cannot be resolved. It is indirectly
referenced from required .class files"

I'm not sure exactly what this means, it seems to me that perhaps when this
method was updated from biojavax to biojava3, it somewhere still references
the RichSequence from biojavax. I can't find a RichSequence class anywhere
in the new BioJava3 API, and I can't find the biojavax jars on the legacy
download page, so I'm not sure how to proceed.

If someone could please provide some assistance, that would be great.

Thank you very much,

Matthew Busse, PhD


From sylvain.foisy at diploide.net  Wed Dec 29 17:22:52 2010
From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.)
Date: Wed, 29 Dec 2010 12:22:52 -0500
Subject: [Biojava-l] QBlast in BioJava3
Message-ID: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>

Hi,

I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.

Best regards

Sylvain





From andreas at sdsc.edu  Wed Dec 29 17:58:43 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 29 Dec 2010 09:58:43 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
Message-ID: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>

Thanks Sylvain,

Matthew, a workaround until we have a fix for this is to add the
http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
from the biojava-legacy project to your classpath. This should allow
your example to work...

Andreas


On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
<sylvain.foisy at diploide.net> wrote:
> Hi,
>
> I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.
>
> Best regards
>
> Sylvain
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From science.translator at gmail.com  Wed Dec 29 19:52:13 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Wed, 29 Dec 2010 11:52:13 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
Message-ID: <AANLkTin6AYfZ56TzqfYHiwx67i7MFu0R7KsU45naKves@mail.gmail.com>

Thank you everyone for your prompt responses. Adding the core-1.8.jar to the
build path took care of the problem.

Cheers!
Matthew

On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Sylvain,
>
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
>
> Andreas
>
>
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the
> problem that you found ASAP to remove the dependency on the old BJ
> architecture about representing Sequence objects. I'll work on this early
> next week, as soon as I'll have finish with my grading... I am more of a
> teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>


From science.translator at gmail.com  Wed Dec 29 21:01:33 2010
From: science.translator at gmail.com (Matthew Busse)
Date: Wed, 29 Dec 2010 13:01:33 -0800
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
Message-ID: <AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>

Hello Sylvain, et al.,

I think I may have found another similar issue.

Here's my program:

package com.multiBLAST.model;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Set;

import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputFormat;
import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
import org.biojava3.ws.alignment.qblast.NCBIQBlastService;

public class BLASTExample {

    public static void main(String [] args) {

        NCBIQBlastService blaster;
        NCBIQBlastOutputProperties outputProperties;
        InputStream is;
        String request = "";
        final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";
        String rid = new String();

        try {
            blaster = new NCBIQBlastService();
            NCBIQBlastAlignmentProperties alignmentProperties = new
NCBIQBlastAlignmentProperties();
            alignmentProperties.setBlastProgram("blastp");
            alignmentProperties.setBlastDatabase("nr");

            request = blaster.sendAlignmentRequest(TESTSEQUENCE,
alignmentProperties);

            System.out.println("Trying to get BLAST results for RID " +
rid);

            boolean wasBlasted = false;

            while (!wasBlasted) {
                wasBlasted = blaster.isReady(rid,
System.currentTimeMillis());
            }

            outputProperties = new NCBIQBlastOutputProperties();
            outputProperties.setOutputFormat(NCBIQBlastOutputFormat.TEXT);

outputProperties.setAlignmentOutputFormat(NCBIQBlastOutputFormat.PAIRWISE);
            outputProperties.setDescriptionNumber(10);
            outputProperties.setAlignmentNumber(10);

            //to show that output options were followed

            Set<String> test = outputProperties.getOutputOptions();

            for(String str : test) {
                System.out.println(str);
            }

            is = blaster.getAlignmentResults(request, outputProperties);

            BufferedReader br = new BufferedReader(new
InputStreamReader(is));

            String line = null;

            while ((line = br.readLine()) != null)    {
                System.out.println(line);
            }

        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}

When I run it, it throws an exception:
java.lang.Exception: The key named PROGRAM is not set in this
RemoteQBlastOutputProperties object
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties.getAlignmentOption(NCBIQBlastAlignmentProperties.java:173)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendActualAlignementRequest(NCBIQBlastService.java:132)
    at
org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendAlignmentRequest(NCBIQBlastService.java:210)
    at com.multiBLAST.model.BLASTExample.main(BLASTExample.java:30)

Because RemoteQBlastOutputProperties is the terminology used in the pre-BJ3
APIs, I'm guessing this is another conversion problem? Or am I missing
something else?

