From jjramirez at estudiantes.uci.cu  Mon Apr  1 10:58:22 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 01 Apr 2013 10:58:22 -0400 (EDT)
Subject: [Biojava-l] Phred Quality Scores and .qual format
In-Reply-To: <CAPXi2mmoc4q7Bb3bXgqeFCOuT0nxP0=j3dPO0RLz+wHcpHLjBA@mail.gmail.com>
Message-ID: <0ed6d39c-4601-4064-8ed0-1b2dea6d9b33@ucimail4.uci.cu>

Thanks for reply

Yes I know it, I'm using Biojava 1.X to read SCF files, but many of my SCF files can't be read by Biojava.
And my other problem is that I need to obtain the Phred Quality Scores from Abi an Scf files, and I don't know how to do this.

Please Help

Thanks



----- Mensaje original -----
De: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
CC: "biojava-l" <biojava-l at lists.open-bio.org>
Enviados: Viernes, 29 de Marzo 2013 7:52:41
Asunto: Re: [Biojava-l] Phred Quality Scores and .qual format


SCF can currently only be read in biojava-legacy. 
I am planning to port the code to BioJave 3 after the switch to git (i.e. next month) 
Until then, I think there are legacy-cookbook examples on how to read scf files. 


Hannes 



On Fri, Mar 29, 2013 at 5:48 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu > wrote: 


Hi guys ! 

I'm investigating for the whole genome assembly using AMOS Project. 

I need to obtain the Phred Quality Scores from Abi an Scf files, to then buil a .qual file, but my dude is obtaining the Scores, I have tried many time but I can't reach it !. 

Sorry for my English. 

Thanks for your time 


-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu 

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


From sbliven at ucsd.edu  Wed Apr  3 19:32:09 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 3 Apr 2013 16:32:09 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
Message-ID: <CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>

The transition to Github is now finished, although we're still working on
getting the documentation up-to-date. If you're currently using a checkout
of trunk from SVN, that checkout will still work but will not receive any
future updates. Please follow the instructions at
http://biojava.org/wiki/Get_source to get a copy of the latest source from
git.

The documentation is rather confusing at the moment, with references to the
old SVN interspersed with recent git instructions. If you run into such a
situation on the wiki, please fix it or mark the article with the
{{outdated}} template so we can get the documentation back up to par.

Thanks!
Spencer


On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Dear community,
>
> On the developer list we have been discussing moving the biojava code to
> github for some time. This transition is currently scheduled to occur this
> weekend. For users who get Biojava via binary jars or maven, this will have
> no effect on your projects. Users who compile the latest version of the
> source themselves may have to get a fresh version from github after April 1:
>
> biojava 3: https://github.com/biojava/biojava
> biojava 1: https://github.com/biojava/biojava-legacy
>
> I'll be working on improving documentation for the transition this week.
> For those interested in the migration process, see
> http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> using git with eclipse is at
> http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And
> http://biojava.org/wiki/Get_source will soon be updated with the new
> instructions for getting the latest source code from git.
>
> Please let me know if anyone has suggestions or concerns.
>
> -Spencer
>

From andreas at sdsc.edu  Wed Apr  3 20:03:21 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 3 Apr 2013 17:03:21 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
Message-ID: <CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>

Thanks Spencer for all your efforts in getting this set up! I hope that
will make the code base even more accessible and should provide a path of
submitting patches more easily from now on.

Let the social coding begin!

Andreas


On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> The transition to Github is now finished, although we're still working on
> getting the documentation up-to-date. If you're currently using a checkout
> of trunk from SVN, that checkout will still work but will not receive any
> future updates. Please follow the instructions at
> http://biojava.org/wiki/Get_source to get a copy of the latest source from
> git.
>
> The documentation is rather confusing at the moment, with references to the
> old SVN interspersed with recent git instructions. If you run into such a
> situation on the wiki, please fix it or mark the article with the
> {{outdated}} template so we can get the documentation back up to par.
>
> Thanks!
> Spencer
>
>
> On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> > Dear community,
> >
> > On the developer list we have been discussing moving the biojava code to
> > github for some time. This transition is currently scheduled to occur
> this
> > weekend. For users who get Biojava via binary jars or maven, this will
> have
> > no effect on your projects. Users who compile the latest version of the
> > source themselves may have to get a fresh version from github after
> April 1:
> >
> > biojava 3: https://github.com/biojava/biojava
> > biojava 1: https://github.com/biojava/biojava-legacy
> >
> > I'll be working on improving documentation for the transition this week.
> > For those interested in the migration process, see
> > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> > using git with eclipse is at
> > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And
> > http://biojava.org/wiki/Get_source will soon be updated with the new
> > instructions for getting the latest source code from git.
> >
> > Please let me know if anyone has suggestions or concerns.
> >
> > -Spencer
> >
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From phidias51 at gmail.com  Wed Apr  3 20:22:27 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Wed, 3 Apr 2013 17:22:27 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
Message-ID: <CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>

Great job you guys.  I've already spotted some minor things.  If only I
could figure out a way to do a code review without doing a commit. :-)

Cheers,

Mark



On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Spencer for all your efforts in getting this set up! I hope that
> will make the code base even more accessible and should provide a path of
> submitting patches more easily from now on.
>
> Let the social coding begin!
>
> Andreas
>
>
> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> > The transition to Github is now finished, although we're still working on
> > getting the documentation up-to-date. If you're currently using a
> checkout
> > of trunk from SVN, that checkout will still work but will not receive any
> > future updates. Please follow the instructions at
> > http://biojava.org/wiki/Get_source to get a copy of the latest source
> from
> > git.
> >
> > The documentation is rather confusing at the moment, with references to
> the
> > old SVN interspersed with recent git instructions. If you run into such a
> > situation on the wiki, please fix it or mark the article with the
> > {{outdated}} template so we can get the documentation back up to par.
> >
> > Thanks!
> > Spencer
> >
> >
> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
> wrote:
> >
> > > Dear community,
> > >
> > > On the developer list we have been discussing moving the biojava code
> to
> > > github for some time. This transition is currently scheduled to occur
> > this
> > > weekend. For users who get Biojava via binary jars or maven, this will
> > have
> > > no effect on your projects. Users who compile the latest version of the
> > > source themselves may have to get a fresh version from github after
> > April 1:
> > >
> > > biojava 3: https://github.com/biojava/biojava
> > > biojava 1: https://github.com/biojava/biojava-legacy
> > >
> > > I'll be working on improving documentation for the transition this
> week.
> > > For those interested in the migration process, see
> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> > > using git with eclipse is at
> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
> And
> > > http://biojava.org/wiki/Get_source will soon be updated with the new
> > > instructions for getting the latest source code from git.
> > >
> > > Please let me know if anyone has suggestions or concerns.
> > >
> > > -Spencer
> > >
> > _______________________________________________
> > 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 sbliven at ucsd.edu  Thu Apr  4 01:57:59 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 3 Apr 2013 22:57:59 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
Message-ID: <CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>

Mark?

If you commit to your own fork and then create a pull request, it
automatically gives you a place for code review.

You could also open up an issue. https://github.com/biojava/biojava/issues

-Spencer


On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:

> Great job you guys.  I've already spotted some minor things.  If only I
> could figure out a way to do a code review without doing a commit. :-)
>
> Cheers,
>
> Mark
>
>
>
> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Thanks Spencer for all your efforts in getting this set up! I hope that
>> will make the code base even more accessible and should provide a path of
>> submitting patches more easily from now on.
>>
>> Let the social coding begin!
>>
>> Andreas
>>
>>
>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>>
>> > The transition to Github is now finished, although we're still working
>> on
>> > getting the documentation up-to-date. If you're currently using a
>> checkout
>> > of trunk from SVN, that checkout will still work but will not receive
>> any
>> > future updates. Please follow the instructions at
>> > http://biojava.org/wiki/Get_source to get a copy of the latest source
>> from
>> > git.
>> >
>> > The documentation is rather confusing at the moment, with references to
>> the
>> > old SVN interspersed with recent git instructions. If you run into such
>> a
>> > situation on the wiki, please fix it or mark the article with the
>> > {{outdated}} template so we can get the documentation back up to par.
>> >
>> > Thanks!
>> > Spencer
>> >
>> >
>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>> wrote:
>> >
>> > > Dear community,
>> > >
>> > > On the developer list we have been discussing moving the biojava code
>> to
>> > > github for some time. This transition is currently scheduled to occur
>> > this
>> > > weekend. For users who get Biojava via binary jars or maven, this will
>> > have
>> > > no effect on your projects. Users who compile the latest version of
>> the
>> > > source themselves may have to get a fresh version from github after
>> > April 1:
>> > >
>> > > biojava 3: https://github.com/biojava/biojava
>> > > biojava 1: https://github.com/biojava/biojava-legacy
>> > >
>> > > I'll be working on improving documentation for the transition this
>> week.
>> > > For those interested in the migration process, see
>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
>> > > using git with eclipse is at
>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>> And
>> > > http://biojava.org/wiki/Get_source will soon be updated with the new
>> > > instructions for getting the latest source code from git.
>> > >
>> > > Please let me know if anyone has suggestions or concerns.
>> > >
>> > > -Spencer
>> > >
>> > _______________________________________________
>> > 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 phidias51 at gmail.com  Thu Apr  4 02:07:04 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Wed, 3 Apr 2013 23:07:04 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
Message-ID: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>

I was wishing I could just kibitz on some of the code without having to
actually fix it. :-)

Just some odd things I noticed in FastaReader and FastaWriter where the
code contains a main instead of relying on the test case to give you an
example.  And comments that are partial or missing.

