From ed at pythoncharmers.com  Sat Mar  4 23:04:36 2017
From: ed at pythoncharmers.com (Ed Schofield)
Date: Sun, 5 Mar 2017 15:04:36 +1100
Subject: [melbourne-pug] Next Melbourne Python meeting - Monday 6 March
Message-ID: <AE36AC4E-68E5-4F16-B37E-874B9DE71FE8@pythoncharmers.com>

Hi everyone!

We're looking forward to another great monthly Python meeting tomorrow!

When: 6pm on Monday 6 March

What:
- Jacqueline Nowak: Python Scripting in Fiji - or image processing for lazy people
- Martin Schweitzer: Python for bioinformatics - and bioinformatics for learning Python
- TBA (possible mystery speaker)

Where: VLSCI, 700 Swanston Street, Carlton

How to get there: Take a tram 5-10 mins north from Melbourne Central station

Dinner afterwards: pizza, then drinks on Lygon Street

We hope you can join us! :-)

Cheers,
    Ed


--
Dr. Edward Schofield
Python Charmers
http://pythoncharmers.com <http://pythoncharmers.com/>
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From lev at levlafayette.com  Sat Mar  4 23:37:32 2017
From: lev at levlafayette.com (luv-ctte)
Date: Sun, 5 Mar 2017 05:37:32 +0100
Subject: [melbourne-pug] =?utf-8?q?it=27s_just_a_bombshell!?=
Message-ID: <1558683904.20170305073732@levlafayette.com>

Dear, 


Have you ever seen something like that? It's  a bombshell you  have to  see! Look at it here  http://pin.webs4actors.com/8081

Sincerely yours, luv-ctte

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From ben+python at benfinney.id.au  Sun Mar  5 17:40:52 2017
From: ben+python at benfinney.id.au (Ben Finney)
Date: Mon, 06 Mar 2017 09:40:52 +1100
Subject: [melbourne-pug] Next Melbourne Python meeting - Monday 6 March
References: <AE36AC4E-68E5-4F16-B37E-874B9DE71FE8@pythoncharmers.com>
Message-ID: <85y3wjibyj.fsf@benfinney.id.au>

Ed Schofield <ed at pythoncharmers.com> writes:

> - TBA (possible mystery speaker)

Is this still open? I have a potential presentation I can give (an app
I've been working on).

-- 
 \       ?My business is to teach my aspirations to conform themselves |
  `\              to fact, not to try and make facts harmonise with my |
_o__)                   aspirations.? ?Thomas Henry Huxley, 1860-09-23 |
Ben Finney


From jni.soma at gmail.com  Sun Mar  5 17:45:26 2017
From: jni.soma at gmail.com (Juan Nunez-Iglesias)
Date: Mon, 6 Mar 2017 09:45:26 +1100
Subject: [melbourne-pug] Next Melbourne Python meeting - Monday 6 March
In-Reply-To: <85y3wjibyj.fsf@benfinney.id.au>
References: <AE36AC4E-68E5-4F16-B37E-874B9DE71FE8@pythoncharmers.com>
 <85y3wjibyj.fsf@benfinney.id.au>
Message-ID: <4896a440-ab79-4d8c-bb79-eac2f8873782@Spark>

Hi Ben, Ed, (and everyone!)

I got confirmation earlier today that Phil Elson, who is visiting BoM from the UK?s Met Office, will give a short talk on Biggus, a library for out-of-core massive array computations.

Ben, perhaps you can sign up for next month?

Juan.

On 6 Mar 2017, 9:41 AM +1100, Ben Finney <ben+python at benfinney.id.au>, wrote:
> Ed Schofield <ed at pythoncharmers.com> writes:
>
> > - TBA (possible mystery speaker)
>
> Is this still open? I have a potential presentation I can give (an app
> I've been working on).
>
> --
> \ ?My business is to teach my aspirations to conform themselves |
> `\ to fact, not to try and make facts harmonise with my |
> _o__) aspirations.? ?Thomas Henry Huxley, 1860-09-23 |
> Ben Finney
>
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug
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From jessicarose74 at yahoo.ca  Fri Mar  3 02:57:21 2017
From: jessicarose74 at yahoo.ca (Jessica Rose)
Date: Fri, 3 Mar 2017 07:57:21 +0000 (UTC)
Subject: [melbourne-pug] help with importing fasta files nito command window
 (python)
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
Message-ID: <1229798348.1019077.1488527841618@mail.yahoo.com>

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. 

thank you and i look forward to any help. ?Jessica Rose, PhD?PDF Department of MicrobiologyFaculty of MedicineTechnion, Haifa+972-52-378-1674
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From william.leslie.ttg at gmail.com  Mon Mar  6 04:43:02 2017
From: william.leslie.ttg at gmail.com (William ML Leslie)
Date: Mon, 6 Mar 2017 20:43:02 +1100
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <1229798348.1019077.1488527841618@mail.yahoo.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
Message-ID: <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>

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.