Many thanks for all your help.

Best,
Matthew

On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Sylvain,
>
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
>
> Andreas
>
>
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the
> problem that you found ASAP to remove the dependency on the old BJ
> architecture about representing Sequence objects. I'll work on this early
> next week, as soon as I'll have finish with my grading... I am more of a
> teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>


From sylvain.foisy at diploide.net  Wed Dec 29 21:15:57 2010
From: sylvain.foisy at diploide.net (Sylvain Foisy Ph. D.)
Date: Wed, 29 Dec 2010 16:15:57 -0500
Subject: [Biojava-l] QBlast in BioJava3
In-Reply-To: <AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>
References: <D0AEE752-0EE9-41FB-94D1-7EF8CCC0CD4C@diploide.net>
	<AANLkTin9XFVwDXswXZ2O9oxeEVUdrpTGR_r1R9B=NPaN@mail.gmail.com>
	<AANLkTi=s8Tj_JM=rT1khr=RiNw=Suq=R77MXUFUH=tYq@mail.gmail.com>
Message-ID: <DA1E2D38-A8E4-4971-9056-863E6347E3CC@diploide.net>

Hi Matthew,

Let me dive in this code again and I'll find the bug. Any rush on this? I am planning to do this early next week/year ;-) You are actually the first reported user of this module beside me! I mostly tested it with nucleotide sequences on the old architecture. Not much work done wince moving to the new code base...

Back to you ASAP

Best regards

Sylvain

On 2010-12-29, at 4:01 PM, Matthew Busse wrote:

> Hello Sylvain, et al., 
> 
> I think I may have found another similar issue. 
> 
> Here's my program:
> 
> package com.multiBLAST.model;
> 
> import java.io.BufferedReader;
> import java.io.InputStream;
> import java.io.InputStreamReader;
> import java.util.Set;
> 
> import org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputFormat;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties;
> import org.biojava3.ws.alignment.qblast.NCBIQBlastService;
> 
> public class BLASTExample {
>     
>     public static void main(String [] args) {
>         
>         NCBIQBlastService blaster;
>         NCBIQBlastOutputProperties outputProperties;
>         InputStream is;
>         String request = "";
>         final String TESTSEQUENCE = "MAQGTLIRVTPEQPTHAVCV";
>         String rid = new String();
>         
>         try {
>             blaster = new NCBIQBlastService();
>             NCBIQBlastAlignmentProperties alignmentProperties = new NCBIQBlastAlignmentProperties();
>             alignmentProperties.setBlastProgram("blastp");
>             alignmentProperties.setBlastDatabase("nr");
>             
>             request = blaster.sendAlignmentRequest(TESTSEQUENCE, alignmentProperties);
>             
>             System.out.println("Trying to get BLAST results for RID " + rid);
>             
>             boolean wasBlasted = false;
>             
>             while (!wasBlasted) {
>                 wasBlasted = blaster.isReady(rid, System.currentTimeMillis());
>             }
>             
>             outputProperties = new NCBIQBlastOutputProperties();
>             outputProperties.setOutputFormat(NCBIQBlastOutputFormat.TEXT);
>             outputProperties.setAlignmentOutputFormat(NCBIQBlastOutputFormat.PAIRWISE);
>             outputProperties.setDescriptionNumber(10);
>             outputProperties.setAlignmentNumber(10);
>             
>             //to show that output options were followed
>             
>             Set<String> test = outputProperties.getOutputOptions();
>             
>             for(String str : test) {
>                 System.out.println(str);
>             }
>             
>             is = blaster.getAlignmentResults(request, outputProperties);
>             
>             BufferedReader br = new BufferedReader(new InputStreamReader(is));
>             
>             String line = null;
>             
>             while ((line = br.readLine()) != null)    {
>                 System.out.println(line);
>             }
>             
>         } catch (Exception ex) {
>             ex.printStackTrace();
>         } 
>     }
> }
> 
> When I run it, it throws an exception:
> java.lang.Exception: The key named PROGRAM is not set in this RemoteQBlastOutputProperties object
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties.getAlignmentOption(NCBIQBlastAlignmentProperties.java:173)
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendActualAlignementRequest(NCBIQBlastService.java:132)
>     at org.biojava3.ws.alignment.qblast.NCBIQBlastService.sendAlignmentRequest(NCBIQBlastService.java:210)
>     at com.multiBLAST.model.BLASTExample.main(BLASTExample.java:30)
> 
> Because RemoteQBlastOutputProperties is the terminology used in the pre-BJ3 APIs, I'm guessing this is another conversion problem? Or am I missing something else?
> 
> Many thanks for all your help.
> 
> Best,
> Matthew
> 
> On Wed, Dec 29, 2010 at 9:58 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Thanks Sylvain,
> 
> Matthew, a workaround until we have a fix for this is to add the
> http://biojava.org/download/maven/org/biojava/core/1.8/core-1.8.jar
> from the biojava-legacy project to your classpath. This should allow
> your example to work...
> 
> Andreas
> 
> 
> On Wed, Dec 29, 2010 at 9:22 AM, Sylvain Foisy Ph. D.
> <sylvain.foisy at diploide.net> wrote:
> > Hi,
> >
> > I am the author/main culprit for the QBlast code in BJ. I have to fix the problem that you found ASAP to remove the dependency on the old BJ architecture about representing Sequence objects. I'll work on this early next week, as soon as I'll have finish with my grading... I am more of a teacher than a coder nowadays.
> >
> > Best regards
> >
> > Sylvain
> >
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> 




