From biojava at hannes.oib.com  Thu Jan  5 01:32:11 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 5 Jan 2012 07:32:11 +0100
Subject: [Biojava-l] BioJava in education
In-Reply-To: <BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>
Message-ID: <CAPXi2mk1bTUe_faYvkGinmnmKQS5entQb0CFgxzngEiEcWJ32A@mail.gmail.com>

I am considering creating a course/presentation series for our
bioinformatics program at the Upper Austria University of Applied
Sciences - presenting various bioinformatics libraries (bioperl,
biopython, biojava...) so any material would be welcome!

Hannes

On Mon, Nov 7, 2011 at 15:48, Amr AL-Hossary <amr_alhossary at hotmail.com> wrote:
> Sorry for the late reply.
> Although I come into it on my own, I had the interest to voluntarily teach
> it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
> I focused on BioJava 1.7 and I May send you the presentation if you like.
> Unfortunately, this department was closed after 2 successive intakes, so I
> didn't update it.
>
>
> Amr
>
> --------------------------------------------------
> From: "Andreas Prlic" <andreas at sdsc.edu>
> Sent: Friday, November 04, 2011 8:21 AM
> To: "Biojava" <biojava-l at lists.open-bio.org>
> Subject: [Biojava-l] BioJava in education
>
>> Hi,
>>
>> Is anybody using BioJava in teaching, or has been introduced to
>> BioJava as part of a course?
>>
>> Andreas
>> _______________________________________________
>> 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 jw12 at sanger.ac.uk  Thu Jan  5 08:44:26 2012
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 5 Jan 2012 13:44:26 +0000
Subject: [Biojava-l] Registrations for DAS Workshop 2012
Message-ID: <3637D8C0-AF24-4D42-90E8-85346C5F706D@sanger.ac.uk>

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Learn of and contribute to current developments in DAS such as: DAS in  
the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative  
annotation projects, DAS alternative formats.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes  
10 February 2012 - 12:00.

If you are interested in giving a 15 minute talk on the second day  
please email Jonathan Warren using jonathan.warren at sanger.ac.uk

Many thanks

The Sanger/EBI DAS team.


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jdr0887 at renci.org  Fri Jan  6 14:11:13 2012
From: jdr0887 at renci.org (Jason)
Date: Fri, 6 Jan 2012 14:11:13 -0500
Subject: [Biojava-l] trim adapter segment
Message-ID: <4F074751.5050803@renci.org>

Hi all,

I am new to BioJava...how would I go about trimming adapter segments?

Thanks,
Jason

From biojava at hannes.oib.com  Mon Jan  9 02:54:49 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Mon, 9 Jan 2012 08:54:49 +0100
Subject: [Biojava-l] trim adapter segment
In-Reply-To: <4F074751.5050803@renci.org>
References: <4F074751.5050803@renci.org>
Message-ID: <CAPXi2mnfTDAZEDXPCXJa1ti-bbP+gV5W3eCPE+r6_T7DTdzx6A@mail.gmail.com>

Hi!

On Fri, Jan 6, 2012 at 20:11, Jason <jdr0887 at renci.org> wrote:

> I am new to BioJava...how would I go about trimming adapter segments?

Could you give a more verbose example? I do not know what you are talking about.

Hannes

From biojava at hannes.oib.com  Wed Jan 11 09:28:55 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 11 Jan 2012 15:28:55 +0100
Subject: [Biojava-l] FASTA Header Parser
Message-ID: <CAPXi2mnn=Pt8t5R38EYSorJgfo-oUFCkgW1eyu1qM_Vy9qZYWQ@mail.gmail.com>

Hi there -

I just came across a puzzling "feature" of the GenericFastaHeaderParser.
It seems to throw away everything in the header after (and including) "length="
(see GenericFastaHeaderParser.java lines 71-76)

... Why?

Also, is there a Fasta Header Parser I can use that does not mess
about with the header?

I really would like to have that as key (still working on my
FASTA/QUAL parsing) and not having that (only in the originalHeader,
not in the Hashmap key) really breaks stuff.

