On 6/03/2017 10:44 PM, Jessica Rose via melbourne-pug 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?
I know nothing about fasta nor biopython but there is a pattern you need
to adopt to import stuff in Python. Python 2.7 and 3.x are slightly
different but you can make them behave more or less the same by
inserting the following incantation at the top of your Python 2.7
script/program ... (not necessary if you are using Python 3)
from __future__ import absolute_import, unicode_literals, division
That imports some Python 3 features into Python 2.
I personally would avoid Idle and go straight to Notepad++ (as suggested
earlier) to write your scripts.
So to your question ... I would try
from biopython import fasta
At that point you have imported the entire fasta suite (aka namespace)
of functions, classes, constants and so on. You call them like this ...
x = fasta.method_one()
Next write your first script in Notepad++ and save it to say
C:\Users\Jessica\beginnings\first.py
Then, in Windows Explorer navigate to that directory and open an
ordinary command prompt. You should see C:\Users\Jessica\beginnings>
Enter "python first.py" and your script should run. If it doesn't you
should see the traceback and be able to fix it.
Check this out ...
https://www.blog.pythonlibrary.org/2016/03/01/python-101-all-about-imports/
Good luck
Mike
Jessica Rose, PhD
PDF Department of Microbiology
Faculty of Medicine
Technion, Haifa
+972-52-378-1674
On Monday, March 6, 2017 1:36 PM, Tim Richardson
<t...@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, <hart...@gmail.com
<mailto:hart...@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....@gmail.com
<mailto:william.leslie....@gmail.com>> wrote:
>
> On 3 March 2017 at 18:57, Jessica Rose via melbourne-pug
> <melbourne-pug@python.org <mailto:melbourne-pug@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:
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