gmane.comp.java.bio.general

Re: reading genbank data

Hannes Brandstätter-Müller — 2013-05-24T07:09:05

I still need to finish up the last task (unfortunately I'm a bit short on
spare time currently) but I guess since it's parsing, I could work on
that...

Hannes


On Fri, May 24, 2013 at 7:36 AM, Andreas Prlic <andreas< at >sdsc.edu> wrote:


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Re: reading genbank data

Andreas Prlic — 2013-05-24T05:36:10

Hi Hannes,

would you be interested in taking this one on?

Thanks,

Andreas


On Thu, May 23, 2013 at 1:14 PM, Hannes Brandstätter-Müller <
biojava< at >hannes.oib.com> wrote:


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Re: reading genbank data

Hannes Brandstätter-Müller — 2013-05-23T20:14:39

Well, it doesn't look like that was ported to biojava 3 yet.

We'll add that to the todo list…


On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber< at >gmail.com> wrote:


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reading genbank data

Ben Bimber — 2013-05-23T18:53:48

Hello,

To date, I have used BioJava3 for very limited work such as read/writing
FASTA files.  I am trying to determine the best method to read and parse
sequence in genbank format using java.  As far as i can tell, legacy
BioJava has classes to support this (RichSequence.IOTools); however, I do
not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
have support for parsing genbank files?

Thanks in advance for any help.

-Ben
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Re: help with fastq

Hannes Brandstätter-Müller — 2013-05-16T18:45:48

Can you show some code, so we can see where the problem is?


On Thu, May 16, 2013 at 3:51 PM, Janier J. Ramírez <
jjramirez< at >estudiantes.uci.cu> wrote:


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help with fastq

Janier J. Ramírez — 2013-05-16T13:51:52

Hi again comunity !

I need this time generate a Fastq file from many fasta files, using illumina scores (one default value).
I ´ve tried this but am having a problem wthis the header and the identifier of the file.
makes Biojava this work ?

greetings

Janier

Re: [Bioperl-l] Workshop on Sustainable Software for Science: Practice and Experiences

Peter Cock — 2013-05-16T09:10:25

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields< at >illinois.edu> wrote:

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter
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Re: Workshop on Sustainable Software for Science: Practice and Experiences

Andreas Prlic — 2013-05-16T04:31:34

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp< at >drycafe.net> wrote:

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Re: File formats parser

Peter Cock — 2013-05-13T16:17:56

On Mon, May 13, 2013 at 3:21 PM, Janier J. Ramírez
<jjramirez< at >estudiantes.uci.cu> wrote:

I'm not sure what exactly is in BioJava for these formats, but I would
suggest you (also) consider Picard for working with SAM/BAM in Java.

Peter

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File formats parser

Janier J. Ramírez — 2013-05-13T14:21:38

There is in Biojava a parser for some of the next file formats ?? :
.sam
.bam
.gig
.ace 


thanks in advance

Re: Getting reverse complement

Hannes Brandstätter-Müller — 2013-05-08T04:21:33

I missed posting my answer to the list too.


Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ramírez :


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Getting reverse complement

Janier J. Ramírez — 2013-05-08T03:51:33

I'm triyng to get the reverse complement from a sequence with gaps (represented as ':'), but biojava thow an IllegalSymbolException, is this a bug or what is the symbol to represent gaps in biojava ?

Here is the error.


org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: ':'
at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
at org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)


Greetings

Janier

Re: AMOScmp problem

Michael Heuer — 2013-05-07T20:43:10

Hello Spencer, Janier

I suppose there will be a biojava-legacy 1.8.3 release as soon as we figure
out the configuration changes necessary to support the release process due
to the svn --> github switch.

   michael


On Tue, May 7, 2013 at 3:27 PM, Spencer Bliven <sbliven< at >ucsd.edu> wrote:


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Re: AMOScmp problem

Spencer Bliven — 2013-05-07T20:27:22

Janier,

Biojava 1 is only receiving bug fixes currently. There are a couple changes
since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
maven repository. There is no release date for 3.0.6 yet, but again you can
use the latest SNAPSHOT from maven if you need new features.


-Spencer


On Tue, May 7, 2013 at 12:31 PM, Janier J. Ramírez <
jjramirez< at >estudiantes.uci.cu> wrote:


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Re: AMOScmp problem

Spencer Bliven — 2013-05-07T19:00:44

Hey Janier,

Sorry no one responded to your last question. Biojava doesn't currently do
full-blown assembly, although the basic pairwise alignment algorithms are
there.

I've never used AMOScmp myself, and so can't advise you on your problem.

-Spencer


On Mon, May 6, 2013 at 6:41 PM, Janier J. Ramírez <
jjramirez< at >estudiantes.uci.cu> wrote:


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AMOScmp problem

Janier J. Ramírez — 2013-05-07T01:41:45

Hi !
I'm interested in the reference based assemblies using AMOScmp, I used tarchive2Amos to obtain the .afg file an I have the reference (.fasta file), but the problem is that the output files (.fasta and .contig) are empty. In the log files there is a WARNING which says that the file FRG.ifo was not found and could not retrieve mate pairs information.
This is very important to me and won't have many time for that.

Please any sugestion for this proble ?

Thanks in advance

Genome Assembly

Janier J. Ramírez — 2013-04-24T18:24:44

Hi !

I´m trying to assemble multiple reads using one as Reference, is this possile using Biojava ?

Greetings


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Today's Topics:

   1. Re: DNA assembly (Chris Friedline)


----------------------------------------------------------------------

Message: 1
Date: Wed, 24 Apr 2013 10:58:22 -0400
From: Chris Friedline <cfriedline< at >vcu.edu>
Subje

Re: DNA assembly

Khalil El Mazouari — 2013-04-24T16:02:36

Hi,

I will combine local alignment + http://biojava.org/wiki/BioJava:CookBook:Core:SequenceCompare . I think this will do the job.

Thanks for your help

khalil




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On 24 Apr 2013, at 16:58, Chris Friedline wrote:



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Re: DNA assembly

Chris Friedline — 2013-04-24T14:58:22

There's also a good deal of alignment quality checking, thresholding, and scoring the overlapping region that is both necessary and but maybe not all that straightforward.  I suggest that you check out the PANDAseq paper, which describes their algorithm.

http://dx.doi.org/10.1186/1471-2105-13-31

Andreas is correct - the basic building blocks are already there.

Chris

On Apr 24, 2013, at 10:48 AM, Andreas Prlic <andreas< at >sdsc.edu> wrote:




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Re: DNA assembly

Andreas Prlic — 2013-04-24T14:48:01

It sounds like as all you need is to get the reverse complement of one of
your sequences and then you do a local alignment. Both should be possible
with BioJava...

Andreas


On Wed, Apr 24, 2013 at 7:29 AM, Khalil El Mazouari <
khalil.elmazouari< at >gmail.com> wrote:

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Re: DNA assembly

Khalil El Mazouari — 2013-04-24T14:29:24

Hi Chris,

my application is deployed as war file. I am trying to avoid, as much as possible, to shell out to other none java programs... for maintainability reasons.

I don't think I need a 'full' genome assembly tools (eg velvet ...), it's overkill for my case: cloned gene is sequenced on both directions. Normally one strand is sufficient. If the sequence quality is not good enough, the 2 strands are used to get the full length gene. There is always a large overlap between the 2 strand sequence. 
I can QC the full length gene.

Best

khalil







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