CODEWITHSUNDEEP
pythonmacospython-2.7biopython
SB2014_Vienna
SB2014_Vienna

Reputation: 1

syntax error trying to run biopython 1.65 from python 2.7.5

Hi I have been through other questions to find the answer to this but I'm a total beginner and I didn't find anything similar to my problem. This might be something obvious but I just have no idea what I'm doing wrong.

I am working on Mac OSX 10.9.4 and using Python 2.7.5 via terminal (here's what my terminal tells me:

Python 2.7.5 (default, Mar 9 2014, 22:15:05) [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin

I am trying to run Biopython 1.65. I downloaded this the source .zip file from the Biopython downloads site (biopython-1.65.zip) and unzipped it.

I am trying to follow the instructions on the Biopython installation page and entering the commands: 

python setup.py build
python setup.py test
sudo python setup.py install

I typed them in - not copied - first making sure that I'm in the correct biopython-1.65 directory but I keep getting this error message (I left out the directory and computer info just for security reasons):

python setup.py build
  File "setup.py", line 489
    python setup.py build
           ^
 SyntaxError: invalid syntax

I have no idea why this doesn't work and I can't find any information as to what I'm doing wrong. there definitely is a file called 'setup.py' in this directory. Any help would be welcome, but please bear in mind I'm a complete beginner so go easy on the jargon please and any step-by-step things to try would be greatly appreciated :) Thanks

Upvotes: 0

Views: 56

Answers (1)

Ignacio Vazquez-Abrams
Ignacio Vazquez-Abrams

Reputation: 798764

You're supposed to run those from the shell, not the Python REPL; they are shell commands, not Python statements.

Upvotes: 2

Related Questions