Hannes

From biojava at hannes.oib.com  Wed Jan 11 09:45:54 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 11 Jan 2012 15:45:54 +0100
Subject: [Biojava-l] FASTA Header Parser
In-Reply-To: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>
References: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>
Message-ID: <CAPXi2mkt=WNUq8Fo9bUq4sgtZJ=w8vTUDx3k04gXD0jJgPrBBg@mail.gmail.com>

nope, the header is in the hashmap in total, except for everything
after length= -- there are whitespaces before that and these are still
left in the header that is used as key.

either make it work like you say or even better, leave the header as-is.

I need to quickly find the sequence, I don't want to iterate over all
my 35k sequences and look up the original headers.

Hannes

On Wed, Jan 11, 2012 at 15:38, Scooter Willis <HWillis at scripps.edu> wrote:
> It should parse until the first space as the unique id. Lots of extra info
> gets added in to the header. You should find a getOriginalHeader method that
> will preserve to contents of the header. I use this when writing the
> sequences back to disk to restore the original header.
>
> You can also do your own custom header parser which we use to support the
> known different fasta headers. If you have extra information in the header
> you can formally associate that with the sequence at the time of the parse.
> We can also add support for your header if it is standard ouput from a
> device.
>
> Thanks
>
> Scooter
>
>
> ----- Reply message -----
> From: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> To: "biojava-l" <biojava-l at lists.open-bio.org>
> Subject: [Biojava-l] FASTA Header Parser
> Date: Wed, Jan 11, 2012 9:30 am
>
>
>
> Hi there -
>
> I just came across a puzzling "feature" of the GenericFastaHeaderParser.
> It seems to throw away everything in the header after (and including)
> "length="
> (see GenericFastaHeaderParser.java lines 71-76)
>
> ... Why?
>
> Also, is there a Fasta Header Parser I can use that does not mess
> about with the header?
>
> I really would like to have that as key (still working on my
> FASTA/QUAL parsing) and not having that (only in the originalHeader,
> not in the Hashmap key) really breaks stuff.
>
> Hannes
> _______________________________________________
> Biojava-l mailing list? -? Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From HWillis at scripps.edu  Wed Jan 11 09:38:21 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Wed, 11 Jan 2012 09:38:21 -0500
Subject: [Biojava-l] FASTA Header Parser
Message-ID: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>

It should parse until the first space as the unique id. Lots of extra info gets added in to the header. You should find a getOriginalHeader method that will preserve to contents of the header. I use this when writing the sequences back to disk to restore the original header.

You can also do your own custom header parser which we use to support the known different fasta headers. If you have extra information in the header you can formally associate that with the sequence at the time of the parse. We can also add support for your header if it is standard ouput from a device.

Thanks

Scooter

----- Reply message -----
From: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
To: "biojava-l" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] FASTA Header Parser
Date: Wed, Jan 11, 2012 9:30 am



Hi there -

I just came across a puzzling "feature" of the GenericFastaHeaderParser.
It seems to throw away everything in the header after (and including) "length="
(see GenericFastaHeaderParser.java lines 71-76)

... Why?

Also, is there a Fasta Header Parser I can use that does not mess
about with the header?

I really would like to have that as key (still working on my
FASTA/QUAL parsing) and not having that (only in the originalHeader,
not in the Hashmap key) really breaks stuff.

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


From mictadlo at gmail.com  Mon Jan 16 01:24:28 2012
From: mictadlo at gmail.com (Mic)
Date: Mon, 16 Jan 2012 16:24:28 +1000
Subject: [Biojava-l] Unique reads
Message-ID: <CAOP6n=hkwDqveq5_WBDP4Go9M4hxYDQQieFiMXcNUyvAgFV7Ng@mail.gmail.com>

Hello,
I read in many papers that they made unique reads before the reads
were align and later on the SNPs were called. However, I could not find out
how they do it.

Which tool can be used to do it?

Thank you in advance.

From mictadlo at gmail.com  Mon Jan 16 08:01:56 2012
From: mictadlo at gmail.com (Mic)
Date: Mon, 16 Jan 2012 23:01:56 +1000
Subject: [Biojava-l] compare sequences
Message-ID: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>

Hello,
Is there anyway a memory efficient way to  compare  sequences like from NGS?

Thank you in advance.

