Patrick McGrath | 5 May 12:57 2015

[Biopython] Reading in chimera generated files


I am trying to use Bio.PDB to read in a PDB file generated from matchmaker in chimera. It seems that Chimera changes the HG to Hg and ZN to Zn in the last column of the pdb file which causes an error:

assert not element or element == element.upper(), element
AssertionError: Hg

Is there any solution to this besides creating a script to manually edit the pdb file generated by chimera?
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Ryan J. Hope | 4 May 19:11 2015

[Biopython] codon optimisation script

Does anyone know of a python script for codon optimization of a FASTA file using a codon usage table as a reference?

Hi, I need a template Python script (or a complete script or perhaps just some advice) for conversion of a gene belonging to R. eutrophia for heterologous expression in C. acetobutylicum. I have a codon usage table as a .txt file copied from Kazusa and the gene I'm interested in as FASTA. If anyone has a .py file they can upload that would be great :)

Kind regards,
Ryan H.

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Linlin Zhao | 30 Apr 16:34 2015

[Biopython] Suggestions for working sequence data

Hi There,

I am new to Biopython, but have some experience with Python. Python is 
my favourite language, I really want to learn and apply Biopython.

I need to work on a large dataset, the whole genomic sequences of all 
bacteria (~2000) from genBank, with size of about 80GB. Each folder 
within the dataset is one organism, which includes several files for 
different types of data.

My task is easy to describe but I need some suggestions of how to work 
on the whole dataset efficiently with Biopython:

1. load FASTA file .ffn (protein genes) in each folder, which looks like 

> gi|158303474|gb|CP000828.1|:3233-4009 Acaryochloris marina MBIC11017, 
> complete genome

According to the address (3233-4009) of this gene, I then go to .fna 
file within the same folder which has the whole genome sequence, and 
read 20 base pairs (3213-3232) as the approximate promoter for the gene. 
Finally I construct a new gene sequence with address 3213-4009, which is 
just adding 20bp in front of the original gene sequence.

2. run motifs, for instance "TACGTC", through all those gene sequences 
to find out their frequency of appearance in all bacterial protein 

I hope my description is clear. Problem in short is that I need to work 
on two files in all 2000 folders, how to load and write file 

Would anyone give some hints?

Thanks in advance,
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Katie Edmonds | 30 Apr 16:15 2015

[Biopython] graphics library suggestions?


I want to write a script that reads a list of genes from a table, including their start and endpoint on the chromosome, and generates vector graphics arrows on a line, with lengths and positions to scale for their size and location in the genome, colored by some value given in the table. Does anyone have any suggestions for a useful library for creating nice vector graphics arrows?

Here's an example of what I'm talking about:

Alternatively, is there already a good tool that does what I want?

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Alaksh Choudhury | 6 Apr 22:16 2015

[Biopython] Problems with using Bio.PDB.NACCESS


I am having trouble using Bio.PDB.NACCESS.

The following is my code:
import Bio.PDB.NACCES as nac
data = nac.run_naccess(structure[0],"1BVU.pdb")

I get the following error:
WindowsError                              Traceback (most recent call last)
<ipython-input-54-1d30779fea29> in <module>()
----> 1 data = nac.run_naccess(structure[0],"1BVU.pdb")

C:\Users\user\AppData\Local\Enthought\Canopy\User\lib\site-packages\Bio\PDB\ in run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
     32     # make temp directory;
---> 33     tmp_path = tempfile.mkdtemp(dir=temp_path)
     35     # file name must end with '.pdb' to work with NACCESS

C:\Users\user\AppData\Local\Enthought\Canopy\App\appdata\\lib\tempfile.pyc in mkdtemp(suffix, prefix, dir)
    331         file = _os.path.join(dir, prefix + name + suffix)
    332         try:
--> 333             _os.mkdir(file, 0700)
    334             return file
    335         except OSError, e:

WindowsError: [Error 3] The system cannot find the path specified: '/tmp/tmpdetkbw' 


Alaksh Choudhury
Graduate Student | Gill lab and Kaar lab
Department of Chemical Engineering
University of Colorado, Boulder

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Mario Latendresse | 4 Apr 17:54 2015

[Biopython] PythonCyc for Pathway Tools

Hello All,

This is not a Biopython specific posting, yet I believe it may interest many Biopython users.

PythonCyc allows you to interact with Pathway Tools using the Python programming language.
The latest version of Pathway Tools (19.0) was just released (for all release notes of Pathway Tools, please see Released Notes).
Please see below for more details on a complete API documentation and a tutorial for PythonCyc.

-- Mario Latendresse
Computer Scientist
SRI International

PythonCyc: A Python Interface for Pathway Tools

It is now possible to use the Python programming language to query and modify an organism database (i.e., a PGDB) of Pathway Tools via the newly developed PythonCyc package. You will need a recent version of Pathway Tools, that is, version 18.5 (November 2014) or version 19.0 (March 2015), to use PythonCyc.

  • PythonCyc is hosted on GitHub. To use PythonCyc, you will have to download it from GitHub and install it on your local computer.
  • The PythonCyc tutorial describes how to install PythonCyc and the main functionalities available.
  • PythonCyc has over 150 functions to interact with Pathway Tools. In particular, you can extract and manipulate all data from PGDBs and modify your own PGDBs by using the well-known Python programming language.
  • You can access MetaFlux, a Flux Balance Analysis tool, via PythonCyc.
  • The complete PythonCyc API documentation is available online.

