biopython on windows

[Jeswin]

Hi guys,

I need the help of the software experts. I am not very familiar with installing python and it's modules on windows. I need Biopython to run a FASTQ to FASTA conversion script. I installed Python 2.7 but I can't install the NumPy module needed for Biopython. I get an error (can't remember exact), but I think it has to do with the C compiler needed to install the module.

So, I found that using pip, you can install the .whl file. But I am not sure which versions of which modules work together. So can anyone tell me how to do get this up and running, like which python, numpy, and biopython versions to get and how to install them with the least trouble.

Thanks

--

In necessariis unitas, in dubiis libertas, in omnibus caritas.
-Marco Antonio Dominis

[Gavin Scott]

Stop right there. Now go get Anaconda (free) which will resolve all
your Python issues. Comes with Python 2.7, NumPy, Pandas, etc., etc.
all out of the box, and you can get things like biopython via "conda
install biopython" in an Anaconda Command Prompt window. No compilers
or other prerequisites required. Windows/Mac/Linux.

https://store.continuum.io/cshop/anaconda/

Once you have it installed, check out iPython Notebook for doing all
your scientific computation. (do a "conda update ipython" to get the
newly released 3.0 too)

http://ipython.org/notebook.html

Best scientific toolset ever!

G.

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[Jeswin]

On Wed, Mar 25, 2015 at 7:19 PM, Gavin Scott <ga...@learn.bio> wrote:

Stop right there. Now go get Anaconda (free) which will resolve all
your Python issues. Comes with Python 2.7, NumPy, Pandas, etc., etc.
all out of the box, and you can get things like biopython via "conda
install biopython" in an Anaconda Command Prompt window. No compilers
or other prerequisites required. Windows/Mac/Linux.

https://store.continuum.io/cshop/anaconda/

Once you have it installed, check out iPython Notebook for doing all
your scientific computation. (do a "conda update ipython" to get the
newly released 3.0 too)

http://ipython.org/notebook.html

Best scientific toolset ever!

G.

For real? Cool. That would be the best solution. I was starting to think cygwin, but the simpler and faster I can get this set up would be the best.

[Nathan McCorkle]

When I need 64-bit binary packages, I go to this University of California site:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython

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--
-Nathan

[Gavin Scott]

On Thu, Mar 26, 2015 at 12:03 AM, Nathan McCorkle <nmz...@gmail.com> wrote:
> When I need 64-bit binary packages, I go to this University of California site:
> http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
> http://www.lfd.uci.edu/~gohlke/pythonlibs/#biopython

Yes,

http://www.lfd.uci.edu/~gohlke/pythonlibs/

is the go-to place for Windows compiled binary Python packages (when
you can't get them via conda). They are generally packaged with a nice
installer that will ask you which Python instance on the system you
want them placed in. These days the only thing I commonly need from
there is psycopg2 (Postgres driver) which for some reason is not
available otherwise and is a pain-in-the-neck to build and install
otherwise.

Fortunately conda completely solves the Python packaging problem for
the (very many) packaged they provide (and others can be found on the
binstar community conda package sharing site). List of official
conda-available packages:

http://docs.continuum.io/anaconda/pkg-docs.html

You can also use pip to install stuff on top of Anaconda if there's no
other solution.

The combination of Python's universality (you can pretty much find
Python packages to do, or talk to, anything), the power of the SciPy
stack (NumPy, Pandas, etc.), the iPython Notebook to drive all this
power and use it for collaboration, and the Anaconda Python
distribution to make access to all of this totally painless, together
make up a system for technical computation which is unmatched at this
time in my opinion. Everyone should really give it a try. Here's an
example iPython Notebook using the public notebook viewer site that
demos the Bokeh plotting library, another another open-source package
from the same people who put Anaconda together:

http://nbviewer.ipython.org/github/bokeh/bokeh-notebooks/blob/master/quickstart/quickstart.ipynb

it shows you the sort of things you can do using the notebook system.

G.

[Cathal (Phone)]

Good time to chip in and point people at pythonanywhere.com, who provide a super batteries-included set of environments including more modern versions than 2.7 (up to 3.4 I think). That includes iPython and I think Biopython, and you can have web-shells and SSH with free accounts quite aside from hosting a webapp.

The drawback? Without a basic paid account you can't make requests to sites outside their whitelist. I don't know offhand whether NBCI is on the whitelist..

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Tom Randall]

Here is an awk that should do it:

awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}'  infile.fastq > outfile.fasta &   

[Jeswin]

On Wed, Mar 25, 2015 at 7:19 PM, Gavin Scott <ga...@learn.bio> wrote:

> Stop right there. Now go get Anaconda (free) which will resolve all
> your Python issues. Comes with Python 2.7, NumPy, Pandas, etc., etc.
> all out of the box, and you can get things like biopython via "conda
> install biopython" in an Anaconda Command Prompt window. No compilers
> or other prerequisites required. Windows/Mac/Linux.
>

This was so helpful. I got the script work. I'll have to make sure the
conversion went well. Thanks so much.

On Thu, Mar 26, 2015 at 11:24 AM, Tom Randall <tara...@gmail.com> wrote:
>
> Here is an awk that should do it:
>
> awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' infile.fastq > outfile.fasta &
>

Would be a good solution, except, I'm on Windows. This is mainly for
my colleagues, who are mainly gui-folk, so I'm trying to keep it as
simple as possible.

[Cathal Garvey]

I love the habitual way you throw the "&" in at the end.

Anyway, I think our OP isn't even using Linux so awk, crazy black magic
even to most Linux users, is out of the question. :)

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[Simon Quellen Field]

Awk runs fine on my Windows machine.

:-)

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Scientific Director, IndieBio Irish Programme
 Got a biology-inspired business idea that $50,000 -
 & 3 months in a well equipped lab could accelerate?
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