Ebert Maximilian | 2 Feb 22:11 2016
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[Biopython] How does pairwise2 alignement returns begin on first matching amino acid?

Hi there,
I aligned two sequences using the following:

from Bio import pairwise2
from Bio.pairwise2 import format_alignment
from Bio.SubsMat import MatrixInfo as matlist

seq1="SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST"
seq2="HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI"
matrix = matlist.blosum62
gap_open = -11
gap_extend = -1
alns = pairwise2.align.localds(seq1, seq2, matrix, gap_open, gap_extend)
for a in alns:
print(format_alignment(*a))
So the result is (hard to see in text mode here is a link to biostars forum entry https://www.biostars.org/p/175229/):

SKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWD-YNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNST-
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
--HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPLTSTFKVLLCGAVLSRVDAGQEQLGRRI
 Score=98
And hence the begin is 9 but I want the beginning to be 2. Also for the end I want it to be the T/R combination and
not K/Q. Any idea how to do this?

Thanks!

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(Continue reading)

Stefanie Lück | 19 Jan 08:52 2016
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[Biopython] BioSeqUtilsMeltingTemp

Hello everybody!

First of all I would like to thank you because of the great documentation of the module I mention above. 

However I have a problem. I am trying to calculate the temperature with Tm_NN by using dangling ends.

I am calling the function like this:

Tm_NN(seq, check=True, strict=True, c_seq=c_seq, shift=1, nn_table=RNA_NN3,
          tmm_table=DNA_TMM1, imm_table=DNA_IMM1, de_table=RNA_DE1,
          dnac1=25, dnac2=0, selfcomp=False, Na=20, K=50, Tris=0, Mg=0,
          dNTPs=0, saltcorr=5)

whereas an example,

seq = GAT
c_seq = TCTA

which means:
-GAT
TCTA

Unfortunately I got a keyerror (KeyError: '.G/TC') because the dictionary does not contain '.G/TC' but 'CT/G.'

Do I have to supply the two sequences in a different way? I can not find what I am doing wrong, I supply seq in 5'-3' and c_seq in 3'-5' direction.

Any help would be very appreciated!
Thanks,
Stefanie
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Ravi Tavakley | 15 Jan 02:33 2016
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[Biopython] Unable to install Biopython on Mac OS X

I am installing Biopython on MacOSX.  “gcc” fails to find “stdio.h” file. I am running MacOSX version 10.11.2 (ElCapitan).
I tried "pip install biopython” and then tried installing from source. gcc fails in both cases. I get the following error message:

gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -Qunused-arguments -Qunused-arguments -I/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.6-x86_64-2.7/Bio/cpairwise2module.o
clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk'
In file included from Bio/cpairwise2module.c:12:
/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h:33:10: fatal error: 
      'stdio.h' file not found
#include <stdio.h>
         ^
1 error generated.
error: command 'gcc' failed with exit status 1

Similar failure occurs with pip install.

Any help will be appreciated. I have python 2.7 with Canopy installed on the system.

Ravi Tavakley
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Ivan Erill | 8 Jan 09:04 2016
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Re: [Biopython] DOI for BioPython

Came across this today; seemed pretty relevant to the topic at hand:

Ivan

On Tue, Jan 5, 2016 at 3:53 PM, Tiago Antao <tra <at> popgen.net> wrote:
On Wed, 23 Dec 2015 10:54:47 +0100
Ivan Erill <ivan.erill <at> gmail.com> wrote:
> That requires analyzing whether there is substantial new stuff to
> warrant a new publication and whether the new pub could make it to a
> journal of at least similar impact. Having an old (2009!) but highly
> cited publication is good, but may backfire if people/funders
> perceive there has been no (citable) progress in the area. Being able
> to cite extensions (e.g. BioPhylo) helps address that problem and
> enticing extension developers to publish, rather than publishing
> updates of Biopython, might be the way to go. Then again, most major
> projects in bioinformatics (e.g. GO, RefSeq, RegulonDB, STRING,
> eggNOG...) publish frequent updates, so why not Biopython? Having
> several Biopython papers might dilute the citation count, but you can
> then state that there have been X biopython publications, so it's a
> tradeoff, as usual.