From p.j.a.cock at googlemail.com  Mon Jan 16 08:30:01 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 16 Jan 2012 13:30:01 +0000
Subject: [Biojava-l] compare sequences
In-Reply-To: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>
References: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Cj+DQY8OdCoPYnWH1JU_73xpW++hcp5KoLrGexfbZqQ@mail.gmail.com>

On Mon, Jan 16, 2012 at 1:01 PM, Mic <mictadlo at gmail.com> wrote:
> Hello,
> Is there anyway a?memory?efficient?way to ?compare ?sequences like from NGS?
>
> Thank you in advance.

Hi Mic,

Could you stop posting such broad questions to multiple mailing
lists simultaneously please? Perhaps you would find Biostars
Q&A more useful? http://biostar.stackexchange.com/

See also: http://dx.doi.org/10.1371/journal.pcbi.1002202

Peter


From mictadlo at gmail.com  Tue Jan 24 03:37:02 2012
From: mictadlo at gmail.com (Mic)
Date: Tue, 24 Jan 2012 18:37:02 +1000
Subject: [Biojava-l] Fastq benchmark
Message-ID: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>

Hello,
I have found the following benchmark (
http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-a-huge-fastq-file/11279#11279
)
and I just wonder whether it is possible to make Java example even faster?

Thank you in advance.

From HWillis at scripps.edu  Tue Jan 24 07:08:22 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 24 Jan 2012 07:08:22 -0500
Subject: [Biojava-l] Fastq benchmark
In-Reply-To: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>
Message-ID: <CB4407F2.129AE%hwillis@scripps.edu>

You can try a FASTA version of the file to measure performance gain.

File file = new File("filename");
Boolean  lazySequenceLoad = true;

LinkedHashMap<String, DNASequence> sequences =
FastaReaderHelper.readFastaDNASequence(file,lazySequenceLoad);

This will go through and index the accession id and not load any sequence
data which means no memory allocation and speed. You can then reference
the DNASequence by name and when you need the sequence data it will use
the file index to load the sequence data from the file for that specific
sequence. The same approach can be applied to FASTQ files.

Scooter

On 1/24/12 3:37 AM, "Mic" <mictadlo at gmail.com> wrote:

>Hello,
>I have found the following benchmark (
>http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-
>a-huge-fastq-file/11279#11279
>)
>and I just wonder whether it is possible to make Java example even faster?
>
>Thank you in advance.
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l



From heuermh at gmail.com  Tue Jan 24 13:00:58 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Tue, 24 Jan 2012 12:00:58 -0600
Subject: [Biojava-l] Fastq benchmark
In-Reply-To: <CB4407F2.129AE%hwillis@scripps.edu>
References: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>
	<CB4407F2.129AE%hwillis@scripps.edu>
Message-ID: <CAOjYwMwYJnmA_eZY7BUfGLAvGWCYnj8mKBssn5J3+vPVo3y9oA@mail.gmail.com>

Hello Mic,

That is an interesting benchmark, and you could probably squeeze a bit
more performance out of fqextract.java by tweaking the data structures
(e.g. provide expected size to the HashMap constructor, use
ImmutableMap from Guava, etc.).

Using bioperl, biopython, bioruby, or biojava for this task will be
much slower than just spitting out lines from a file since they are
all validating the FASTQ format against the specification.

   michael


On Tue, Jan 24, 2012 at 6:08 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> You can try a FASTA version of the file to measure performance gain.
>
> File file = new File("filename");
> Boolean ?lazySequenceLoad = true;
>
> LinkedHashMap<String, DNASequence> sequences =
> FastaReaderHelper.readFastaDNASequence(file,lazySequenceLoad);
>
> This will go through and index the accession id and not load any sequence
> data which means no memory allocation and speed. You can then reference
> the DNASequence by name and when you need the sequence data it will use
> the file index to load the sequence data from the file for that specific
> sequence. The same approach can be applied to FASTQ files.
>
> Scooter
>
> On 1/24/12 3:37 AM, "Mic" <mictadlo at gmail.com> wrote:
>
>>Hello,
>>I have found the following benchmark (
>>http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-
>>a-huge-fastq-file/11279#11279
>>)
>>and I just wonder whether it is possible to make Java example even faster?
>>
>>Thank you in advance.