Are the checkstyle and findbugs plugins configured to run as part of the
build?

Mark
On Apr 3, 2013 10:58 PM, "Spencer Bliven" <sbliven at ucsd.edu> wrote:

> Mark?
>
> If you commit to your own fork and then create a pull request, it
> automatically gives you a place for code review.
>
> You could also open up an issue. https://github.com/biojava/biojava/issues
>
> -Spencer
>
>
> On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>
>> Great job you guys.  I've already spotted some minor things.  If only I
>> could figure out a way to do a code review without doing a commit. :-)
>>
>> Cheers,
>>
>> Mark
>>
>>
>>
>> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>>> Thanks Spencer for all your efforts in getting this set up! I hope that
>>> will make the code base even more accessible and should provide a path of
>>> submitting patches more easily from now on.
>>>
>>> Let the social coding begin!
>>>
>>> Andreas
>>>
>>>
>>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>>>
>>> > The transition to Github is now finished, although we're still working
>>> on
>>> > getting the documentation up-to-date. If you're currently using a
>>> checkout
>>> > of trunk from SVN, that checkout will still work but will not receive
>>> any
>>> > future updates. Please follow the instructions at
>>> > http://biojava.org/wiki/Get_source to get a copy of the latest source
>>> from
>>> > git.
>>> >
>>> > The documentation is rather confusing at the moment, with references
>>> to the
>>> > old SVN interspersed with recent git instructions. If you run into
>>> such a
>>> > situation on the wiki, please fix it or mark the article with the
>>> > {{outdated}} template so we can get the documentation back up to par.
>>> >
>>> > Thanks!
>>> > Spencer
>>> >
>>> >
>>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>>> wrote:
>>> >
>>> > > Dear community,
>>> > >
>>> > > On the developer list we have been discussing moving the biojava
>>> code to
>>> > > github for some time. This transition is currently scheduled to occur
>>> > this
>>> > > weekend. For users who get Biojava via binary jars or maven, this
>>> will
>>> > have
>>> > > no effect on your projects. Users who compile the latest version of
>>> the
>>> > > source themselves may have to get a fresh version from github after
>>> > April 1:
>>> > >
>>> > > biojava 3: https://github.com/biojava/biojava
>>> > > biojava 1: https://github.com/biojava/biojava-legacy
>>> > >
>>> > > I'll be working on improving documentation for the transition this
>>> week.
>>> > > For those interested in the migration process, see
>>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
>>> > > using git with eclipse is at
>>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>>> And
>>> > > http://biojava.org/wiki/Get_source will soon be updated with the new
>>> > > instructions for getting the latest source code from git.
>>> > >
>>> > > Please let me know if anyone has suggestions or concerns.
>>> > >
>>> > > -Spencer
>>> > >
>>> > _______________________________________________
>>> > 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 biojava at hannes.oib.com  Thu Apr  4 05:50:30 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 4 Apr 2013 11:50:30 +0200
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
Message-ID: <CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>

On Thu, Apr 4, 2013 at 8:07 AM, Mark Fortner <phidias51 at gmail.com> wrote:

> I was wishing I could just kibitz on some of the code without having to
> actually fix it. :-)
>
> Just some odd things I noticed in FastaReader and FastaWriter where the
> code contains a main instead of relying on the test case to give you an
> example.  And comments that are partial or missing.
>
> Are the checkstyle and findbugs plugins configured to run as part of the
> build?
>
> Mark


Last time I looked, I noticed that there were some different code styles
going on. Is that now fixed (and which style are we using? is a formatter
for eclipse checked in somewhere?)

Hannes

From andreas at sdsc.edu  Thu Apr  4 10:54:51 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 07:54:51 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
	<CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>
Message-ID: <CALthepxpZ-j-5b37iFx39+RTCqMXz4YFYJjz_WkRNmtHHBpRbg@mail.gmail.com>

Hi Hannes,

there is an eclipse formatting template available from here:

http://biojava.org/wiki/BioJava3:Coding_Conventions

Andreas


On Thu, Apr 4, 2013 at 2:50 AM, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> On Thu, Apr 4, 2013 at 8:07 AM, Mark Fortner <phidias51 at gmail.com> wrote:
>
> > I was wishing I could just kibitz on some of the code without having to
> > actually fix it. :-)
> >
> > Just some odd things I noticed in FastaReader and FastaWriter where the
> > code contains a main instead of relying on the test case to give you an
> > example.  And comments that are partial or missing.
> >
> > Are the checkstyle and findbugs plugins configured to run as part of the
> > build?
> >
> > Mark
>
>
> Last time I looked, I noticed that there were some different code styles
> going on. Is that now fixed (and which style are we using? is a formatter
> for eclipse checked in somewhere?)
>
> Hannes
> _______________________________________________
> 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  Thu Apr  4 10:56:14 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 07:56:14 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
Message-ID: <CALthepx4RdMPiGeY4cWGb6Luzr6_AYw722-grbV+_JAJd4DzdQ@mail.gmail.com>

Hi Mark,

running checkstyle and findbugs as part of the build is a good idea... I'll
look into that.

Andreas


On Wed, Apr 3, 2013 at 11:07 PM, Mark Fortner <phidias51 at gmail.com> wrote:

> I was wishing I could just kibitz on some of the code without having to
> actually fix it. :-)
>
> Just some odd things I noticed in FastaReader and FastaWriter where the
> code contains a main instead of relying on the test case to give you an
> example.  And comments that are partial or missing.
>
> Are the checkstyle and findbugs plugins configured to run as part of the
> build?
>
> Mark
> On Apr 3, 2013 10:58 PM, "Spencer Bliven" <sbliven at ucsd.edu> wrote:
>
>> Mark?
>>
>> If you commit to your own fork and then create a pull request, it
>> automatically gives you a place for code review.
>>
>> You could also open up an issue.
>> https://github.com/biojava/biojava/issues
>>
>> -Spencer
>>
>>
>> On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>>
>>> Great job you guys.  I've already spotted some minor things.  If only I
>>> could figure out a way to do a code review without doing a commit. :-)
>>>
>>> Cheers,
>>>
>>> Mark
>>>
>>>
>>>
>>> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>
>>>> Thanks Spencer for all your efforts in getting this set up! I hope that
>>>> will make the code base even more accessible and should provide a path
>>>> of
>>>> submitting patches more easily from now on.
>>>>
>>>> Let the social coding begin!
>>>>
>>>> Andreas
>>>>
>>>>
>>>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu>
>>>> wrote:
>>>>
>>>> > The transition to Github is now finished, although we're still
>>>> working on
>>>> > getting the documentation up-to-date. If you're currently using a
>>>> checkout
>>>> > of trunk from SVN, that checkout will still work but will not receive
>>>> any
>>>> > future updates. Please follow the instructions at
>>>> > http://biojava.org/wiki/Get_source to get a copy of the latest
>>>> source from
>>>> > git.
>>>> >
>>>> > The documentation is rather confusing at the moment, with references
>>>> to the
>>>> > old SVN interspersed with recent git instructions. If you run into
>>>> such a
>>>> > situation on the wiki, please fix it or mark the article with the
>>>> > {{outdated}} template so we can get the documentation back up to par.
>>>> >
>>>> > Thanks!
>>>> > Spencer
>>>> >
>>>> >
>>>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>>>> wrote:
>>>> >
>>>> > > Dear community,
>>>> > >
>>>> > > On the developer list we have been discussing moving the biojava
>>>> code to
>>>> > > github for some time. This transition is currently scheduled to
>>>> occur
>>>> > this
>>>> > > weekend. For users who get Biojava via binary jars or maven, this
>>>> will
>>>> > have
>>>> > > no effect on your projects. Users who compile the latest version of
>>>> the
>>>> > > source themselves may have to get a fresh version from github after
>>>> > April 1:
>>>> > >
>>>> > > biojava 3: https://github.com/biojava/biojava
>>>> > > biojava 1: https://github.com/biojava/biojava-legacy
>>>> > >
>>>> > > I'll be working on improving documentation for the transition this
>>>> week.
>>>> > > For those interested in the migration process, see
>>>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information
>>>> about
>>>> > > using git with eclipse is at
>>>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>>>> And
>>>> > > http://biojava.org/wiki/Get_source will soon be updated with the
>>>> new
>>>> > > instructions for getting the latest source code from git.
>>>> > >
>>>> > > Please let me know if anyone has suggestions or concerns.
>>>> > >
>>>> > > -Spencer
>>>> > >
>>>> > _______________________________________________
>>>> > 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 sbliven at ucsd.edu  Fri Apr  5 00:13:46 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Thu, 4 Apr 2013 21:13:46 -0700
Subject: [Biojava-l] Gource Video
Message-ID: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>

I've been staring at the BioJava history so much I thought I'd take a break
and have some fun with it. Here's a video, made with Gource, showing all
the commits to SVN over the current life of BioJava.

http://www.youtube.com/watch?v=hhH9T_JimY0

-Spencer

From andreas at sdsc.edu  Fri Apr  5 00:23:03 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 21:23:03 -0700
Subject: [Biojava-l] Gource Video
In-Reply-To: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
References: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
Message-ID: <CALthepz7vbLoRvay8mG9Ai2sfLbPG3Sv67mB8D-0dYveG8bo2A@mail.gmail.com>

Fun!

Interesting to see how the shape of the project evolves and changes over
time!