From andreas.prlic at gmail.com  Thu Dec 30 18:27:09 2010
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Thu, 30 Dec 2010 10:27:09 -0800
Subject: [Biojava-l] BioJava3 - Structure - Bug
In-Reply-To: <AANLkTi=Em4QBXkfuKf=ot-YfEPA5kCKWuG9ACuzd-zLi@mail.gmail.com>
References: <AANLkTi=Em4QBXkfuKf=ot-YfEPA5kCKWuG9ACuzd-zLi@mail.gmail.com>
Message-ID: <AANLkTi=6-if=E-yprYEcwhFkAD0EQsD7N4Zf+8Mnci04@mail.gmail.com>

Hi Jose,

Thanks for spotting this. I disabled the get/setPDBline a while ago
since it essentially doubles memory usage. It would be better to have
an Atom.toPDB or a FileConvert.toPDB(Atom) class that builds up the
String output dynamically.. I will flag the method calls as
deprecated.

Andreas


2010/12/30 Jos? Augusto Salim <jose.asalim at gmail.com>:
> Hi Andreas,
>
> I have used BioJava3 and I find some kind of bug on it. When I try to use
> the function getPBDline from Atom interface it return a blank string, it
> because in PDBFileParser when a new AtomImpl is created no pdbLine is set.
> So, I change the code for it works, just but the line:
>
> atom.setPDBline(line.trim());
>
> in PDBFileParser.java
>
> I'm sending the file for you.
>
> thanks for BioJava3 it has been very useful for my work.
>
> best regardless,
>
> ===
> Jos? Augusto Salim
> Computer Engineer
> -------------------------------
> http://www.thezeitgeistmovement.com
> http://www.zeitgeistmovie.com
>
>



From philipp.comans at mytum.de  Fri Dec 31 17:07:46 2010
From: philipp.comans at mytum.de (Philipp Comans)
Date: Fri, 31 Dec 2010 18:07:46 +0100
Subject: [Biojava-l] Error parsing GFF3 file
Message-ID: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>

Hello everyone,

I am trying to parse the file available here: ftp://ftp.jgi-psf.org/pub/JGI_data/Amphimedon_queenslandica/annotation/Aqu1.gff3.gz
with the following commands:

import java.util.Iterator;

import org.biojava3.genome.parsers.gff.FeatureI;
import org.biojava3.genome.parsers.gff.FeatureList;
import org.biojava3.genome.parsers.gff.GFF3Reader;

public class GFFReader3 {

	public static void main(String[] args) throws Exception {
		
		FeatureList features = (FeatureList) GFF3Reader.read("/Users/philipp/Dropbox/IDP/JGI_data/annotation/Smiles.gff3");
		Iterator<FeatureI> featureIterator = features.iterator();
		
		FeatureI currentFeature = null;
		
		while (featureIterator.hasNext()) {
			currentFeature = featureIterator.next();
			System.out.println(currentFeature);
		}