From biojava at hannes.oib.com  Thu Jan  5 06:32:11 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 5 Jan 2012 07:32:11 +0100
Subject: [Biojava-l] BioJava in education
In-Reply-To: <BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>
Message-ID: <CAPXi2mk1bTUe_faYvkGinmnmKQS5entQb0CFgxzngEiEcWJ32A@mail.gmail.com>

I am considering creating a course/presentation series for our
bioinformatics program at the Upper Austria University of Applied
Sciences - presenting various bioinformatics libraries (bioperl,
biopython, biojava...) so any material would be welcome!

Hannes

On Mon, Nov 7, 2011 at 15:48, Amr AL-Hossary <amr_alhossary at hotmail.com> wrote:
> Sorry for the late reply.
> Although I come into it on my own, I had the interest to voluntarily teach
> it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
> I focused on BioJava 1.7 and I May send you the presentation if you like.
> Unfortunately, this department was closed after 2 successive intakes, so I
> didn't update it.
>
>
> Amr
>
> --------------------------------------------------
> From: "Andreas Prlic" <andreas at sdsc.edu>
> Sent: Friday, November 04, 2011 8:21 AM
> To: "Biojava" <biojava-l at lists.open-bio.org>
> Subject: [Biojava-l] BioJava in education
>
>> Hi,
>>
>> Is anybody using BioJava in teaching, or has been introduced to
>> BioJava as part of a course?
>>
>> Andreas
>> _______________________________________________
>> 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 jw12 at sanger.ac.uk  Thu Jan  5 13:44:26 2012
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 5 Jan 2012 13:44:26 +0000
Subject: [Biojava-l] Registrations for DAS Workshop 2012
Message-ID: <3637D8C0-AF24-4D42-90E8-85346C5F706D@sanger.ac.uk>

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Learn of and contribute to current developments in DAS such as: DAS in  
the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative  
annotation projects, DAS alternative formats.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes  
10 February 2012 - 12:00.

If you are interested in giving a 15 minute talk on the second day  
please email Jonathan Warren using jonathan.warren at sanger.ac.uk

Many thanks

The Sanger/EBI DAS team.


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jdr0887 at renci.org  Fri Jan  6 19:11:13 2012
From: jdr0887 at renci.org (Jason)
Date: Fri, 6 Jan 2012 14:11:13 -0500
Subject: [Biojava-l] trim adapter segment
Message-ID: <4F074751.5050803@renci.org>

Hi all,

I am new to BioJava...how would I go about trimming adapter segments?

Thanks,
Jason


From biojava at hannes.oib.com  Mon Jan  9 07:54:49 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Mon, 9 Jan 2012 08:54:49 +0100
Subject: [Biojava-l] trim adapter segment
In-Reply-To: <4F074751.5050803@renci.org>
References: <4F074751.5050803@renci.org>
Message-ID: <CAPXi2mnfTDAZEDXPCXJa1ti-bbP+gV5W3eCPE+r6_T7DTdzx6A@mail.gmail.com>

Hi!

On Fri, Jan 6, 2012 at 20:11, Jason <jdr0887 at renci.org> wrote:

> I am new to BioJava...how would I go about trimming adapter segments?

Could you give a more verbose example? I do not know what you are talking about.

Hannes


From biojava at hannes.oib.com  Wed Jan 11 14:28:55 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 11 Jan 2012 15:28:55 +0100
Subject: [Biojava-l] FASTA Header Parser
Message-ID: <CAPXi2mnn=Pt8t5R38EYSorJgfo-oUFCkgW1eyu1qM_Vy9qZYWQ@mail.gmail.com>

Hi there -

I just came across a puzzling "feature" of the GenericFastaHeaderParser.
It seems to throw away everything in the header after (and including) "length="
(see GenericFastaHeaderParser.java lines 71-76)

... Why?

Also, is there a Fasta Header Parser I can use that does not mess
about with the header?

I really would like to have that as key (still working on my
FASTA/QUAL parsing) and not having that (only in the originalHeader,
not in the Hashmap key) really breaks stuff.

Hannes


From biojava at hannes.oib.com  Wed Jan 11 14:45:54 2012
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 11 Jan 2012 15:45:54 +0100
Subject: [Biojava-l] FASTA Header Parser
In-Reply-To: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>
References: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>
Message-ID: <CAPXi2mkt=WNUq8Fo9bUq4sgtZJ=w8vTUDx3k04gXD0jJgPrBBg@mail.gmail.com>

nope, the header is in the hashmap in total, except for everything
after length= -- there are whitespaces before that and these are still
left in the header that is used as key.

either make it work like you say or even better, leave the header as-is.