Andreas


On Thu, Apr 4, 2013 at 9:13 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> I've been staring at the BioJava history so much I thought I'd take a break
> and have some fun with it. Here's a video, made with Gource, showing all
> the commits to SVN over the current life of BioJava.
>
> http://www.youtube.com/watch?v=hhH9T_JimY0
>
> -Spencer
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From andreas.draeger at uni-tuebingen.de  Mon Apr  8 00:37:32 2013
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Mon, 08 Apr 2013 06:37:32 +0200
Subject: [Biojava-l] Gource Video
In-Reply-To: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
References: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
Message-ID: <5162498C.8050008@uni-tuebingen.de>

Am 4/5/13 6:13 AM, schrieb Spencer Bliven:
> I've been staring at the BioJava history so much I thought I'd take a break
> and have some fun with it. Here's a video, made with Gource, showing all
> the commits to SVN over the current life of BioJava.
>
> http://www.youtube.com/watch?v=hhH9T_JimY0
>
This is really cool. Thanks for doing tis kind of visualization! It is 
incredible, what can be done with SVN history!

-- 
Dr. Andreas Dr?ger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-78982
Fax:   +49-7071-29-5091


From p.j.a.cock at googlemail.com  Tue Apr  9 06:20:43 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:20:43 +0100
Subject: [Biojava-l] OBF not accepted for GSoC 2013
Message-ID: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>

Dear all,

Unfortunately this year we have not been accepted on the Google
Summer of Code scheme:

I'm sure the rest of the OBF board and the other Bio* developers
will join me in thanking Pjotr Prins for his efforts as the OBF
GSoC administrator co-ordinating our application this year, as
well as last year's administrator Rob Bruels and the other mentors
for their efforts.

For those of you not subscribed to the OBF's GSoC mailing list,
I am forwarding Pjotr's email from last night (also below):
http://lists.open-bio.org/pipermail/gsoc/2013/000211.html

In all 177 organisations were accepted (about the same as the
last few years), and they will be listed here (once they have filled
out their profile information):
https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013

To potential students this summer, the good news is that some
related organisations have been accepted, such as NESCent,
the National Resource for Network Biology (NRNB - known for
Cytoscape), SciRuby (Ruby Science Foundation), so there is
still some scope for doing a bioinformatics related project in
GSoC 2013, perhaps even with a Bio* developer as a co-mentor.

Thank you all,

Peter
(Biopython developer, OBF board member)

---------- Forwarded message ----------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: Mon, Apr 8, 2013 at 9:13 PM
Subject: Re: GSoC 2013 is ON
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: ..., OBF GSoC <gsoc at lists.open-bio.org>


Sadly, our application got rejected by GSoC this year. I am not sure
what the reason was, but I am convinced our application was similar to
that of other years. Maybe the project ideas could have been better
presented. I am not sure at this stage. I'll make a list of successful
projects to see if we can digest some truths.

The upside is that FOSS is going strong! And that the field is getting
increasingly competitive. As an open source geezer I can only be
happy, even if it hurts our own application.

Sorry everyone, and many thanks for the trouble you took getting
projects written up. Let's not feel discouraged for next year.

Pj.

From andreas at sdsc.edu  Tue Apr  9 13:11:33 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 9 Apr 2013 10:11:33 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
Message-ID: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>

Hi,

As you probably have seen by now the Open Bioinformatics Foundation's
application for Google Summer of Code 2013 did not get accepted. While this
means we won't be able to sponsor any students this year, this does not
mean we are not going to be active in the coming months. I believe the
current migration to Github has opened us up for a different style of
development and let's focus on extending our community around that.

Andreas

From phidias51 at gmail.com  Tue Apr  9 13:18:12 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Tue, 9 Apr 2013 10:18:12 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
Message-ID: <CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>

Andreas,
Perhaps a hackathon might be a good way to extend the community.

Cheers,

Mark



On Tue, Apr 9, 2013 at 10:11 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi,
>
> As you probably have seen by now the Open Bioinformatics Foundation's
> application for Google Summer of Code 2013 did not get accepted. While this
> means we won't be able to sponsor any students this year, this does not
> mean we are not going to be active in the coming months. I believe the
> current migration to Github has opened us up for a different style of
> development and let's focus on extending our community around that.
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From p.j.a.cock at googlemail.com  Tue Apr  9 14:13:38 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 19:13:38 +0100
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
Message-ID: <CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>

On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
> Andreas,
> Perhaps a hackathon might be a good way to extend the community.
>
> Cheers,
>
> Mark

How about trying to get a good BioJava turn out at the
pre-BOSC 2013 CodeFest then?
http://www.open-bio.org/wiki/Codefest_2013

Peter

From sbliven at ucsd.edu  Tue Apr  9 14:42:23 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 9 Apr 2013 11:42:23 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
Message-ID: <CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>

That would be fun. Is there an additional cost beyond the conference
registration? The website only mentions hotel rates.

-Spencer


On Tue, Apr 9, 2013 at 11:13 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
> > Andreas,
> > Perhaps a hackathon might be a good way to extend the community.
> >
> > Cheers,
> >
> > Mark
>
> How about trying to get a good BioJava turn out at the
> pre-BOSC 2013 CodeFest then?
> http://www.open-bio.org/wiki/Codefest_2013
>
> Peter
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From p.j.a.cock at googlemail.com  Tue Apr  9 14:56:34 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 19:56:34 +0100
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
	<CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
Message-ID: <CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>

> On Tue, Apr 9, 2013 at 11:13 AM, Peter Cock wrote:
>>
>> On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>> >
>> > Andreas,
>> > Perhaps a hackathon might be a good way to extend the community.
>> >
>> > Cheers,
>> >
>> > Mark
>>
>> How about trying to get a good BioJava turn out at the
>> pre-BOSC 2013 CodeFest then?
>> http://www.open-bio.org/wiki/Codefest_2013
>>
>> Peter

On Tue, Apr 9, 2013 at 7:42 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> That would be fun. Is there an additional cost beyond the conference
> registration? The website only mentions hotel rates.
>
> -Spencer

This is quite an informal hackathon - but we do need people to
register to make sure we can cope with the expected numbers.
I've CC'd Brad Chapman who is the main CodeFest 2013 organiser.

There are conference registration fees for BOSC and the main
ISBM/ECCB conference, but *not* for this pre-BOSC CodeFest.
You would have to pay your accommodation, food and travel
costs.

We're hoping and expecting the CodeFest attendees will also
attend BOSC, but this is a not formal requirement. If that is
difficult due to finances, note that for students this year there
are three prizes covering the BOSC fees and money towards
travel, plus if your abstract is accepted you can ask for the
BOSC registration to be waived - see:
http://www.open-bio.org/wiki/BOSC_2013

NOTE: The BOSC abstract submission *DEADLINE* is this Friday!

Having lots of Bio* people together should be good fun :)

Peter

From chapmanb at 50mail.com  Tue Apr  9 20:11:59 2013
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 09 Apr 2013 20:11:59 -0400
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
	<CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
	<CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>
Message-ID: <8738uzmegg.fsf@fastmail.fm>


Spencer, Mark and Peter;

>> That would be fun. Is there an additional cost beyond the conference
>> registration? The website only mentions hotel rates.

http://www.open-bio.org/wiki/Codefest_2013

> This is quite an informal hackathon - but we do need people to
> register to make sure we can cope with the expected numbers.
>
> There are conference registration fees for BOSC and the main
> ISBM/ECCB conference, but *not* for this pre-BOSC CodeFest.
> You would have to pay your accommodation, food and travel
> costs.

+1 to everything Peter said. You are very welcome and there is no cost
to attend. It's two days to discuss, meet other developers, and work on
code together. We're appreciative of everyone who wants to donate
their time to help work on open source projects. Hope you can make it
out,
Brad

From kohchuanhock at gmail.com  Fri Apr 12 10:23:17 2013
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Fri, 12 Apr 2013 14:23:17 +0000 (UTC)
Subject: [Biojava-l] Invitation to connect on LinkedIn
Message-ID: <2018124687.16072581.1365776597303.JavaMail.app@ela4-bed84.prod>

LinkedIn
------------



I'd like to add you to my professional network on LinkedIn.

- Chuan Hock

Chuan Hock Koh
Software Engineer at DeNA
Japan

Confirm that you know Chuan Hock Koh:
https://www.linkedin.com/e/-u6hnvb-hffg4f1b-5w/isd/12422496303/xv1pynGp/?hs=false&tok=12OicutkG_llI1

--
You are receiving Invitation to Connect emails. Click to unsubscribe:
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(c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.


  

From khalil.elmazouari at gmail.com  Tue Apr 23 15:38:54 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Tue, 23 Apr 2013 21:38:54 +0200
Subject: [Biojava-l] DNA assembly
Message-ID: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>

Hi,

I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?

Thanks




-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.





From sbliven at ucsd.edu  Tue Apr 23 17:38:25 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 23 Apr 2013 14:38:25 -0700
Subject: [Biojava-l] DNA assembly
In-Reply-To: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
Message-ID: <CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>

If you just have two contiguous sequences to align, you should just use a
global sequence alignment. See
http://biojava.org/wiki/BioJava:CookBook3:PSAfor how to do this in
BioJava, or it might be easier to just use one of the
online services for this such as http://www.ebi.ac.uk/Tools/psa/.

On the other hand, if you actually want to do genome assembly (ie from many
overlapping reads), then there are much more computationally efficient
methods. BioJava isn't really intended for large-scale genome assembly, so
you'd want to use a sequence assembly
tool<http://en.wikipedia.org/wiki/Sequence_assembly>(eg Velvet).

