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How to fix error message "from: can't read /var/mail/pwn" [duplicate]

I am running a (bio)python script which results in the following error:
from: can't read /var/mail/Bio
seeing as my script doesn't have anything to with mail, I don't understand why my script is looking in /var/mail.
What seems to be the problem here? i doubt it will help as the script doesn't seem to be the problem, but here's my script anyway:
from Bio import SeqIO
from Bio.SeqUtils import ProtParam
handle = open("examplefasta.fasta")
for record in SeqIO.parse(handle, "fasta"):
seq = str(record.seq)
X = ProtParam.ProteinAnalysis(seq)
print X.count_amino_acids()
print X.get_amino_acids_percent()
print X.molecular_weight()
print X.aromaticity()
print X.instability_index()
print X.flexibility()
print X.isoelectric_point()
print X.secondary_structure_fraction()
what is the problem here? bad python setup? I really don't think it's the script.

No, it's not the script, it's the fact that your script is not executed by Python at all. If your script is stored in a file named script.py, you have to execute it as python script.py, otherwise the default shell will execute it and it will bail out at the from keyword. (Incidentally, from is the name of a command line utility which prints names of those who have sent mail to the given username, so that's why it tries to access the mailboxes).
Another possibility is to add the following line to the top of the script:
#!/usr/bin/env python
This will instruct your shell to execute the script via python instead of trying to interpret it on its own.

I ran into a similar error when trying to run a command.
After reading the answer by Tamás,
I realized I was not trying this command in Python but in the shell (this can happen to those new to Linux).
Solution was to first enter in the Python shell with the command python
and when you get these >>>
then run any Python commands.

Same here. I had this error when running an import command from terminal without activating python3 shell through manage.py in a django project (yes, I am a newbie yet). As one must expect, activating shell allowed the command to be interpreted correctly.
./manage.py shell
and only then
>>> from django.contrib.sites.models import Site

Put this at the top of your .py file (for Python 2.x)
#!/usr/bin/env python
or for Python 3.x
#!/usr/bin/env python3
This should look up the Python environment. Without it, it will execute the code as if it were not Python code, but shell code. If you need to specify a manual location of the Python environment, put
#!/#path/#to/#python

for Mac OS just go to applications and just run these Scripts Install Certificates.command and Update Shell Profile.command, now it will work.

For Flask users, before writing the commands, first make sure you enter the Flask shell using:
flask shell

why the same powershell command run on the powershell console but not using os.system?

I would like to include a command to create a 7zip archive withinin a Python script. Since I am working on Windows, I need to pass the command to the powershell console. I am planning to do it with os.system (I am aware that this is not the best way to do it and that I should use subprocess, but I really just need a quick fix and it would not be time effective for me to learn to use a new module in this context).
The following command works if run from the powershell console
&'C:\\Program Files\\7-Zip\\7z' a -mx=0 X:/myarch.zip X:/myarch
So I recreate the same string within python like this:
cmdl = r"&'C:\\Program Files\\7-Zip\\7z' a -mx=0 X:/myarch.zip X:/myarch"
The string is interpreted as follow:
"&'C:\\\\Program Files\\\\7-Zip\\\\7z' a -mx=0 X:/myarch.zip X:/myarch"
Now, if I copy-paste the above string within the powershell console, it runs without problems. However, if I run it within python using os.system(cmdl) I got the following error
"The filename, directory name, or volume label syntax is incorrect"
Why is this the case and how can I fix this issue ?

os.system is meant for executing cmd commands, cmd commands can be ran in powershell maybe after all powershell is a bit advanced but I'm sure that you can't run a cmd command in powershell, henceforth your code is not working.
However a creative solution for executing a powershell command from python(not using python) would be to write your command into a .ps file(powershell script)and then run it using os.startfile()(use this code: os.startfile("script.ps"))

Program to run another through command prompt

I am not even sure if this question is answerable.
Basically in my game I am using the colorama features to make it look nice, but the colorama features only work when you access python in command prompt, so my question is how I can get python program to run another via command prompt, is this doable or not? I have tried installing win32 but that is in python 2 format and I am using 3.4 so I was getting syntax errors that I wasnt sure how to fix.