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Alexey Morozov | 31 Mar 10:39 2015

[Biopython] Lots of pairwise alignments

Dear colleagues, what's the fastest way to produce a lot of pairwise alignmnents from (bio)python? Bio::pairwise2 is pretty slow and allows only for linear gap penalties, not affine ones. So currently I launch a bunch of subprocesses of NWalign or needle. It works, but is about twice slower then clustalw pairwise alignments. Which, alas, clustal discards after building guide tree and doesn't print.

Is this the fastest way it can be or I have missed some other tool?

Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Björn Johansson | 30 Mar 08:41 2015

Re: [Biopython] Biopython Digest, Vol 147, Issue 13


has pcr functionality.

have a look at the documentation


On Sun, Mar 29, 2015 at 1:00 PM, <biopython-request <at>> wrote:
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Determine thermocycler sequence for PCR (Horea Christian)


Message: 1
Date: Sat, 28 Mar 2015 23:20:52 +0100
From: Horea Christian <h.chr <at>>
To: biopython <at>
Subject: [Biopython] Determine thermocycler sequence for PCR
Message-ID: <1427581252.22280.12.camel <at>>
Content-Type: text/plain; charset="utf-8"

Hi, do you guys know any good literature reference that provides a
reliable equation to determine the ideal step temperatures and durations
for a PCR given the primers and the amplicon?

I see annealing temps can be calculated with biopython via
SeqUtils.MeltingTemp, which is nice, but it would be even greater if we
could provide assistance with designing more of the PCR protocol. I am
asking this also because I have a set of new primers over here which
likely need a new thermocycler protocol, and all I found via google was
very vague.

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End of Biopython Digest, Vol 147, Issue 13

Björn Johansson
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Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
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Goutham atla | 29 Mar 20:09 2015

[Biopython] Biopython genepop help

Dear All,

I am trying to use genePop module of Biopython. I am trying to create a Record object.

I am little bit confused as I did not find any examples on how to use Record class.

If I have a file named "test.genepop", how should I create a Record object out of that file ?

My ultimate goal is to replace 0000 0000 000 notation to some thing like 9 9 9 to indicate missing data. Is there any simpler way of doing it ?

Goutham Atla
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Horea Christian | 28 Mar 23:20 2015

[Biopython] Determine thermocycler sequence for PCR

Hi, do you guys know any good literature reference that provides a reliable equation to determine the ideal step temperatures and durations for a PCR given the primers and the amplicon?

I see annealing temps can be calculated with biopython via SeqUtils.MeltingTemp, which is nice, but it would be even greater if we could provide assistance with designing more of the PCR protocol. I am asking this also because I have a set of new primers over here which likely need a new thermocycler protocol, and all I found via google was very vague.

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[Biopython] SciPy 2015 Call for Propsals & Registration Open - tutorial & talk submissions due April 1st - Life & Medical Sciences Mini-Symposia planned

Wanted to share the Call for Proposals and registration info about the 2015
SciPy Conference (below) - more info on the conference website at Thought you might have some interesting
proposals for the computational life and medical sciences minisymposia?

Best regards, 

Courtenay Godshall
SciPy 2015 Communications Co-Chair


**SciPy 2015 Conference (Scientific Computing with Python) Call for
Proposals and Registration Open: Submit Your Tutorial and Talk Ideas by
April 1, 2015 at**  

SciPy 2015, the fourteenth annual Scientific Computing with Python
conference, will be held July 6-12, 2015 in Austin, Texas. SciPy is a
community dedicated to the advancement of scientific computing through open
source Python software for mathematics, science, and engineering. The annual
SciPy Conference brings together over 500 participants from industry,
academia, and government to showcase their latest projects, learn from
skilled users and developers, and collaborate on code development. The full
program will consist of two days of tutorials by followed by three days of
presentations, and concludes with two days of developer sprints. More info
available on the conference website at; you can
also sign up on the website for mailing list updates or follow  <at> scipyconf on
Twitter. We hope you'll join us - early bird registration is open until May
15, 2015 at 

We encourage you to submit tutorial or talk proposals in the categories
below; please also share with others who you'd like to see participate!
Submit via the conference website  <at>

The SciPy experience kicks off with two days of tutorials. These sessions
provide extremely affordable access to expert training, and consistently
receive fantastic feedback from participants. We're looking for submissions
on topics from introductory to advanced - we'll have attendees across the
gamut looking to learn. Whether you are a major contributor to a scientific
Python library or an expert-level user, this is a great opportunity to share
your knowledge and stipends are available. Submit Your Tutorial Proposal on
the SciPy 2015 website:

*SCIPY TALK AND POSTER SUBMISSIONS - DUE April 1, 2015* SciPy 2015 will
include 3 major topic tracks and 7 mini-symposia tracks. Submit Your Talk
Proposal on the SciPy 2015 website:

Major topic tracks include:
- Scientific Computing in Python (General track)
- Python in Data Science
- Quantitative and Computational Social Sciences

Mini-symposia will include the applications of Python in:
- Astronomy and astrophysics
- Computational life and medical sciences
- Engineering
- Geographic information systems (GIS)
- Geophysics
- Oceanography and meteorology
- Visualization, vision and imaging

If you have any questions or comments, feel free to contact us at:
scipy-organizers <at>

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