-Spencer


On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <
khalil.elmazouari at gmail.com> wrote:

> Hi,
>
> I would like to assemble 2 overlapping DNA sequences. Is there something
> in biojava that may help in this task?
>
> Thanks
>
>
>
>
> -----
>
> Confidentiality Notice: This e-mail and any files transmitted with it are
> private and confidential and are solely for the use of the addressee. It
> may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From khalil.elmazouari at gmail.com  Wed Apr 24 04:08:49 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 10:08:49 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
Message-ID: <C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>

Hi,

It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.

Best

khalil




-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.



On 23 Apr 2013, at 23:38, Spencer Bliven wrote:

> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> 
> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> 
> -Spencer
> 
> 
> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> Hi,
> 
> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> 
> Thanks
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 



From cfriedline at vcu.edu  Wed Apr 24 10:04:23 2013
From: cfriedline at vcu.edu (Chris Friedline)
Date: Wed, 24 Apr 2013 10:04:23 -0400
Subject: [Biojava-l] DNA assembly
In-Reply-To: <C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
Message-ID: <9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>

Khalil,

Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.

www.mothur.org
https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler

PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.

Chris

On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:

> Hi,
> 
> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> 
> Best
> 
> khalil
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> 
>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>> 
>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>> 
>> -Spencer
>> 
>> 
>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> Hi,
>> 
>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>> 
>> Thanks
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> 
>> _______________________________________________
>> 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 khalil.elmazouari at gmail.com  Wed Apr 24 10:29:24 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 16:29:24 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
Message-ID: <87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>

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







-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.



On 24 Apr 2013, at 16:04, Chris Friedline wrote:

> Khalil,
> 
> Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> 
> www.mothur.org
> https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> 
> PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> 
> Chris
> 
> On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> 
>> Hi,
>> 
>> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
>> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
>> 
>> Best
>> 
>> khalil
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
>> 
>>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>>> 
>>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>>> 
>>> -Spencer
>>> 
>>> 
>>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>>> Hi,
>>> 
>>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>>> 
>>> Thanks
>>> 
>>> 
>>> 
>>> 
>>> -----
>>> 
>>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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  Wed Apr 24 10:48:01 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 24 Apr 2013 07:48:01 -0700
Subject: [Biojava-l] DNA assembly
In-Reply-To: <87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
Message-ID: <CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>

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:

> 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
>
>
>
>
>
>
>
> -----
>
> Confidentiality Notice: This e-mail and any files transmitted with it are
> private and confidential and are solely for the use of the addressee. It
> may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
>
>
>
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
>
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in
> the results?  We are in the process of publishing a paper which uses
> PANDAseq to assemble overlapping PE reads.  The latest version of mothur
> also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right
> from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <
> khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a
> DNA fragment sequenced from both ends with an overlapping region. I want to
> assemble the 2 reads in order to get the full length sequence. This
> assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need
> somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it
> are private and confidential and are solely for the use of the addressee.
> It may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just
> use a global sequence alignment. See
> http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in
> BioJava, or it might be easier to just use one of the online services for
> this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from
> many overlapping reads), then there are much more computationally efficient
> methods. BioJava isn't really intended for large-scale genome assembly, so
> you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <
> khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there
> something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it
> are private and confidential and are solely for the use of the addressee.
> It may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> >
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From cfriedline at vcu.edu  Wed Apr 24 10:58:22 2013
From: cfriedline at vcu.edu (Chris Friedline)
Date: Wed, 24 Apr 2013 10:58:22 -0400
Subject: [Biojava-l] DNA assembly
In-Reply-To: <CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
	<CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
Message-ID: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>

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:

> 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:
> 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
> 
> 
> 
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
> 
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> >
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 




From khalil.elmazouari at gmail.com  Wed Apr 24 12:02:36 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 18:02:36 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
	<CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
	<DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>
Message-ID: <9E71B866-B121-404D-8D53-083CEECC9C1D@gmail.com>

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




-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.



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

> 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:
> 
>> 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:
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
>> 
>> > Khalil,
>> >
>> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
>> >
>> > www.mothur.org
>> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
>> >
>> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
>> >
>> > Chris
>> >
>> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> >
>> >> Hi,
>> >>
>> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
>> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
>> >>
>> >> Best
>> >>
>> >> khalil
>> >>
>> >>
>> >>
>> >>
>> >> -----
>> >>
>> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> >>
>> >>
>> >>
>> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
>> >>
>> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>> >>>
>> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>> >>>
>> >>> -Spencer
>> >>>
>> >>>
>> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> >>> Hi,
>> >>>
>> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>> >>>
>> >>> Thanks
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> -----
>> >>>
>> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> 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
>> >
>> >
>> >
>> >
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
>> 
> 
> 



From jjramirez at estudiantes.uci.cu  Wed Apr 24 14:24:44 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Wed, 24 Apr 2013 14:24:44 -0400 (EDT)
Subject: [Biojava-l] Genome Assembly
In-Reply-To: <mailman.5.1366819203.20525.biojava-l@lists.open-bio.org>
Message-ID: <fc80660b-bbc6-4d59-8991-40236304e6a1@ucimail4.uci.cu>

Hi !

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

Greetings


----- Mensaje original -----
De: biojava-l-request at lists.open-bio.org
Para: biojava-l at lists.open-bio.org
Enviados: Mi?rcoles, 24 de Abril 2013 11:00:03
Asunto: Biojava-l Digest, Vol 123, Issue 10

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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>
Subject: Re: [Biojava-l] DNA assembly
To: Andreas Prlic <andreas at sdsc.edu>
Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
	Khalil El Mazouari <khalil.elmazouari at gmail.com>
Message-ID: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA at vcu.edu>
Content-Type: text/plain;	charset=iso-8859-1

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:

> 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:
> 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
> 
> 
> 
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
> 
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> >
> 
> 
> _______________________________________________
> 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


End of Biojava-l Digest, Vol 123, Issue 10
******************************************
http://www.uci.cu
http://www.uci.cu


From jjramirez at estudiantes.uci.cu  Mon Apr  1 14:58:22 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 01 Apr 2013 10:58:22 -0400 (EDT)
Subject: [Biojava-l] Phred Quality Scores and .qual format
In-Reply-To: <CAPXi2mmoc4q7Bb3bXgqeFCOuT0nxP0=j3dPO0RLz+wHcpHLjBA@mail.gmail.com>
Message-ID: <0ed6d39c-4601-4064-8ed0-1b2dea6d9b33@ucimail4.uci.cu>

Thanks for reply

Yes I know it, I'm using Biojava 1.X to read SCF files, but many of my SCF files can't be read by Biojava.
And my other problem is that I need to obtain the Phred Quality Scores from Abi an Scf files, and I don't know how to do this.

Please Help

Thanks



----- Mensaje original -----
De: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com>
Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
CC: "biojava-l" <biojava-l at lists.open-bio.org>
Enviados: Viernes, 29 de Marzo 2013 7:52:41
Asunto: Re: [Biojava-l] Phred Quality Scores and .qual format


SCF can currently only be read in biojava-legacy. 
I am planning to port the code to BioJave 3 after the switch to git (i.e. next month) 
Until then, I think there are legacy-cookbook examples on how to read scf files. 


Hannes 



On Fri, Mar 29, 2013 at 5:48 AM, Janier J. Ram?rez < jjramirez at estudiantes.uci.cu > wrote: 


Hi guys ! 

I'm investigating for the whole genome assembly using AMOS Project. 

I need to obtain the Phred Quality Scores from Abi an Scf files, to then buil a .qual file, but my dude is obtaining the Scores, I have tried many time but I can't reach it !. 

Sorry for my English. 

Thanks for your time 


-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu 

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



From sbliven at ucsd.edu  Wed Apr  3 23:32:09 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 3 Apr 2013 16:32:09 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
Message-ID: <CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>

The transition to Github is now finished, although we're still working on
getting the documentation up-to-date. If you're currently using a checkout
of trunk from SVN, that checkout will still work but will not receive any
future updates. Please follow the instructions at
http://biojava.org/wiki/Get_source to get a copy of the latest source from
git.

The documentation is rather confusing at the moment, with references to the
old SVN interspersed with recent git instructions. If you run into such a
situation on the wiki, please fix it or mark the article with the
{{outdated}} template so we can get the documentation back up to par.

Thanks!
Spencer


On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Dear community,
>
> On the developer list we have been discussing moving the biojava code to
> github for some time. This transition is currently scheduled to occur this
> weekend. For users who get Biojava via binary jars or maven, this will have
> no effect on your projects. Users who compile the latest version of the
> source themselves may have to get a fresh version from github after April 1:
>
> biojava 3: https://github.com/biojava/biojava
> biojava 1: https://github.com/biojava/biojava-legacy
>
> I'll be working on improving documentation for the transition this week.
> For those interested in the migration process, see
> http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> using git with eclipse is at
> http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And
> http://biojava.org/wiki/Get_source will soon be updated with the new
> instructions for getting the latest source code from git.
>
> Please let me know if anyone has suggestions or concerns.
>
> -Spencer
>


From andreas at sdsc.edu  Thu Apr  4 00:03:21 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 3 Apr 2013 17:03:21 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
Message-ID: <CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>

Thanks Spencer for all your efforts in getting this set up! I hope that
will make the code base even more accessible and should provide a path of
submitting patches more easily from now on.

Let the social coding begin!