I think there is a severe issue of fairness here: there are quite a few
people that contributed a lot and are profiting nothing from the
project. It would be only fair that they could have a citable paper.

Of course, deciding on the author list and ordering is a massive can of
worms... The only thing we know is that Peter would be first (and
second and third ;) ).


--
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have no expectation to receive a reply outside yours" - <at> tomstafford

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Martin Mokrejs | 3 Jan 20:51 2016
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[Biopython] Feeding XML stream from BLAST directly into SeqIO.parse()

Hi,
   I want to avoid creation of the huge XML files and feed BLAST results directly into SeqIO. I think the
following clearly sends all output into _stdout.

_stdout, _stderr = subprocess.Popen(_cmdline, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()

   Wrapping _stdout with cStringIO.StringIO would give a file-like object to be fed into SeqIO.parse() but
that does not help with the primary problem I have: how to delay BLASTN output or maybe just limit the buffer
of Popen? so that it would not consume all of my computer memory.

   I know one can prepare the left- and right-side of a UNIX pipe separately but I am not running SeqIO.parse()
on the right hand-side of a pipe as a separate process [an example could be:
http://seqanswers.com/forums/showpost.php?s=9904bb037c254042dfe282d032f8c07d&p=140253&postcount=6
I use something like this elsewhere but I cannot think of a way to do it now instead of moving the
SeqIO.parse() caller into a separate program and executing it as the consumer on the right side of a pipe.
Sounds not very elegant.
Can I do it directly inside my python? Just passing a handle/iterator to SeqIO.parse()?

   What do you think of this: http://eyalarubas.com/python-subproc-nonblock.html

   In Biopython's TUTORIAL I only see in section 7.3 result_handle using an existing disk file. Chapter 8
dedicated to SearchIO does not go beyond file-based examples either. Is it so uncommon? ;-)

Thank you for clues,
Martin
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Ivan Erill | 23 Dec 10:54 2015
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Re: [Biopython] Biopython Digest, Vol 156, Issue 19

More seriously, I'd be much happier with a convention where you'd cite the
major biopython paper, the specific module papers if there are any, and
include the hash of the revision you used. This should be included in the
wiki page where we define 'citation guidelines'. It is simple, helps
everyone (although occasional contributors might feel robbed), and is fully
reproducible.
This seems very sensible in terms of ensuring reproducibility and maintaining impact without added complications.

That being said, and at the risk of opening a can of worms, I find it
very unfair that many people that have recently contributed hard to the
project are not on the author list of the 2009 paper (you, for
example. Bow is another). That would be fixed with a new paper. Deciding
on the author list would be the can of worms. We all can agree that it
would be another Cock et al paper, but getting the list of people that
are the "et al" would be complex.
That requires analyzing whether there is substantial new stuff to warrant a new publication and whether the new pub could make it to a journal of at least similar impact. Having an old (2009!) but highly cited publication is good, but may backfire if people/funders perceive there has been no (citable) progress in the area. Being able to cite extensions (e.g. BioPhylo) helps address that problem and enticing extension developers to publish, rather than publishing updates of Biopython, might be the way to go. Then again, most major projects in bioinformatics (e.g. GO, RefSeq, RegulonDB, STRING, eggNOG...) publish frequent updates, so why not Biopython? Having several Biopython papers might dilute the citation count, but you can then state that there have been X biopython publications, so it's a tradeoff, as usual.

Regarding the can of worms, most journals currently accept author "lists" that may be maintained externally. A paper could be signed by the major contributors of the current version (and/or whomever actually takes the time to write the darn thing) followed by a "list" author pointing to the historical contributor list.