	}

}

The error I get is:
31.12.2010 18:05:10 org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading /Users/philipp/Dropbox/IDP/JGI_data/annotation/Aqu1.gff3
Exception in thread "main" java.lang.IllegalArgumentException: Improper location parameters: (-1864985,746)
	at org.biojava3.genome.parsers.gff.Location.<init>(Location.java:75)
	at org.biojava3.genome.parsers.gff.Location.union(Location.java:258)
	at org.biojava3.genome.parsers.gff.FeatureList.add(FeatureList.java:49)
	at org.biojava3.genome.parsers.gff.GFF3Reader.read(GFF3Reader.java:59)
	at GFFReader3.main(GFFReader3.java:11)

I find this very strange because the file is a valid GFF document according to
http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

Is this a bug or am I doing something wrong?
Thanks for your help, I wish you a happy New Year!

Philipp


From willishf at ufl.edu  Fri Dec 31 18:21:48 2010
From: willishf at ufl.edu (Scooter Willis)
Date: Fri, 31 Dec 2010 13:21:48 -0500
Subject: [Biojava-l] Error parsing GFF3 file
In-Reply-To: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>
References: <6D0D6C61-35E4-406A-8554-4C8AB82449F0@mytum.de>
Message-ID: <AANLkTi=DZi1ue=8FkCGmLGW0Gs8=Pz5q6wwkckDJtp-0@mail.gmail.com>

Phillip

I think it is complaining about the negative location (-1864985,746). Is
this a circular genome? That seems to be a rather large sequence segment and
I think it is correct to complain about the negative location. We tried to
plan ahead on circular genomes and genes that cross the boundary begin/end
boundary and at the same time not have the programmer brain explode trying
to handle all the combinations that exist.  It gets really fun when you have
a negative strand.

One of the challenges of a valid gff3 file is that you can make sure
ontology is correct and the file format is correct but when you try and
bring it all together to do something with the data(turn it into a protein)
you need to check harder.

If this is a valid location can you send me the gff3 segment and the DNA
sequence that describes the features and I will see what I can do to make it
work without previous reference to head exploding. Let me know what the end
goal is on parsing gff3 file and what is missing when you try and map to a
GeneSequence/ProteinSequence.

Thanks

Scooter

On Fri, Dec 31, 2010 at 12:07 PM, Philipp Comans <philipp.comans at mytum.de>wrote:

> Hello everyone,
>
> I am trying to parse the file available here:
> ftp://ftp.jgi-psf.org/pub/JGI_data/Amphimedon_queenslandica/annotation/Aqu1.gff3.gz
> with the following commands:
>
> import java.util.Iterator;
>
> import org.biojava3.genome.parsers.gff.FeatureI;
> import org.biojava3.genome.parsers.gff.FeatureList;
> import org.biojava3.genome.parsers.gff.GFF3Reader;
>
> public class GFFReader3 {
>
>        public static void main(String[] args) throws Exception {
>
>                FeatureList features = (FeatureList)
> GFF3Reader.read("/Users/philipp/Dropbox/IDP/JGI_data/annotation/Smiles.gff3");
>                Iterator<FeatureI> featureIterator = features.iterator();
>
>                FeatureI currentFeature = null;
>
>                while (featureIterator.hasNext()) {
>                        currentFeature = featureIterator.next();
>                        System.out.println(currentFeature);
>                }
>
>        }
>
> }
>
> The error I get is:
> 31.12.2010 18:05:10 org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/philipp/Dropbox/IDP/JGI_data/annotation/Aqu1.gff3
> Exception in thread "main" java.lang.IllegalArgumentException: Improper
> location parameters: (-1864985,746)
>        at org.biojava3.genome.parsers.gff.Location.<init>(Location.java:75)
>        at org.biojava3.genome.parsers.gff.Location.union(Location.java:258)
>        at
> org.biojava3.genome.parsers.gff.FeatureList.add(FeatureList.java:49)
>        at
> org.biojava3.genome.parsers.gff.GFF3Reader.read(GFF3Reader.java:59)
>        at GFFReader3.main(GFFReader3.java:11)
>
> I find this very strange because the file is a valid GFF document according
> to
> http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online
>
> Is this a bug or am I doing something wrong?
> Thanks for your help, I wish you a happy New Year!
>
> Philipp
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>