Andreas


On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> The transition to Github is now finished, although we're still working on
> getting the documentation up-to-date. If you're currently using a checkout
> of trunk from SVN, that checkout will still work but will not receive any
> future updates. Please follow the instructions at
> http://biojava.org/wiki/Get_source to get a copy of the latest source from
> git.
>
> The documentation is rather confusing at the moment, with references to the
> old SVN interspersed with recent git instructions. If you run into such a
> situation on the wiki, please fix it or mark the article with the
> {{outdated}} template so we can get the documentation back up to par.
>
> Thanks!
> Spencer
>
>
> On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> > Dear community,
> >
> > On the developer list we have been discussing moving the biojava code to
> > github for some time. This transition is currently scheduled to occur
> this
> > weekend. For users who get Biojava via binary jars or maven, this will
> have
> > no effect on your projects. Users who compile the latest version of the
> > source themselves may have to get a fresh version from github after
> April 1:
> >
> > biojava 3: https://github.com/biojava/biojava
> > biojava 1: https://github.com/biojava/biojava-legacy
> >
> > I'll be working on improving documentation for the transition this week.
> > For those interested in the migration process, see
> > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> > using git with eclipse is at
> > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git. And
> > http://biojava.org/wiki/Get_source will soon be updated with the new
> > instructions for getting the latest source code from git.
> >
> > Please let me know if anyone has suggestions or concerns.
> >
> > -Spencer
> >
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From phidias51 at gmail.com  Thu Apr  4 00:22:27 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Wed, 3 Apr 2013 17:22:27 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
Message-ID: <CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>

Great job you guys.  I've already spotted some minor things.  If only I
could figure out a way to do a code review without doing a commit. :-)

Cheers,

Mark



On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Thanks Spencer for all your efforts in getting this set up! I hope that
> will make the code base even more accessible and should provide a path of
> submitting patches more easily from now on.
>
> Let the social coding begin!
>
> Andreas
>
>
> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>
> > The transition to Github is now finished, although we're still working on
> > getting the documentation up-to-date. If you're currently using a
> checkout
> > of trunk from SVN, that checkout will still work but will not receive any
> > future updates. Please follow the instructions at
> > http://biojava.org/wiki/Get_source to get a copy of the latest source
> from
> > git.
> >
> > The documentation is rather confusing at the moment, with references to
> the
> > old SVN interspersed with recent git instructions. If you run into such a
> > situation on the wiki, please fix it or mark the article with the
> > {{outdated}} template so we can get the documentation back up to par.
> >
> > Thanks!
> > Spencer
> >
> >
> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
> wrote:
> >
> > > Dear community,
> > >
> > > On the developer list we have been discussing moving the biojava code
> to
> > > github for some time. This transition is currently scheduled to occur
> > this
> > > weekend. For users who get Biojava via binary jars or maven, this will
> > have
> > > no effect on your projects. Users who compile the latest version of the
> > > source themselves may have to get a fresh version from github after
> > April 1:
> > >
> > > biojava 3: https://github.com/biojava/biojava
> > > biojava 1: https://github.com/biojava/biojava-legacy
> > >
> > > I'll be working on improving documentation for the transition this
> week.
> > > For those interested in the migration process, see
> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
> > > using git with eclipse is at
> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
> And
> > > http://biojava.org/wiki/Get_source will soon be updated with the new
> > > instructions for getting the latest source code from git.
> > >
> > > Please let me know if anyone has suggestions or concerns.
> > >
> > > -Spencer
> > >
> > _______________________________________________
> > 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 sbliven at ucsd.edu  Thu Apr  4 05:57:59 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Wed, 3 Apr 2013 22:57:59 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
Message-ID: <CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>

Mark?

If you commit to your own fork and then create a pull request, it
automatically gives you a place for code review.

You could also open up an issue. https://github.com/biojava/biojava/issues

-Spencer


On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:

> Great job you guys.  I've already spotted some minor things.  If only I
> could figure out a way to do a code review without doing a commit. :-)
>
> Cheers,
>
> Mark
>
>
>
> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Thanks Spencer for all your efforts in getting this set up! I hope that
>> will make the code base even more accessible and should provide a path of
>> submitting patches more easily from now on.
>>
>> Let the social coding begin!
>>
>> Andreas
>>
>>
>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>>
>> > The transition to Github is now finished, although we're still working
>> on
>> > getting the documentation up-to-date. If you're currently using a
>> checkout
>> > of trunk from SVN, that checkout will still work but will not receive
>> any
>> > future updates. Please follow the instructions at
>> > http://biojava.org/wiki/Get_source to get a copy of the latest source
>> from
>> > git.
>> >
>> > The documentation is rather confusing at the moment, with references to
>> the
>> > old SVN interspersed with recent git instructions. If you run into such
>> a
>> > situation on the wiki, please fix it or mark the article with the
>> > {{outdated}} template so we can get the documentation back up to par.
>> >
>> > Thanks!
>> > Spencer
>> >
>> >
>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>> wrote:
>> >
>> > > Dear community,
>> > >
>> > > On the developer list we have been discussing moving the biojava code
>> to
>> > > github for some time. This transition is currently scheduled to occur
>> > this
>> > > weekend. For users who get Biojava via binary jars or maven, this will
>> > have
>> > > no effect on your projects. Users who compile the latest version of
>> the
>> > > source themselves may have to get a fresh version from github after
>> > April 1:
>> > >
>> > > biojava 3: https://github.com/biojava/biojava
>> > > biojava 1: https://github.com/biojava/biojava-legacy
>> > >
>> > > I'll be working on improving documentation for the transition this
>> week.
>> > > For those interested in the migration process, see
>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
>> > > using git with eclipse is at
>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>> And
>> > > http://biojava.org/wiki/Get_source will soon be updated with the new
>> > > instructions for getting the latest source code from git.
>> > >
>> > > Please let me know if anyone has suggestions or concerns.
>> > >
>> > > -Spencer
>> > >
>> > _______________________________________________
>> > 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 phidias51 at gmail.com  Thu Apr  4 06:07:04 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Wed, 3 Apr 2013 23:07:04 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
Message-ID: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>

I was wishing I could just kibitz on some of the code without having to
actually fix it. :-)

Just some odd things I noticed in FastaReader and FastaWriter where the
code contains a main instead of relying on the test case to give you an
example.  And comments that are partial or missing.

Are the checkstyle and findbugs plugins configured to run as part of the
build?

Mark
On Apr 3, 2013 10:58 PM, "Spencer Bliven" <sbliven at ucsd.edu> wrote:

> Mark?
>
> If you commit to your own fork and then create a pull request, it
> automatically gives you a place for code review.
>
> You could also open up an issue. https://github.com/biojava/biojava/issues
>
> -Spencer
>
>
> On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>
>> Great job you guys.  I've already spotted some minor things.  If only I
>> could figure out a way to do a code review without doing a commit. :-)
>>
>> Cheers,
>>
>> Mark
>>
>>
>>
>> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>>> Thanks Spencer for all your efforts in getting this set up! I hope that
>>> will make the code base even more accessible and should provide a path of
>>> submitting patches more easily from now on.
>>>
>>> Let the social coding begin!
>>>
>>> Andreas
>>>
>>>
>>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>>>
>>> > The transition to Github is now finished, although we're still working
>>> on
>>> > getting the documentation up-to-date. If you're currently using a
>>> checkout
>>> > of trunk from SVN, that checkout will still work but will not receive
>>> any
>>> > future updates. Please follow the instructions at
>>> > http://biojava.org/wiki/Get_source to get a copy of the latest source
>>> from
>>> > git.
>>> >
>>> > The documentation is rather confusing at the moment, with references
>>> to the
>>> > old SVN interspersed with recent git instructions. If you run into
>>> such a
>>> > situation on the wiki, please fix it or mark the article with the
>>> > {{outdated}} template so we can get the documentation back up to par.
>>> >
>>> > Thanks!
>>> > Spencer
>>> >
>>> >
>>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>>> wrote:
>>> >
>>> > > Dear community,
>>> > >
>>> > > On the developer list we have been discussing moving the biojava
>>> code to
>>> > > github for some time. This transition is currently scheduled to occur
>>> > this
>>> > > weekend. For users who get Biojava via binary jars or maven, this
>>> will
>>> > have
>>> > > no effect on your projects. Users who compile the latest version of
>>> the
>>> > > source themselves may have to get a fresh version from github after
>>> > April 1:
>>> > >
>>> > > biojava 3: https://github.com/biojava/biojava
>>> > > biojava 1: https://github.com/biojava/biojava-legacy
>>> > >
>>> > > I'll be working on improving documentation for the transition this
>>> week.
>>> > > For those interested in the migration process, see
>>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information about
>>> > > using git with eclipse is at
>>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>>> And
>>> > > http://biojava.org/wiki/Get_source will soon be updated with the new
>>> > > instructions for getting the latest source code from git.
>>> > >
>>> > > Please let me know if anyone has suggestions or concerns.
>>> > >
>>> > > -Spencer
>>> > >
>>> > _______________________________________________
>>> > 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 biojava at hannes.oib.com  Thu Apr  4 09:50:30 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 4 Apr 2013 11:50:30 +0200
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
Message-ID: <CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>

On Thu, Apr 4, 2013 at 8:07 AM, Mark Fortner <phidias51 at gmail.com> wrote:

> I was wishing I could just kibitz on some of the code without having to
> actually fix it. :-)
>
> Just some odd things I noticed in FastaReader and FastaWriter where the
> code contains a main instead of relying on the test case to give you an
> example.  And comments that are partial or missing.
>
> Are the checkstyle and findbugs plugins configured to run as part of the
> build?
>
> Mark


Last time I looked, I noticed that there were some different code styles
going on. Is that now fixed (and which style are we using? is a formatter
for eclipse checked in somewhere?)

