Syntax error

[spenagon]

How can I solve this error?

File "orthofinder.py", line 229
with open(clustersFilename, 'rb') as clusterFile, open(newFilename, "wb") as output:
^
SyntaxError: invalid syntax

[davidemms]

Are you using an old version of python? If you're having problems with the 'with' statement it might be that that's the problem (https://www.python.org/dev/peps/pep-0343/). If so then it's best to install and use version 2.7.

Date: Thu, 6 Aug 2015 02:24:56 -0700
From: notifications@github.com
To: OrthoFinder@noreply.github.com
Subject: [OrthoFinder] Syntax error (#1)

How can I solve this error?

File "orthofinder.py", line 229

with open(clustersFilename, 'rb') as clusterFile, open(newFilename, "wb") as output:

                                                ^

SyntaxError: invalid syntax

—
Reply to this email directly or view it on GitHub.

[spenagon]

I am using python version 2.6.5. When I change lines of with I get another error:
File "orthofinder.py", line 1031
fastaFileIndices = {filename:iSpecies for iSpecies, filename in enumerate(originalFastaFilenames_justNames)}
^
SyntaxError: invalid syntax

[davidemms]

Hi spenagon

I've just checked and the dictionary comprehension (the syntax you've posted) was introduced in versions 2.7, released 2010. I will put a note in the README file to tell users that they'll need to use version 2.7 but will download some older versions of python and see if I can make the code backwards compatible with these.

David

[davidemms]

Closing this issue now that README now makes clear the python version requirements.