Re: invalid syntax

[Rob Lanfear]

Hi,

Can you post the whole output on your terminal please. Thanks! 

Also, the fastest way to fix this is usually to send me your .cfg file and alignment off-list, and I can take a look.

Cheers,

Rob

On Tuesday, December 18, 2012 2:46:36 AM UTC+11, zoologia...@gmail.com wrote:

I have tried to run PartitionFinder on Mac but I couldn't do it. I type python with a space and then Drap and drop the file PartitionFinder.py and the folder with the alignements but I obtain this error:

SyntaxError: invalid syntax

I can't find this SyntaxError

Thanks fot your help!

[Rob Lanfear]

Since I may not be available for the next few days, I'll post a self-help solution here too.

These syntax errors are usually something to do with having your input files set up incorrectly. To avoid this, here are a few things you should do:

1. Read the manual carefully, particularly the part about alignment formatting. Then check your alignment meets the correct format by looking at the PhyML website. Finally, compare your alignment to those in the example folders.  The format should be the same.

2. Run through the tutorial here: www.robertlanfear.com/partitionfinder/tutorial  This is a very detailed tutorial, and hopefully by running through it you should be able to identify where you've gone wrong with your dataset.

I'll try to answer email regularly over the next few days, but it might be January before I'm back online.

Cheers,

Rob

--
Rob Lanfear
Research Fellow,
Ecology, Evolution, and Genetics,
Research School of Biology,
Australian National University

phone: +61 (0)2 6125 3611

www.robertlanfear.com

[zoologia...@gmail.com]

Dear Rob, 

I have the same syntax error with the examples files (included in PartitionFinder) and file you described in the tutorial. It is the next:

Last login: Tue Dec 18 09:31:57 on ttys001

u008XXX:~ YYYYYYYYYY$ python 

Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) 

[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> /Applications/PartitionFinder/PartitionFinder.py  /Users/YYYYYYYYYYYYY/Desktop/Armadillo  

  File "<stdin>", line 1

    /Applications/PartitionFinder/PartitionFinder.py  /Users/YYYYYYYYYYYYY/Desktop/Armadillo  

    ^

SyntaxError: invalid syntax

>>>  

Should I modify the file PartitionFinder.py?

Thank you in advance

[zoologia...@gmail.com]

Dear Rob,

I have found the problem. It was an error mine!! I typed ENTER after python. Sorry for my mistake, and thank your very much for your help and time

[Rob Lanfear]

Hi!

Glad you found the problem. It's a steep learning curve sometimes to start using the commandline, but it sounds like you have it figured out!

Cheers,

Rob

On 18 December 2012 22:00, <zoologia...@gmail.com> wrote:

Dear Rob,

I have found the problem. It was an error mine!! I typed ENTER after python. Sorry for my mistake, and thank your very much for your help and time