[melbourne-pug] help with importing fasta files nito command window (python)

[Fabion Kauker]

Hi Jessica

without knowing your environment and a error it will be hard to diagnose.

It would be helpful if you could share:
0) OS (read you are using windows)
1) Python install process
 a) Python version (launch python and it should be the first thing shown in
the cmd line)
2) Pip version installed
 a) type "pip --version" and then "pip freeze" to see which libraries are
installed.
3) Current error

It may be easier to install anaconda
<https://tracking.cirrusinsight.com/4c433fe1-2452-4bab-a18d-8a7fe44b9019/continuum-io-downloads>,
it comes complete with a bunch of libraries and you can easily create
<https://tracking.cirrusinsight.com/4c433fe1-2452-4bab-a18d-8a7fe44b9019/conda-io-docs-downloads-conda-cheatsheet-pdf>
environments.

For pyfasta it should be as simple as:
conda install -c bioconda pyfasta=0.5.2

There also appears to be a bio version
<https://tracking.cirrusinsight.com/4c433fe1-2452-4bab-a18d-8a7fe44b9019/bioconda-github-io>
for conda.

Hope this helps

Fabion




On Mon, Mar 6, 2017 at 10:44 PM, Jessica Rose via melbourne-pug <
melbourne-pug at python.org> wrote:

> yeah that pip command gives me trouble too! i really am a newbie at all
> this so sorry for seeming slow.
>
> when i have my command window open (idle) what do i type in to import
> fasta from biopython?
>
> Jessica Rose, PhD
> PDF Department of Microbiology
> Faculty of Medicine
> Technion, Haifa
> +972-52-378-1674 <+972%2052-378-1674>
>
>
> On Monday, March 6, 2017 1:36 PM, Tim Richardson <tim at growthpath.com.au>
> wrote:
>
>
> The module is not installed. Read pyfasta installation instructions.
> Usually it will be
> pip install pyfasta
>
>
> On Mon, 6 Mar. 2017, 21:57 Rory Hart, <hartror at gmail.com> wrote:
>
> Oh dear you've asked programmers about what text editor they prefer, let
> the religious wars begin!
>
> I would suggest sublime 3 personally. It is straightforward to use out of
> the box and later you can install a bunch of plugins once you get a bit
> more advanced that can help your coding.
>
> I assume by your name you are a lady (or identify as such), are you aware
> of the PyLadies Meetup?
>
> > On 6 Mar. 2017, at 8:43 pm, William ML Leslie <
> william.leslie.ttg at gmail.com> wrote:
> >
> > On 3 March 2017 at 18:57, Jessica Rose via melbourne-pug
> > <melbourne-pug at python.org> wrote:
> >> Hi there, I am having trouble with importing or reading text files
> (fasta
> >> files) when writing code with python. I am very new to this and have
> been
> >> practicing python code writing from the command window with great
> success.
> >> but the time has come for me to apply what i have learned to real
> files. I
> >> am a protein biologist and am starting to get more into bioinformatics.
> >> python is definitely the way for me to go.
> >>
> >> i have looked at every online site and tried just about everything
> >> suggested. Do you think there is an easy solution to my problem? I am
> >> working primarily on a windows operating system.
> >>
> >
> > Hello! It is great that you are getting to saving your programs to a
> file.
> >
> > What are you trying so far?  Are you using notepad.exe?  Note that
> > wordpad and MS Word will not work!  Some people also like notepad++
> > when on Windows.
> >
> > When you save your file, make sure the 'save as type' select list
> > shows 'all files *.*' if it doesn't have anything for python.  then
> > you can add a .py extension on your file.
> >
> > Have you ever used the printscreen feature to get an image of the
> > problem you are seeing?
> >
> > --
> > William Leslie
> >
> > Notice:
> > Likely much of this email is, by the nature of copyright, covered
> > under copyright law.  You absolutely MAY reproduce any part of it in
> > accordance with the copyright law of the nation you are reading this
> > in.  Any attempt to DENY YOU THOSE RIGHTS would be illegal without
> > prior contractual agreement.
> > _______________________________________________
> > melbourne-pug mailing list
> > melbourne-pug at python.org
> > https://mail.python.org/mailman/listinfo/melbourne-pug
>
> _______________________________________________
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>
> --
> Tim Richardson, Director
> GrowthPath - Profit Engineers
>
>
>
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>
>


-- 

*Fabion Kauker                 *

*Optimisation Consultant*
*Biarri Networks*
M +1 415 489 8434
E fabion.kauker at biarri.com
W www.biarrinetworks.com
A 180 Sansome St.
  San Francisco
  CA 94104
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