Hannes


From andreas at sdsc.edu  Thu Apr  4 14:54:51 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 07:54:51 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
	<CAPXi2mkTcv0NwEbbQ12fW0GmN9vw0o0pydZfa2ekDpGtxZBHNg@mail.gmail.com>
Message-ID: <CALthepxpZ-j-5b37iFx39+RTCqMXz4YFYJjz_WkRNmtHHBpRbg@mail.gmail.com>

Hi Hannes,

there is an eclipse formatting template available from here:

http://biojava.org/wiki/BioJava3:Coding_Conventions

Andreas


On Thu, Apr 4, 2013 at 2:50 AM, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> On Thu, Apr 4, 2013 at 8:07 AM, Mark Fortner <phidias51 at gmail.com> wrote:
>
> > I was wishing I could just kibitz on some of the code without having to
> > actually fix it. :-)
> >
> > Just some odd things I noticed in FastaReader and FastaWriter where the
> > code contains a main instead of relying on the test case to give you an
> > example.  And comments that are partial or missing.
> >
> > Are the checkstyle and findbugs plugins configured to run as part of the
> > build?
> >
> > Mark
>
>
> Last time I looked, I noticed that there were some different code styles
> going on. Is that now fixed (and which style are we using? is a formatter
> for eclipse checked in somewhere?)
>
> Hannes
> _______________________________________________
> 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  Thu Apr  4 14:56:14 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 07:56:14 -0700
Subject: [Biojava-l] Biojava moving to Github
In-Reply-To: <CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
References: <CA+P6ar=_U1q5DZ8JNSBiwRxgYXOobPD0t_8jyUuKkUiR4jjMLw@mail.gmail.com>
	<CA+P6ar=apmTLdfxvAz8QwE8DZD1RgKbVxs9zxz4VEyUWuorAUA@mail.gmail.com>
	<CALthepw0CgMac7sBYPJObkN+0Nj2mh5GM_cDAr3+JqoPDYJ4nA@mail.gmail.com>
	<CAOwy01urn8utVB2EAxcBSwu79i+kimMoDgAUD0EJT1h82N3W3g@mail.gmail.com>
	<CA+P6ar=23Gs6tC1amOiFn99yk7p_JMANYxTpaxhTDj=rEN8zNg@mail.gmail.com>
	<CAOwy01sJaUWWPT5xmWLFz39HJRpFrBbspH_KX0iNm6=BmE4uYQ@mail.gmail.com>
Message-ID: <CALthepx4RdMPiGeY4cWGb6Luzr6_AYw722-grbV+_JAJd4DzdQ@mail.gmail.com>

Hi Mark,

running checkstyle and findbugs as part of the build is a good idea... I'll
look into that.

Andreas


On Wed, Apr 3, 2013 at 11:07 PM, Mark Fortner <phidias51 at gmail.com> wrote:

> I was wishing I could just kibitz on some of the code without having to
> actually fix it. :-)
>
> Just some odd things I noticed in FastaReader and FastaWriter where the
> code contains a main instead of relying on the test case to give you an
> example.  And comments that are partial or missing.
>
> Are the checkstyle and findbugs plugins configured to run as part of the
> build?
>
> Mark
> On Apr 3, 2013 10:58 PM, "Spencer Bliven" <sbliven at ucsd.edu> wrote:
>
>> Mark?
>>
>> If you commit to your own fork and then create a pull request, it
>> automatically gives you a place for code review.
>>
>> You could also open up an issue.
>> https://github.com/biojava/biojava/issues
>>
>> -Spencer
>>
>>
>> On Wed, Apr 3, 2013 at 5:22 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>>
>>> Great job you guys.  I've already spotted some minor things.  If only I
>>> could figure out a way to do a code review without doing a commit. :-)
>>>
>>> Cheers,
>>>
>>> Mark
>>>
>>>
>>>
>>> On Wed, Apr 3, 2013 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>
>>>> Thanks Spencer for all your efforts in getting this set up! I hope that
>>>> will make the code base even more accessible and should provide a path
>>>> of
>>>> submitting patches more easily from now on.
>>>>
>>>> Let the social coding begin!
>>>>
>>>> Andreas
>>>>
>>>>
>>>> On Wed, Apr 3, 2013 at 4:32 PM, Spencer Bliven <sbliven at ucsd.edu>
>>>> wrote:
>>>>
>>>> > The transition to Github is now finished, although we're still
>>>> working on
>>>> > getting the documentation up-to-date. If you're currently using a
>>>> checkout
>>>> > of trunk from SVN, that checkout will still work but will not receive
>>>> any
>>>> > future updates. Please follow the instructions at
>>>> > http://biojava.org/wiki/Get_source to get a copy of the latest
>>>> source from
>>>> > git.
>>>> >
>>>> > The documentation is rather confusing at the moment, with references
>>>> to the
>>>> > old SVN interspersed with recent git instructions. If you run into
>>>> such a
>>>> > situation on the wiki, please fix it or mark the article with the
>>>> > {{outdated}} template so we can get the documentation back up to par.
>>>> >
>>>> > Thanks!
>>>> > Spencer
>>>> >
>>>> >
>>>> > On Tue, Mar 26, 2013 at 10:35 AM, Spencer Bliven <sbliven at ucsd.edu>
>>>> wrote:
>>>> >
>>>> > > Dear community,
>>>> > >
>>>> > > On the developer list we have been discussing moving the biojava
>>>> code to
>>>> > > github for some time. This transition is currently scheduled to
>>>> occur
>>>> > this
>>>> > > weekend. For users who get Biojava via binary jars or maven, this
>>>> will
>>>> > have
>>>> > > no effect on your projects. Users who compile the latest version of
>>>> the
>>>> > > source themselves may have to get a fresh version from github after
>>>> > April 1:
>>>> > >
>>>> > > biojava 3: https://github.com/biojava/biojava
>>>> > > biojava 1: https://github.com/biojava/biojava-legacy
>>>> > >
>>>> > > I'll be working on improving documentation for the transition this
>>>> week.
>>>> > > For those interested in the migration process, see
>>>> > > http://biojava.org/wiki/SVN_to_GIT_Migration. Some information
>>>> about
>>>> > > using git with eclipse is at
>>>> > > http://biojava.org/wiki/BioJava3_eclipse#Anonymous_access_with_Git.
>>>> And
>>>> > > http://biojava.org/wiki/Get_source will soon be updated with the
>>>> new
>>>> > > instructions for getting the latest source code from git.
>>>> > >
>>>> > > Please let me know if anyone has suggestions or concerns.
>>>> > >
>>>> > > -Spencer
>>>> > >
>>>> > _______________________________________________
>>>> > 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 sbliven at ucsd.edu  Fri Apr  5 04:13:46 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Thu, 4 Apr 2013 21:13:46 -0700
Subject: [Biojava-l] Gource Video
Message-ID: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>

I've been staring at the BioJava history so much I thought I'd take a break
and have some fun with it. Here's a video, made with Gource, showing all
the commits to SVN over the current life of BioJava.

http://www.youtube.com/watch?v=hhH9T_JimY0

-Spencer


From andreas at sdsc.edu  Fri Apr  5 04:23:03 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 4 Apr 2013 21:23:03 -0700
Subject: [Biojava-l] Gource Video
In-Reply-To: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
References: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
Message-ID: <CALthepz7vbLoRvay8mG9Ai2sfLbPG3Sv67mB8D-0dYveG8bo2A@mail.gmail.com>

Fun!

Interesting to see how the shape of the project evolves and changes over
time!

Andreas


On Thu, Apr 4, 2013 at 9:13 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> I've been staring at the BioJava history so much I thought I'd take a break
> and have some fun with it. Here's a video, made with Gource, showing all
> the commits to SVN over the current life of BioJava.
>
> http://www.youtube.com/watch?v=hhH9T_JimY0
>
> -Spencer
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas.draeger at uni-tuebingen.de  Mon Apr  8 04:37:32 2013
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Mon, 08 Apr 2013 06:37:32 +0200
Subject: [Biojava-l] Gource Video
In-Reply-To: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
References: <CA+P6arkhVOnQoxZeevygR-WSWD2=c7Ovy0B7+okAky5oPUE4Gw@mail.gmail.com>
Message-ID: <5162498C.8050008@uni-tuebingen.de>

Am 4/5/13 6:13 AM, schrieb Spencer Bliven:
> I've been staring at the BioJava history so much I thought I'd take a break
> and have some fun with it. Here's a video, made with Gource, showing all
> the commits to SVN over the current life of BioJava.
>
> http://www.youtube.com/watch?v=hhH9T_JimY0
>
This is really cool. Thanks for doing tis kind of visualization! It is 
incredible, what can be done with SVN history!

-- 
Dr. Andreas Dr?ger
University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-78982
Fax:   +49-7071-29-5091



From p.j.a.cock at googlemail.com  Tue Apr  9 10:20:43 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 11:20:43 +0100
Subject: [Biojava-l] OBF not accepted for GSoC 2013
Message-ID: <CAKVJ-_6-+nyJk+7tp5YOyy7i7N7GtkRswZ_2Vs0uTuqGEV4wWQ@mail.gmail.com>

Dear all,

Unfortunately this year we have not been accepted on the Google
Summer of Code scheme:

I'm sure the rest of the OBF board and the other Bio* developers
will join me in thanking Pjotr Prins for his efforts as the OBF
GSoC administrator co-ordinating our application this year, as
well as last year's administrator Rob Bruels and the other mentors
for their efforts.