Ivan


On Wed, Dec 23, 2015 at 3:38 AM, <biopython-request <at> mailman.open-bio.org> wrote:
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Today's Topics:

   1. Re: DOI for BioPython (c.buhtz <at> posteo.jp)
   2. Re: DOI for BioPython (Fields, Christopher J)
   3. Re: DOI for BioPython (Iddo Friedberg)
   4. Re: DOI for BioPython (Tiago Antao)
   5. Re: DOI for BioPython (Jo?o Rodrigues)


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

Message: 1
Date: Tue, 22 Dec 2015 18:35:30 +0100
From: <c.buhtz <at> posteo.jp>
To: biopython <at> mailman.open-bio.org
Subject: Re: [Biopython] DOI for BioPython
Message-ID: <3pQ4bR6MwMz5vNM <at> dovecot03.posteo.de>
Content-Type: text/plain; charset=UTF-8

On 2015-12-22 16:38 Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com>
wrote:
> What's better: citing the paper that describes the algorithm(s) or
> the pull request that fixed a typo in the documentation?

The latter because a DOI/Reference is about reproducibility.
--
GnuPGP-Key ID 0751A8EC



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

Message: 2
Date: Tue, 22 Dec 2015 18:30:47 +0000
From: "Fields, Christopher J" <cjfields <at> illinois.edu>
To: Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com>
Cc: "biopython <at> mailman.open-bio.org" <biopython <at> mailman.open-bio.org>
Subject: Re: [Biopython] DOI for BioPython
Message-ID: <1E2AA25C-2269-4281-A364-0FEE6F673EE1 <at> illinois.edu>
Content-Type: text/plain; charset="utf-8"

I agree re: tracking citations, etc, particularly for funding.  However, for attributing credit for developers it?s actually tricky, particularly with large projects that have an evolving group of core developers.

My personal example: I wasn?t on the original bioperl citation (joined after), yet I am now essentially managing bioperl development when I can.  My commits and releases are the things I could to point to, so it?s nice to have something of a compromise (e.g. an updated DOI via Zenodo).  Not to mention it shows that development has continued past the point of publication (sometimes with significant changes to the API), which as we all know isn?t true for a significant chunk of published software.

So in my opinion it?s never a bad thing to have an updated (officially sanctioned!) citation reflecting contributions from new developers or significant changes to the codebase.  The original citation will never go away.

chris

On Dec 22, 2015, at 10:38 AM, Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com<mailto:j.p.g.l.m.rodrigues <at> gmail.com>> wrote:


Having all citations concentrated in one paper with all the major contributors helps tracking citation data, which helps those major contributors and OBF in future funding ventures. Further, a new release does not change the entire code base, so if you were to use Bio.PDB in say release X and Y, where there weren't any changes to this module, you'd cite two different DOIs, which wouldn't make any sense from any point of view.

Also, Peter's paper is not *his* paper about the software. It's the entire team, or almost, on that paper and it describes the different modules and their purpose and functionality.

What's better: citing the paper that describes the algorithm(s) or the pull request that fixed a typo in the documentation?

Cheers,

Jo?o

A ter, 22/12/2015, 16:05,  <c.buhtz <at> posteo.jp<mailto:c.buhtz <at> posteo.jp>> escreveu:
On 2015-12-22 15:10 Peter Cock <p.j.a.cock <at> googlemail.com<mailto:p.j.a.cock <at> googlemail.com>> wrote:
> You can just say Biopython version 1.66 (for example) and
> cite the paper Cock et al 2009 and its DOI:

I need to cite the software not your paper about the software.
It is unscientific to do it like that. And somebody could say I just
want to say "thank you" in the way to increase your ImpfactFactor.

If there is no DOI I will just name the main website an the release
identifier (version number).

> Using Zenodo.org<http://zenodo.org> we'd have to register a DOI for each
> release, which does not seem that useful.

Exactly that would be useful and what DOIs are for - especially for a
scientific software like BioPython.
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Message: 3
Date: Tue, 22 Dec 2015 13:29:13 -0600
From: Iddo Friedberg <idoerg <at> gmail.com>
To: biopython <at> mailman.open-bio.org
Subject: Re: [Biopython] DOI for BioPython
Message-ID:
        <CABm4-MRaG3jqz1iEgWcz22fxQogHouwynYnpiiEZKysNYs6TxA <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

COI: I am a paper co-author.