I need to quickly find the sequence, I don't want to iterate over all
my 35k sequences and look up the original headers.

Hannes

On Wed, Jan 11, 2012 at 15:38, Scooter Willis <HWillis at scripps.edu> wrote:
> It should parse until the first space as the unique id. Lots of extra info
> gets added in to the header. You should find a getOriginalHeader method that
> will preserve to contents of the header. I use this when writing the
> sequences back to disk to restore the original header.
>
> You can also do your own custom header parser which we use to support the
> known different fasta headers. If you have extra information in the header
> you can formally associate that with the sequence at the time of the parse.
> We can also add support for your header if it is standard ouput from a
> device.
>
> Thanks
>
> Scooter
>
>
> ----- Reply message -----
> From: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
> To: "biojava-l" <biojava-l at lists.open-bio.org>
> Subject: [Biojava-l] FASTA Header Parser
> Date: Wed, Jan 11, 2012 9:30 am
>
>
>
> Hi there -
>
> I just came across a puzzling "feature" of the GenericFastaHeaderParser.
> It seems to throw away everything in the header after (and including)
> "length="
> (see GenericFastaHeaderParser.java lines 71-76)
>
> ... Why?
>
> Also, is there a Fasta Header Parser I can use that does not mess
> about with the header?
>
> I really would like to have that as key (still working on my
> FASTA/QUAL parsing) and not having that (only in the originalHeader,
> not in the Hashmap key) really breaks stuff.
>
> Hannes
> _______________________________________________
> Biojava-l mailing list? -? Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From HWillis at scripps.edu  Wed Jan 11 14:38:21 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Wed, 11 Jan 2012 09:38:21 -0500
Subject: [Biojava-l] FASTA Header Parser
Message-ID: <ECC85847-4319-4BB3-B3C4-415812C978F7@scripps.edu>

It should parse until the first space as the unique id. Lots of extra info gets added in to the header. You should find a getOriginalHeader method that will preserve to contents of the header. I use this when writing the sequences back to disk to restore the original header.

You can also do your own custom header parser which we use to support the known different fasta headers. If you have extra information in the header you can formally associate that with the sequence at the time of the parse. We can also add support for your header if it is standard ouput from a device.

Thanks

Scooter

----- Reply message -----
From: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
To: "biojava-l" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] FASTA Header Parser
Date: Wed, Jan 11, 2012 9:30 am



Hi there -

I just came across a puzzling "feature" of the GenericFastaHeaderParser.
It seems to throw away everything in the header after (and including) "length="
(see GenericFastaHeaderParser.java lines 71-76)

... Why?

Also, is there a Fasta Header Parser I can use that does not mess
about with the header?

I really would like to have that as key (still working on my
FASTA/QUAL parsing) and not having that (only in the originalHeader,
not in the Hashmap key) really breaks stuff.

Hannes
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From mictadlo at gmail.com  Mon Jan 16 06:24:28 2012
From: mictadlo at gmail.com (Mic)
Date: Mon, 16 Jan 2012 16:24:28 +1000
Subject: [Biojava-l] Unique reads
Message-ID: <CAOP6n=hkwDqveq5_WBDP4Go9M4hxYDQQieFiMXcNUyvAgFV7Ng@mail.gmail.com>

Hello,
I read in many papers that they made unique reads before the reads
were align and later on the SNPs were called. However, I could not find out
how they do it.

Which tool can be used to do it?

Thank you in advance.


From mictadlo at gmail.com  Mon Jan 16 13:01:56 2012
From: mictadlo at gmail.com (Mic)
Date: Mon, 16 Jan 2012 23:01:56 +1000
Subject: [Biojava-l] compare sequences
Message-ID: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>

Hello,
Is there anyway a memory efficient way to  compare  sequences like from NGS?

Thank you in advance.


From p.j.a.cock at googlemail.com  Mon Jan 16 13:30:01 2012
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 16 Jan 2012 13:30:01 +0000
Subject: [Biojava-l] compare sequences
In-Reply-To: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>
References: <CAOP6n=hFnz_6hPC+D8m_p+QLizc_-hngNCh5OUgj8hEUQ6vf7Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Cj+DQY8OdCoPYnWH1JU_73xpW++hcp5KoLrGexfbZqQ@mail.gmail.com>

On Mon, Jan 16, 2012 at 1:01 PM, Mic <mictadlo at gmail.com> wrote:
> Hello,
> Is there anyway a?memory?efficient?way to ?compare ?sequences like from NGS?
>
> Thank you in advance.