From hartror at gmail.com  Mon Mar  6 05:56:36 2017
From: hartror at gmail.com (Rory Hart)
Date: Mon, 6 Mar 2017 21:56:36 +1100
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
Message-ID: <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>

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

From tim at growthpath.com.au  Mon Mar  6 06:36:24 2017
From: tim at growthpath.com.au (Tim Richardson)
Date: Mon, 06 Mar 2017 11:36:24 +0000
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
 <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
Message-ID: <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>

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
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug
>
-- 

Tim Richardson, Director
GrowthPath - Profit Engineers
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From jessicarose74 at yahoo.ca  Mon Mar  6 06:44:37 2017
From: jessicarose74 at yahoo.ca (Jessica Rose)
Date: Mon, 6 Mar 2017 11:44:37 +0000 (UTC)
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
 <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
 <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>
Message-ID: <167025825.2704260.1488800677020@mail.yahoo.com>

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 MicrobiologyFaculty of MedicineTechnion, Haifa+972-52-378-1674 

    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
_______________________________________________
melbourne-pug mailing list
melbourne-pug at python.org
https://mail.python.org/mailman/listinfo/melbourne-pug

-- 
Tim Richardson, Director
GrowthPath - Profit Engineers

   
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From miked at dewhirst.com.au  Tue Mar  7 03:03:26 2017
From: miked at dewhirst.com.au (Mike Dewhirst)
Date: Tue, 7 Mar 2017 19:03:26 +1100
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <167025825.2704260.1488800677020@mail.yahoo.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
 <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
 <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>
 <167025825.2704260.1488800677020@mail.yahoo.com>
Message-ID: <7c09b19e-ca2d-d59a-636e-f5e7e99f5678@dewhirst.com.au>

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 
> <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 
> <mailto: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
>     <mailto:william.leslie.ttg at gmail.com>> wrote:
>     >
>     > On 3 March 2017 at 18:57, Jessica Rose via melbourne-pug
>     > <melbourne-pug at python.org <mailto: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 <mailto:melbourne-pug at python.org>
>     > https://mail.python.org/mailman/listinfo/melbourne-pug
>
>     _______________________________________________
>     melbourne-pug mailing list
>     melbourne-pug at python.org <mailto:melbourne-pug at python.org>
>     https://mail.python.org/mailman/listinfo/melbourne-pug
>
> -- 
> Tim Richardson, Director
> GrowthPath - Profit Engineers
>
>
>
>
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug


From fabion.kauker at biarri.com  Mon Mar  6 23:26:55 2017
From: fabion.kauker at biarri.com (Fabion Kauker)
Date: Tue, 7 Mar 2017 15:26:55 +1100
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <167025825.2704260.1488800677020@mail.yahoo.com>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
 <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
 <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>
 <167025825.2704260.1488800677020@mail.yahoo.com>
Message-ID: <CACpVpkDz5aC+z_b9YRDokdPCN_6xihQrrTL1JkT67hM7aOUO4g@mail.gmail.com>

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
>
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug
>
> --
> Tim Richardson, Director
> GrowthPath - Profit Engineers
>
>
>
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug
>
>


-- 

*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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From jessicarose74 at yahoo.ca  Tue Mar  7 04:15:30 2017
From: jessicarose74 at yahoo.ca (Jessica Rose)
Date: Tue, 7 Mar 2017 09:15:30 +0000 (UTC)
Subject: [melbourne-pug] help with importing fasta files nito command
 window (python)
In-Reply-To: <7c09b19e-ca2d-d59a-636e-f5e7e99f5678@dewhirst.com.au>
References: <1229798348.1019077.1488527841618.ref@mail.yahoo.com>
 <1229798348.1019077.1488527841618@mail.yahoo.com>
 <CAHgd1hEs6+Xt7wR-C75uKUNkrYCAC2-9Dt8Gry3CwdXN+tSHCQ@mail.gmail.com>
 <9130D036-DC2D-4F40-8605-6BBBA6BAC376@gmail.com>
 <CAJKXMoLBuwYDRKbd748KMJ=amA-pmFsD0aS7Oe7vvuckJZ_thA@mail.gmail.com>
 <167025825.2704260.1488800677020@mail.yahoo.com>
 <7c09b19e-ca2d-d59a-636e-f5e7e99f5678@dewhirst.com.au>
Message-ID: <72399258.1290675.1488878130576@mail.yahoo.com>