My $0.02 is that citing the paper is much more beneficial for the project,
for the reason Leighton said: a highly cited paper does help justify work
on the project to funding agencies as well as institutions. Speaking for
myself, I have cited the paper in two funded grant applications, one which
has resulted in some code contribution (the GAF parser) and one which
hopefully will benefit Biopython as well (recently funded to do some work
on GO, need to talk about that in the dev list). As Leighton said, funders
& bosses judge importance by citation count. While Biopython is not
directly funded, some of us manage to spend some time on it using our own
grants.


To facilitate reproducibility, a major version citation is sufficient, IMO,
as those are archived. If you used some non-major version on github, you
can fork/clone the version of your liking to your own github,  assign it a
DOI yourself, and cite that. For reasons mentioned, I would advocate citing
both the paper and the DOI you have assigned.

On Tue, Dec 22, 2015 at 11:35 AM, <c.buhtz <at> posteo.jp> wrote:

> On 2015-12-22 16:38 Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com>
> wrote:
> > What's better: citing the paper that describes the algorithm(s) or
> > the pull request that fixed a typo in the documentation?
>
> The latter because a DOI/Reference is about reproducibility.
> --
> GnuPGP-Key ID 0751A8EC
>
> _______________________________________________
> Biopython mailing list  -  Biopython <at> mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>



--
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.
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Message: 4
Date: Tue, 22 Dec 2015 18:03:48 -0700
From: Tiago Antao <tra <at> popgen.net>
To: Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com>
Cc: biopython <at> mailman.open-bio.org
Subject: Re: [Biopython] DOI for BioPython
Message-ID: <20151222180348.5d044506 <at> urso>
Content-Type: text/plain; charset=UTF-8

On Tue, 22 Dec 2015 16:38:37 +0000
Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com> wrote:

> Also, Peter's paper is not *his* paper about the software. It's the
> entire team, or almost, on that paper and it describes the different
> modules and their purpose and functionality.

One can discuss if it is good or bad, but basic pragmatism dictates
that the proper citing object is the 2009 paper, period. This for the
reasons stated here by others already. Myself I would not be able to
have contributed over the years if there was not a high-cited paper to
put forward as a justification.

Having another (non-paper) citing object will damage the project and
has my full frontal objection. Things in science work as they work, and
while I might object to paper citation metrics, that is the
world we live in. I believe Biopython already lives too much on the
volunteering of a few individuals, removing the only thing that
provides "income" would be fatal. We actually need more (not less)
forms of "income".

That being said, and at the risk of opening a can of worms, I find it
very unfair that many people that have recently contributed hard to the
project are not on the author list of the 2009 paper (you, for
example. Bow is another). That would be fixed with a new paper. Deciding
on the author list would be the can of worms. We all can agree that it
would be another Cock et al paper, but getting the list of people that
are the "et al" would be complex.

Tiago



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

Message: 5
Date: Wed, 23 Dec 2015 02:38:22 +0000
From: Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com>
To: Tiago Antao <tra <at> popgen.net>
Cc: biopython <at> mailman.open-bio.org
Subject: Re: [Biopython] DOI for BioPython
Message-ID:
        <CAB=-b2aEPQRGOc+jpoGMDda-zeXYjnwPOcsP9fqo+WtutfzFYg <at> mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Since this is a python library I'd go with the mantra of there is only one
way to do things, thus, one citation to keep things simple :)

More seriously, I'd be much happier with a convention where you'd cite the
major biopython paper, the specific module papers if there are any, and
include the hash of the revision you used. This should be included in the
wiki page where we define 'citation guidelines'. It is simple, helps
everyone (although occasional contributors might feel robbed), and is fully
reproducible.

Including DOIs for every release is only partially reproducible, since it
relies on a third party service to map between the DOI and the release,
which adds an unnecessary, in my opinion, extra layer of complexity. Also,
it doesn't help those that do not know biopython to learn about it since
they will have to Google it's publication.

It's a good discussion and a good point to raise, but there are still major
rules in science we have to play by in order to keep people interested and
generally move forward.

As Tiago, I'm also against implementing pre-release DOIs. It'll create too
much entropy that has no real benefits other than ideology.

