Pathmanaban Ramasamy | 20 Apr 00:04 2014
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[Biopython] Graph representation

Dear Biopython users,
     Can anyone help me  how to represent residue contact map of pdb files
in adjacency list? Also need some  good references/articles related.

Thanks in advance,
Pathmanaban.
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Vikram K | 19 Apr 16:31 2014
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[Biopython] cosmic data

Dear Biopython users,
is there any biopython module which can be used to help analyze cosmic
data?

Regards
Vikram
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Cannatella, David | 16 Apr 00:37 2014
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[Biopython] Biopython and OSX Mavericks problem.

I've had the same problem as Mike Shaffer (8 April) on the discussion list (see my errors below).

I had tried the possible solutions mentioned (including the export commands below), including those on
the stackoverflow site, but none has worked so far.

Some posted solutions have included installing other versions of python, etc., but this is not practical
for several reasons.

Is re-installing an earlier version of XCode a viable option for me?
Or is it likely that there might be a fix in BioPython in the next month?

Thanks in advance,
Dave

=========
export CPPFLAGS=-Qunused-arguments
export CFLAGS=-Qunused-arguments

===============
...
building 'Bio.cpairwise2' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common
-fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall
-Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes
-DENABLE_DTRACE -arch x86_64 -arch i386 -pipe
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c
Bio/cpairwise2module.c -o build/temp.macosx-10.9-intel-2.7/Bio/cpairwise2module.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'cc' failed with exit status 1
(Continue reading)

Csaba Kiss | 15 Apr 16:58 2014

[Biopython] python advice needed

Hi!
I need some advice how to get better in python. I have written a 
software package to analyze antibody deep sequencing data. This was my 
first experience with python and I am not a programmer. The end result 
works, however, if a professional coder looks at the scripts, it is 
obvious that it was written by an amateur. I am planning to re-write the 
code into a better format that is extendable and more user and coder 
friendly. At the moment the script only relies on biopython to get the 
sequences and quality values out of sff and fastq files, the rest is 
custom written. I would like to rely more on biopython and also perhaps 
extend biopython with new features.
The problem I am having is object oriented python and classes. I 
understand the concept of both, but it's completely different to 
actually use it. I would like to ask help from scientist who are in a 
similar situation, as myself. I am a molecular biologist with interest 
in coding, but little background. Do you have any good tutorials books 
about python classes and OOP? For example, when I learned python I found 
the Google python class, extremely valuable. I practically looked at the 
videos and solved the problems and that sent me on my way to python:
https://developers.google.com/edu/python/?csw=1

Any help would be appreciated:
Csaba

--

-- 
Best Regards:
Csaba Kiss PhD, MSc, BSc
TA-43, HRL-1, MS888
Los Alamos National Laboratory
Work: 1-505-667-9898
(Continue reading)

George Devaniranjan | 11 Apr 17:58 2014
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[Biopython] SVDSuperimposer()

I was wondering if there is a faster way to do the following.

I am minimizing a protein structure and one of the 'measurements" is that
the minimized structure be as close to the starting value as possible.

Currently I use SVDSuperimposer.SVDSuperimposer() to calculate the RMSD
difference.

When I checked the various "energy terms" that are used to evaluate the
structure I find that the bottleneck is
indeed SVDSuperimposer.SVDSuperimposer().

Is there a way to do this more efficiently ?

Thank you
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Andrew Mather | 11 Apr 10:28 2014
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[Biopython] Install problems (Numpy problem ?)

Hi,

I'm attempting to install 1.63 from a git cloned directory into Python 2.7.

Numpy 1.8.0 appears to have installed correctly and can be imported at
the prompt.

However the BioPython build fails with the message below:

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC
-I/usr/local/lib/python2.7/site-packages/numpy/core/include
-I/usr/local/include/python2.7 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-x86_64-2.7/Bio/Cluster/clustermodule.o
In file included from
/usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:4,
                 from
/usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from
/usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from Bio/Cluster/clustermodule.c:3:
/usr/local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:114:10:
error: #error Unsupported size for type off_t
error: command 'gcc' failed with exit status 1

Any advice would be gratefully received, as we're in the middle of
racing to commission a new system and running out of time.