For those of you not subscribed to the OBF's GSoC mailing list,
I am forwarding Pjotr's email from last night (also below):
http://lists.open-bio.org/pipermail/gsoc/2013/000211.html

In all 177 organisations were accepted (about the same as the
last few years), and they will be listed here (once they have filled
out their profile information):
https://google-melange.appspot.com/gsoc/accepted_orgs/google/gsoc2013

To potential students this summer, the good news is that some
related organisations have been accepted, such as NESCent,
the National Resource for Network Biology (NRNB - known for
Cytoscape), SciRuby (Ruby Science Foundation), so there is
still some scope for doing a bioinformatics related project in
GSoC 2013, perhaps even with a Bio* developer as a co-mentor.

Thank you all,

Peter
(Biopython developer, OBF board member)

---------- Forwarded message ----------
From: Pjotr Prins <pjotr2010 at thebird.nl>
Date: Mon, Apr 8, 2013 at 9:13 PM
Subject: Re: GSoC 2013 is ON
To: Pjotr Prins <pjotr2010 at thebird.nl>
Cc: ..., OBF GSoC <gsoc at lists.open-bio.org>


Sadly, our application got rejected by GSoC this year. I am not sure
what the reason was, but I am convinced our application was similar to
that of other years. Maybe the project ideas could have been better
presented. I am not sure at this stage. I'll make a list of successful
projects to see if we can digest some truths.

The upside is that FOSS is going strong! And that the field is getting
increasingly competitive. As an open source geezer I can only be
happy, even if it hurts our own application.

Sorry everyone, and many thanks for the trouble you took getting
projects written up. Let's not feel discouraged for next year.

Pj.


From andreas at sdsc.edu  Tue Apr  9 17:11:33 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 9 Apr 2013 10:11:33 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
Message-ID: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>

Hi,

As you probably have seen by now the Open Bioinformatics Foundation's
application for Google Summer of Code 2013 did not get accepted. While this
means we won't be able to sponsor any students this year, this does not
mean we are not going to be active in the coming months. I believe the
current migration to Github has opened us up for a different style of
development and let's focus on extending our community around that.

Andreas


From phidias51 at gmail.com  Tue Apr  9 17:18:12 2013
From: phidias51 at gmail.com (Mark Fortner)
Date: Tue, 9 Apr 2013 10:18:12 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
Message-ID: <CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>

Andreas,
Perhaps a hackathon might be a good way to extend the community.

Cheers,

Mark



On Tue, Apr 9, 2013 at 10:11 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi,
>
> As you probably have seen by now the Open Bioinformatics Foundation's
> application for Google Summer of Code 2013 did not get accepted. While this
> means we won't be able to sponsor any students this year, this does not
> mean we are not going to be active in the coming months. I believe the
> current migration to Github has opened us up for a different style of
> development and let's focus on extending our community around that.
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From p.j.a.cock at googlemail.com  Tue Apr  9 18:13:38 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 19:13:38 +0100
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
Message-ID: <CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>

On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
> Andreas,
> Perhaps a hackathon might be a good way to extend the community.
>
> Cheers,
>
> Mark

How about trying to get a good BioJava turn out at the
pre-BOSC 2013 CodeFest then?
http://www.open-bio.org/wiki/Codefest_2013

Peter


From sbliven at ucsd.edu  Tue Apr  9 18:42:23 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 9 Apr 2013 11:42:23 -0700
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
Message-ID: <CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>

That would be fun. Is there an additional cost beyond the conference
registration? The website only mentions hotel rates.

-Spencer


On Tue, Apr 9, 2013 at 11:13 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
> > Andreas,
> > Perhaps a hackathon might be a good way to extend the community.
> >
> > Cheers,
> >
> > Mark
>
> How about trying to get a good BioJava turn out at the
> pre-BOSC 2013 CodeFest then?
> http://www.open-bio.org/wiki/Codefest_2013
>
> Peter
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From p.j.a.cock at googlemail.com  Tue Apr  9 18:56:34 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 9 Apr 2013 19:56:34 +0100
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
	<CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
Message-ID: <CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>

> On Tue, Apr 9, 2013 at 11:13 AM, Peter Cock wrote:
>>
>> On Tue, Apr 9, 2013 at 6:18 PM, Mark Fortner <phidias51 at gmail.com> wrote:
>> >
>> > Andreas,
>> > Perhaps a hackathon might be a good way to extend the community.
>> >
>> > Cheers,
>> >
>> > Mark
>>
>> How about trying to get a good BioJava turn out at the
>> pre-BOSC 2013 CodeFest then?
>> http://www.open-bio.org/wiki/Codefest_2013
>>
>> Peter

On Tue, Apr 9, 2013 at 7:42 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> That would be fun. Is there an additional cost beyond the conference
> registration? The website only mentions hotel rates.
>
> -Spencer

This is quite an informal hackathon - but we do need people to
register to make sure we can cope with the expected numbers.
I've CC'd Brad Chapman who is the main CodeFest 2013 organiser.

There are conference registration fees for BOSC and the main
ISBM/ECCB conference, but *not* for this pre-BOSC CodeFest.
You would have to pay your accommodation, food and travel
costs.

We're hoping and expecting the CodeFest attendees will also
attend BOSC, but this is a not formal requirement. If that is
difficult due to finances, note that for students this year there
are three prizes covering the BOSC fees and money towards
travel, plus if your abstract is accepted you can ask for the
BOSC registration to be waived - see:
http://www.open-bio.org/wiki/BOSC_2013

NOTE: The BOSC abstract submission *DEADLINE* is this Friday!

Having lots of Bio* people together should be good fun :)

Peter


From chapmanb at 50mail.com  Wed Apr 10 00:11:59 2013
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 09 Apr 2013 20:11:59 -0400
Subject: [Biojava-l] [GSoC] OBF not accepted for GSoC 2013
In-Reply-To: <CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>
References: <CALthepypHb7e1pSOKdy8gZYpkBrze_E__gR+MmgLCBWP7ar6+A@mail.gmail.com>
	<CAOwy01vGvRK-pkHWtT2=wCGFxtduhf9-33zNh4Psx9TdzQnNvA@mail.gmail.com>
	<CAKVJ-_6gAqp66on28gu9agoPwzZabsCqfPCP4qDakvv9Du3U7Q@mail.gmail.com>
	<CA+P6arkmZGYPZ4KMOL9cD2ep9wnKiWHawy+m0U0Ung7Sgpv9kQ@mail.gmail.com>
	<CAKVJ-_7DR0drdMEvjqqPHw5x=CSi1Lj757=m_B3G-6AfWJ+2vw@mail.gmail.com>
Message-ID: <8738uzmegg.fsf@fastmail.fm>


Spencer, Mark and Peter;

>> That would be fun. Is there an additional cost beyond the conference
>> registration? The website only mentions hotel rates.

http://www.open-bio.org/wiki/Codefest_2013

> This is quite an informal hackathon - but we do need people to
> register to make sure we can cope with the expected numbers.
>
> There are conference registration fees for BOSC and the main
> ISBM/ECCB conference, but *not* for this pre-BOSC CodeFest.
> You would have to pay your accommodation, food and travel
> costs.

+1 to everything Peter said. You are very welcome and there is no cost
to attend. It's two days to discuss, meet other developers, and work on
code together. We're appreciative of everyone who wants to donate
their time to help work on open source projects. Hope you can make it
out,
Brad


From kohchuanhock at gmail.com  Fri Apr 12 14:23:17 2013
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Fri, 12 Apr 2013 14:23:17 +0000 (UTC)
Subject: [Biojava-l] Invitation to connect on LinkedIn
Message-ID: <2018124687.16072581.1365776597303.JavaMail.app@ela4-bed84.prod>

LinkedIn
------------



I'd like to add you to my professional network on LinkedIn.

- Chuan Hock

Chuan Hock Koh
Software Engineer at DeNA
Japan

Confirm that you know Chuan Hock Koh:
https://www.linkedin.com/e/-u6hnvb-hffg4f1b-5w/isd/12422496303/xv1pynGp/?hs=false&tok=12OicutkG_llI1

--
You are receiving Invitation to Connect emails. Click to unsubscribe:
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(c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.


  


From khalil.elmazouari at gmail.com  Tue Apr 23 19:38:54 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Tue, 23 Apr 2013 21:38:54 +0200
Subject: [Biojava-l] DNA assembly
Message-ID: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>

Hi,

I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?

Thanks




-----

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From sbliven at ucsd.edu  Tue Apr 23 21:38:25 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 23 Apr 2013 14:38:25 -0700
Subject: [Biojava-l] DNA assembly
In-Reply-To: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
Message-ID: <CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>

If you just have two contiguous sequences to align, you should just use a
global sequence alignment. See
http://biojava.org/wiki/BioJava:CookBook3:PSAfor how to do this in
BioJava, or it might be easier to just use one of the
online services for this such as http://www.ebi.ac.uk/Tools/psa/.

On the other hand, if you actually want to do genome assembly (ie from many
overlapping reads), then there are much more computationally efficient
methods. BioJava isn't really intended for large-scale genome assembly, so
you'd want to use a sequence assembly
tool<http://en.wikipedia.org/wiki/Sequence_assembly>(eg Velvet).