A qua, 23/12/2015, 01:03, Tiago Antao <tra <at> popgen.net> escreveu:

> On Tue, 22 Dec 2015 16:38:37 +0000
> Jo?o Rodrigues <j.p.g.l.m.rodrigues <at> gmail.com> wrote:
>
> > Also, Peter's paper is not *his* paper about the software. It's the
> > entire team, or almost, on that paper and it describes the different
> > modules and their purpose and functionality.
>
> One can discuss if it is good or bad, but basic pragmatism dictates
> that the proper citing object is the 2009 paper, period. This for the
> reasons stated here by others already. Myself I would not be able to
> have contributed over the years if there was not a high-cited paper to
> put forward as a justification.
>
> Having another (non-paper) citing object will damage the project and
> has my full frontal objection. Things in science work as they work, and
> while I might object to paper citation metrics, that is the
> world we live in. I believe Biopython already lives too much on the
> volunteering of a few individuals, removing the only thing that
> provides "income" would be fatal. We actually need more (not less)
> forms of "income".
>
> That being said, and at the risk of opening a can of worms, I find it
> very unfair that many people that have recently contributed hard to the
> project are not on the author list of the 2009 paper (you, for
> example. Bow is another). That would be fixed with a new paper. Deciding
> on the author list would be the can of worms. We all can agree that it
> would be another Cock et al paper, but getting the list of people that
> are the "et al" would be complex.
>
> Tiago
>
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c.buhtz | 22 Dec 15:46 2015
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[Biopython] DOI for BioPython

Is there a DOI (DigitalObjectIdentifier) available for BioPython?

Zenodo.org offers that in cooperation with GitHub. This would make it
much easier and more professional in publications using BioPython to
handle the data.
--

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c.buhtz | 20 Dec 20:32 2015
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[Biopython] [Entrez] HTTPError 414

I create a "long" search term for Entrez.eSearch which results in an
URL 9998 characters long (search on 32 journals per ISSN).

Using this url (per copy and paste) in Firefox works without any
problems.

But using it with BioPython or more spcific urllib I get an HTTPError
414 back.

I am not sure but I think urllib itself doesn't check the URL-length.
It is the NCBI-server who throw back the 414.

But why does the server handle urllib and Firefox different?
--

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c.buhtz | 19 Dec 10:59 2015
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[Biopython] [Entrez] use the handle twice

I want to use the handle returned by Entrez.efetch() twice.

First time, write the xml to a file

	f.write(handle._handle.read())

But I want to know how much records are in there.

	records = Entrez.read(handle)
	print(records['Count'])

This doesn't work here because the handle is "empty" after the first
read()-call.

Open an read the xml-file would be a resource wasting workaround and not
a solution.
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Peter Cock | 15 Dec 19:45 2015
Gravatar

[Biopython] Labels/tags on issues on GitHub?

Vincent is suggesting we start tagging our issues on GitHub
with things like Bug, Enhancement, Docs, etc.

See https://github.com/biopython/biopython/issues/730

For an example of a project doing this in great details, see
https://github.com/numpy/numpy/issues - if anyone knows
where there system is documented please post the URL.

Peter
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Felix Heeger | 15 Dec 11:34 2015
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[Biopython] problem with KEGG.REST.kegg_conv

Hi,

first of all thanks for the awesome library. 

Here is my problem: I am trying to to use the KEGG.REST.kegg_conv
function to translate NCBI GIs to kegg gene names.

For example I think this should work:

> kegg_conv("genes","ncbi-gi:16130957")

But I get an error from Biopython:

> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.7/dist-packages/Bio/KEGG/REST.py", line 252, in kegg_conv
>     raise Exception("Bad argument target_db or source_db for kegg conv request.")
> Exception: Bad argument target_db or source_db for kegg conv request.

Looking at the code, I think the only accepted input for the function
would look something like this:

> kegg_conv("genes","ncbi-gi")

This does indeed not cause a error from Biopython, but is clearly
missing the information *which* GI I want to convert and also gives my
a HTTP Error because Kegg does not accept the resulting URL
(http://rest.kegg.jp/conv/genes/ncbi-gi).

Is this a problem with the kegg_conv function or am I missing something?

Cheers,
felix

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