Hi guys. I am all good. Still trying to get the bigger picture but have successfully imported a number of files for translation from RNA to protein. Yay me and you.?
Next in line...?Jessica Rose, PhD?PDF Department of MicrobiologyFaculty of MedicineTechnion, Haifa+972-52-378-1674 

    On Tuesday, March 7, 2017 10:03 AM, Mike Dewhirst <miked at dewhirst.com.au> wrote:
 

 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 
> <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 
> <mailto: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
>? ? <mailto:william.leslie.ttg at gmail.com>> wrote:
>? ? >
>? ? > On 3 March 2017 at 18:57, Jessica Rose via melbourne-pug
>? ? > <melbourne-pug at python.org <mailto: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 <mailto:melbourne-pug at python.org>
>? ? > https://mail.python.org/mailman/listinfo/melbourne-pug
>
>? ? _______________________________________________
>? ? melbourne-pug mailing list
>? ? melbourne-pug at python.org <mailto:melbourne-pug at python.org>
>? ? https://mail.python.org/mailman/listinfo/melbourne-pug
>
> -- 
> Tim Richardson, Director
> GrowthPath - Profit Engineers
>
>
>
>
> _______________________________________________
> melbourne-pug mailing list
> melbourne-pug at python.org
> https://mail.python.org/mailman/listinfo/melbourne-pug



   
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From walker.michael.luke at gmail.com  Fri Mar 10 22:51:37 2017
From: walker.michael.luke at gmail.com (walker.michael.luke)
Date: Sat, 11 Mar 2017 14:51:37 +1100
Subject: [melbourne-pug] Modeller For hire
Message-ID: <ju56kf1y6p1prrohv4kdrc5u.1489204297432@email.android.com>


    
Hello fellow python-charmers,As my first post to this list, I would like to hear about any modelling positions that anyone knows of, or is hiring for.?
I spent several years modelling hormone transport in plants using python 2.7 as part of a larger group project modelling plant growth, before doing a masters thesis at Melbourne University in bioinformatics. This latter involved a lot of statistical modelling and machine learning in the R programming language.
I also have Java and Fortran and a little bit of C++ and MatLab. I also have experience with molecular dynamics and brownian motion simulations of ion transport through cell membranes.?
Prior to modelling I was a theoretical physicist, with publications in international journals. My experience has been largely academic up to this point, but I would be keen on a position in the private sector.
I currently work at La Trobe University doing molecular modelling in the context of drug design. This position ends in October and I am available on Mondays up until then.
I can be reached at this email address or on 0457353331.
Thank you?Michael Walker?
Sent from my Samsung G360G on the Telstra Mobile Network
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From tleeuwenburg at gmail.com  Mon Mar 20 07:41:58 2017
From: tleeuwenburg at gmail.com (Tennessee Leeuwenburg)
Date: Mon, 20 Mar 2017 22:41:58 +1100
Subject: [melbourne-pug] PyCon Australia 2017 is calling for proposals
Message-ID: <CADhgxgdc1aGHmCoyeQSMOCAhopfcEamwDh8rrVPKpVQiFybkjA@mail.gmail.com>

Welcome all -- coders, tinkerers, contributors, presenters, thinkers,
teachers and artists... our call for proposals is finally here!

In just a few more months, PyCon AU will be in full swing. We have
developed both our community engagement and technical depth year on year,
consolidating in people?s hearts and minds the value of coming along to
this fantastic event. Those who have presented or attended before can
attest to the high calibre of our speakers, the quality of our technical
content, and also the welcoming and inclusive approach to new speakers and
people from a broad variety of backgrounds.

Please follow this link <https://2017.pycon-au.org/program/cfp/> for more
details on how to submit a proposal for PyCon AU 2017.

Regardless of whether you are intending to submit a proposal, please help
us spread the word on twitter, Facebook and email, by sharing a link to
this page, along with the hashtag #pyconau.

Finally, although the website gnomes and bugfinding goblins have been
working hard to achieve a smooth user experience, Murphy is as harsh
lawmaker, and it?s possible you might need to contact us with questions or
raise issues. Please email program at pycon-au.org should you need to reach us.
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