I am not sure why is this happening, I mean, colorama not working without starting from prompt.
Perhaps something with environment variables PATH or something.
This is one suggestion, and I am not sure that it will work as we will not be changing the window program is running in, just invoking cmd.exe i.e. command prompt to start within it and start python and your script again.
But it is worth a try:
# Start of your program:
import sys, os
if "started_with_prompt" not in sys.argv:
cmd = 'cmd /C "'+sys.executable+' '+" ".join(sys.argv)+' started_with_prompt"'
os.system(cmd)
sys.exit()
print "the rest of your program"
If this doesn't work, there are tricks that can be used through subprocess module to do the similar thing.
Also, you should look at cmd.exe's help to see whether you should use some other switch than /C to enable environment and/or registry extensions.
But, essentially, you should be able to get the same result by making a shortcut with the command like one in cmd variable, or a batch file that starts Python. Like this:
#echo off
cmd /C "C:\Python27\python.exe path_to_your_script.py"
I think both would work, but somehow that you wouldn't like this solution.
Well, I think that shortcut would need a full path to cmd.exe which is:
C:\Windows\system32\cmd.exe
Let me know if it doesn't work.

using bash commands in python on mac: error 127

I am using am using Python 2.7 on MacOS and want to use a bash command within a python script.
command = "someProgram --option1 value 1 --option2 value 2"
I had to include the path of this program in my bash_profile in order to run it. I tested so far:
os.system(command)
and
subprocess.check_call(command.split(" "),shell=True)
Neither worked. The latter threw error 127 and the first one only returned 32512. A google search told me that this occurs when the command is not known.
If I now start this command within the terminal everything works perfectly fine.
Do I have to include something such that python can find this command? Why is this behavior?

With shell=True the cmd needs to be a string.
subprocess.check_call(command, shell=True)
where command is of type str

Thanks for your help. The final solution is kind of stupid. I started spyder via the anaconda GUI. If I do so the above code does not work.
If I run this directly via the console or start spyder via the console everything is fine. It seems that the bash_profile is not loaded when spyder is loaded but requires the console to do so

subprocess: PyDev console vs. cmd.exe

I'm trying to call a process from python using subprocess.call as shown below:
from subprocess import call
exePath = 'C:\\Test\\EXE.exe'
inPath = 'C:\\Test\\IN.in'
outPath = 'C:\\Test\\OUT.out'
call([exePath, inPath, outPath])
This prints a few lines from EXE.exe followed by "The handle is invalid" -- but as a string, not as an error, which makes me think it might be a message from the EXE.exe:
Unzipping Solution...
0.0% The handle is invalid.
However when I open cmd.exe and paste in:
C:\Test\EXE.exe C:\Test\IN.in C:\Test\OUT.out
it works fine.
Can someone point me in the right direction?
Thanks!
I'm running Python 2.7 64-bit on Windows 7.
EDIT:
It looks now like a problem in PyDev where the console cannot handle the the stdout from the process overwriting lines. The code runs fine from IDLE. Still looking for a fix for PyDev...

I think you're having this issue because PyDev is not a real terminal (i.e.: in Python, os.isatty() will return False when run from PyDev).
If the exe really relies on having a terminal, currently there's not much that PyDev can do...
For now, you can make your call from Python as:
In windows:
popen = subprocess.Popen(['myexe', 'params'], creationflags=subprocess.CREATE_NEW_CONSOLE)
popen.wait()
In Linux (as the CREATE_NEW_CONSOLE is not available):
args = ['xterm', '-e'] + ['myexe', 'params']
popen = subprocess.Popen(args)
popen.wait()
so that it works regardless of who's calling it :)
I think Aptana Studio does have an actual terminal replacement, but there's no PyDev integration to launch things on it...