Thanks,
Andrew
(Continue reading)

Asma Riyaz | 10 Apr 20:29 2014
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[Biopython] Phylo Tree: Need to align Taxa for visual representation

Hi,

I am using Bio.Phylo package to display a tree, and I am having problems
representing it the way I want it to be.

Here is my code:

    gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
,width_ratios=[1,1,-2,2],hspace=0,wspace=0)
    phyl_ax=plt.subplot(gs[0])
    Phylo.draw(tree, axes=phyl_ax, do_show=False,show_confidence=False)

With the above code I am able to produce, wrong.png
I would like the tree to be displayed similar to correct.png (I got this of
a 3rd party software MEGA) and want to automate the process (hence Phylo)

I have tried several of rcParams settings with line specifically but no
success.

Appreciate any help provided.
Asma
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Tommy Carstensen | 8 Apr 23:23 2014
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[Biopython] random access to bgz file

I read the Biopython tutorial:
http://biopython.org/DIST/docs/tutorial/Tutorial.html

It does not explain how to do random access to a bgz file. Can someone point me to a tutorial on how to do this?
Thank you.

Best wishes,
Tommy

--

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

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Tommy Carstensen | 8 Apr 23:24 2014
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[Biopython] random access to bgz file

I read the Biopython tutorial:
http://biopython.org/DIST/docs/tutorial/Tutorial.html

It does not explain how to do random access to a bgz file. Can someone point me to a tutorial on how to do this?
Thank you.

Best wishes,
Tommy

--

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

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Mike Shaffer | 8 Apr 23:05 2014

[Biopython] Installation Problems in Mavericks

Hello,
I am attempting to install biopython and I am getting this error.  I have
install xcode command line tools and verified that it is installed using
pkgutil.  I found some people saying that this problem was solved by
installing xcode command line tools but this didn't work.  Some seemed to
say that this was just because of the new version of Apple's complier.  Any
work arounds or tips would be greatly appreciated.  Full read out from
running setup.py build is below:

python setup.py build

running build

running build_py

running build_ext

building 'Bio.cpairwise2' extension

cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os
-pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd
-DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes
-Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes
-DENABLE_DTRACE -arch x86_64 -arch i386 -pipe
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-c Bio/cpairwise2module.c -o
build/temp.macosx-10.9-intel-2.7/Bio/cpairwise2module.o

clang: error: unknown argument: '-mno-fused-madd'
[-Wunused-command-line-argument-hard-error-in-future]
(Continue reading)

Tiago Antao | 8 Apr 17:22 2014
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[Biopython] Job: Bioinformatics/PopGen of Disease vectors (Tropical Medicine)

Dear all,

We currently have a position here for a bioinformatician with a good
population genetics background.
The Liverpool School of Tropical Medicine works with neglected tropical
diseases and in our department we are mainly focused on disease vectors
(mosquitoes, flies, ...).
The postdoc accepting this position would be the first in the group
(and the second in the department) doing bioinformatics, thus with a lot
of freedom to choose their preferred tools. So, if you are a
Biopythoneer you would most probably be able to use (Bio)python.

Liverpool is one of the cheapest cities in the UK and has been ranked
as one of the top 5 big cities to live in the UK:

http://www.telegraph.co.uk/news/uknews/10386993/Bristol-is-best-city-to-live-in-the-UK.html

As to the position, you can find more details here:

http://www.jobs.ac.uk/job/AIL535/post-doctoral-research-assistant-in-bioinformatics-and-population-genetics/

Charles' page (the PI), can be found here:
http://www.lstmliverpool.ac.uk/research/departments/staff-profiles/charles-wondji

For questions, please do not hesitate to contact Charles directly (or
me if you prefer, but I am not directly related to the position).

Tiago
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(Continue reading)


Gmane