-Spencer


On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <
khalil.elmazouari at gmail.com> wrote:

> Hi,
>
> I would like to assemble 2 overlapping DNA sequences. Is there something
> in biojava that may help in this task?
>
> Thanks
>
>
>
>
> -----
>
> Confidentiality Notice: This e-mail and any files transmitted with it are
> private and confidential and are solely for the use of the addressee. It
> may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From khalil.elmazouari at gmail.com  Wed Apr 24 08:08:49 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 10:08:49 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
Message-ID: <C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>

Hi,

It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.

Best

khalil




-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.



On 23 Apr 2013, at 23:38, Spencer Bliven wrote:

> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> 
> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> 
> -Spencer
> 
> 
> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> Hi,
> 
> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> 
> Thanks
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 




From cfriedline at vcu.edu  Wed Apr 24 14:04:23 2013
From: cfriedline at vcu.edu (Chris Friedline)
Date: Wed, 24 Apr 2013 10:04:23 -0400
Subject: [Biojava-l] DNA assembly
In-Reply-To: <C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
Message-ID: <9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>

Khalil,

Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.

www.mothur.org
https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler

PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.

Chris

On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:

> Hi,
> 
> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> 
> Best
> 
> khalil
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> 
>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>> 
>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>> 
>> -Spencer
>> 
>> 
>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> Hi,
>> 
>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>> 
>> Thanks
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> 
>> _______________________________________________
>> 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 khalil.elmazouari at gmail.com  Wed Apr 24 14:29:24 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 16:29:24 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
Message-ID: <87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>

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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On 24 Apr 2013, at 16:04, Chris Friedline wrote:

> Khalil,
> 
> Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> 
> www.mothur.org
> https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> 
> PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> 
> Chris
> 
> On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> 
>> Hi,
>> 
>> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
>> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
>> 
>> Best
>> 
>> khalil
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
>> 
>>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>>> 
>>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>>> 
>>> -Spencer
>>> 
>>> 
>>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>>> Hi,
>>> 
>>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>>> 
>>> Thanks
>>> 
>>> 
>>> 
>>> 
>>> -----
>>> 
>>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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  Wed Apr 24 14:48:01 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 24 Apr 2013 07:48:01 -0700
Subject: [Biojava-l] DNA assembly
In-Reply-To: <87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
Message-ID: <CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>

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:

> 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
>
>
>
>
>
>
>
> -----
>
> Confidentiality Notice: This e-mail and any files transmitted with it are
> private and confidential and are solely for the use of the addressee. It
> may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
>
>
>
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
>
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in
> the results?  We are in the process of publishing a paper which uses
> PANDAseq to assemble overlapping PE reads.  The latest version of mothur
> also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right
> from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <
> khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a
> DNA fragment sequenced from both ends with an overlapping region. I want to
> assemble the 2 reads in order to get the full length sequence. This
> assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need
> somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it
> are private and confidential and are solely for the use of the addressee.
> It may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just
> use a global sequence alignment. See
> http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in
> BioJava, or it might be easier to just use one of the online services for
> this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from
> many overlapping reads), then there are much more computationally efficient
> methods. BioJava isn't really intended for large-scale genome assembly, so
> you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <
> khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there
> something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it
> are private and confidential and are solely for the use of the addressee.
> It may contain material which is legally privileged. If you are not the
> addressee or the person responsible for delivering to the addressee, please
> notify that you have received this e-mail in error and that any use of it
> is strictly prohibited. It would be helpful if you could notify the author
> by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> >
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From cfriedline at vcu.edu  Wed Apr 24 14:58:22 2013
From: cfriedline at vcu.edu (Chris Friedline)
Date: Wed, 24 Apr 2013 10:58:22 -0400
Subject: [Biojava-l] DNA assembly
In-Reply-To: <CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
	<CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
Message-ID: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>

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:

> 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:
> 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
> 
> 
> 
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
> 
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
> >
> >
> >
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> 
> 





From khalil.elmazouari at gmail.com  Wed Apr 24 16:02:36 2013
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Wed, 24 Apr 2013 18:02:36 +0200
Subject: [Biojava-l] DNA assembly
In-Reply-To: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>
References: <719C8670-0C96-4725-AC00-7AF18A876581@gmail.com>
	<CA+P6arkNzfQf=i1F3pdEhCjYQGFJiXZOSxcT61DCG-FuZo5-zA@mail.gmail.com>
	<C179E72D-A566-4CD7-BC0D-A26DE4CAD1DB@gmail.com>
	<9E2776A1-68AD-4D45-9B8C-B9E94126835D@vcu.edu>
	<87E40EAD-BA01-40E4-AB28-69C2E4C2FF19@gmail.com>
	<CALthepy5P_OO=6z4vUFzYzthOLRAyM+Fpw=Q8y=JPxCoFNSaQA@mail.gmail.com>
	<DCB620AB-AE14-4A23-BCEE-BEB45D404BBA@vcu.edu>
Message-ID: <9E71B866-B121-404D-8D53-083CEECC9C1D@gmail.com>

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




-----

Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.



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

> 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:
> 
>> 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:
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -----
>> 
>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> 
>> 
>> 
>> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
>> 
>> > Khalil,
>> >
>> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
>> >
>> > www.mothur.org
>> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
>> >
>> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
>> >
>> > Chris
>> >
>> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> >
>> >> Hi,
>> >>
>> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
>> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
>> >>
>> >> Best
>> >>
>> >> khalil
>> >>
>> >>
>> >>
>> >>
>> >> -----
>> >>
>> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> >>
>> >>
>> >>
>> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
>> >>
>> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
>> >>>
>> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
>> >>>
>> >>> -Spencer
>> >>>
>> >>>
>> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
>> >>> Hi,
>> >>>
>> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
>> >>>
>> >>> Thanks
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> -----
>> >>>
>> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> 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
>> >
>> >
>> >
>> >
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> 
>> 
> 
> 




From jjramirez at estudiantes.uci.cu  Wed Apr 24 18:24:44 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Wed, 24 Apr 2013 14:24:44 -0400 (EDT)
Subject: [Biojava-l] Genome Assembly
In-Reply-To: <mailman.5.1366819203.20525.biojava-l@lists.open-bio.org>
Message-ID: <fc80660b-bbc6-4d59-8991-40236304e6a1@ucimail4.uci.cu>

Hi !

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

Greetings


----- Mensaje original -----
De: biojava-l-request at lists.open-bio.org
Para: biojava-l at lists.open-bio.org
Enviados: Mi?rcoles, 24 de Abril 2013 11:00:03
Asunto: Biojava-l Digest, Vol 123, Issue 10

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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>
Subject: Re: [Biojava-l] DNA assembly
To: Andreas Prlic <andreas at sdsc.edu>
Cc: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>,
	Khalil El Mazouari <khalil.elmazouari at gmail.com>
Message-ID: <DCB620AB-AE14-4A23-BCEE-BEB45D404BBA at vcu.edu>
Content-Type: text/plain;	charset=iso-8859-1

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:

> 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:
> 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
> 
> 
> 
> 
> 
> 
> 
> -----
> 
> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> 
> 
> 
> On 24 Apr 2013, at 16:04, Chris Friedline wrote:
> 
> > Khalil,
> >
> > Why not just shell out to programs designed for this purpose and pull in the results?  We are in the process of publishing a paper which uses PANDAseq to assemble overlapping PE reads.  The latest version of mothur also does this.
> >
> > www.mothur.org
> > https://github.com/neufeld/pandaseq/wiki/PANDAseq-Assembler
> >
> > PANDAseq is particularly nice in this case, because you could read right from stderr and stdout streams.  It's also wicked fast.
> >
> > Chris
> >
> > On Apr 24, 2013, at 4:08 AM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> It's not a global sequence alignment nor genome assembly. It's just a DNA fragment sequenced from both ends with an overlapping region. I want to assemble the 2 reads in order to get the full length sequence. This assembly is a part of a complex analysis process that uses biojava.
> >> I agree, there a lot of simple option how to achieve this. But I need somthing in java/biojava.
> >>
> >> Best
> >>
> >> khalil
> >>
> >>
> >>
> >>
> >> -----
> >>
> >> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>
> >>
> >>
> >> On 23 Apr 2013, at 23:38, Spencer Bliven wrote:
> >>
> >>> If you just have two contiguous sequences to align, you should just use a global sequence alignment. See http://biojava.org/wiki/BioJava:CookBook3:PSA for how to do this in BioJava, or it might be easier to just use one of the online services for this such as http://www.ebi.ac.uk/Tools/psa/.
> >>>
> >>> On the other hand, if you actually want to do genome assembly (ie from many overlapping reads), then there are much more computationally efficient methods. BioJava isn't really intended for large-scale genome assembly, so you'd want to use a sequence assembly tool (eg Velvet).
> >>>
> >>> -Spencer
> >>>
> >>>
> >>> On Tue, Apr 23, 2013 at 12:38 PM, Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:
> >>> Hi,
> >>>
> >>> I would like to assemble 2 overlapping DNA sequences. Is there something in biojava that may help in this task?
> >>>
> >>> Thanks
> >>>
> >>>
> >>>
> >>>
> >>> -----
> >>>
> >>> Confidentiality Notice: This e-mail and any files transmitted with it are private and confidential and are solely for the use of the addressee. It may contain material which is legally privileged. If you are not the addressee or the person responsible for delivering to the addressee, please notify that you have received this e-mail in error and that any use of it is strictly prohibited. It would be helpful if you could notify the author by replying to it.
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
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End of Biojava-l Digest, Vol 123, Issue 10
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