Hi Mic,

Could you stop posting such broad questions to multiple mailing
lists simultaneously please? Perhaps you would find Biostars
Q&A more useful? http://biostar.stackexchange.com/

See also: http://dx.doi.org/10.1371/journal.pcbi.1002202

Peter



From mictadlo at gmail.com  Tue Jan 24 08:37:02 2012
From: mictadlo at gmail.com (Mic)
Date: Tue, 24 Jan 2012 18:37:02 +1000
Subject: [Biojava-l] Fastq benchmark
Message-ID: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>

Hello,
I have found the following benchmark (
http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-a-huge-fastq-file/11279#11279
)
and I just wonder whether it is possible to make Java example even faster?

Thank you in advance.


From HWillis at scripps.edu  Tue Jan 24 12:08:22 2012
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 24 Jan 2012 07:08:22 -0500
Subject: [Biojava-l] Fastq benchmark
In-Reply-To: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>
Message-ID: <CB4407F2.129AE%hwillis@scripps.edu>

You can try a FASTA version of the file to measure performance gain.

File file = new File("filename");
Boolean  lazySequenceLoad = true;

LinkedHashMap<String, DNASequence> sequences =
FastaReaderHelper.readFastaDNASequence(file,lazySequenceLoad);

This will go through and index the accession id and not load any sequence
data which means no memory allocation and speed. You can then reference
the DNASequence by name and when you need the sequence data it will use
the file index to load the sequence data from the file for that specific
sequence. The same approach can be applied to FASTQ files.

Scooter

On 1/24/12 3:37 AM, "Mic" <mictadlo at gmail.com> wrote:

>Hello,
>I have found the following benchmark (
>http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-
>a-huge-fastq-file/11279#11279
>)
>and I just wonder whether it is possible to make Java example even faster?
>
>Thank you in advance.
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/biojava-l




From heuermh at gmail.com  Tue Jan 24 18:00:58 2012
From: heuermh at gmail.com (Michael Heuer)
Date: Tue, 24 Jan 2012 12:00:58 -0600
Subject: [Biojava-l] Fastq benchmark
In-Reply-To: <CB4407F2.129AE%hwillis@scripps.edu>
References: <CAOP6n=gr4SFrPHaWxqRdFXMHEOdkM4yf+zrbyPs3dgUxsRcBxg@mail.gmail.com>
	<CB4407F2.129AE%hwillis@scripps.edu>
Message-ID: <CAOjYwMwYJnmA_eZY7BUfGLAvGWCYnj8mKBssn5J3+vPVo3y9oA@mail.gmail.com>

Hello Mic,

That is an interesting benchmark, and you could probably squeeze a bit
more performance out of fqextract.java by tweaking the data structures
(e.g. provide expected size to the HashMap constructor, use
ImmutableMap from Guava, etc.).

Using bioperl, biopython, bioruby, or biojava for this task will be
much slower than just spitting out lines from a file since they are
all validating the FASTQ format against the specification.

   michael


On Tue, Jan 24, 2012 at 6:08 AM, Scooter Willis <HWillis at scripps.edu> wrote:
> You can try a FASTA version of the file to measure performance gain.
>
> File file = new File("filename");
> Boolean ?lazySequenceLoad = true;
>
> LinkedHashMap<String, DNASequence> sequences =
> FastaReaderHelper.readFastaDNASequence(file,lazySequenceLoad);
>
> This will go through and index the accession id and not load any sequence
> data which means no memory allocation and speed. You can then reference
> the DNASequence by name and when you need the sequence data it will use
> the file index to load the sequence data from the file for that specific
> sequence. The same approach can be applied to FASTQ files.
>
> Scooter
>
> On 1/24/12 3:37 AM, "Mic" <mictadlo at gmail.com> wrote:
>
>>Hello,
>>I have found the following benchmark (
>>http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-
>>a-huge-fastq-file/11279#11279
>>)
>>and I just wonder whether it is possible to make Java example even faster?
>>
>>Thank you in advance.