sites_file argument not working about pixy HOT 5 CLOSED

Hi Jesse,

The logical flow of all those checks is confusing but I think this is working as intended: without a bed file (whether or not you have a sites file), you'll need to specify a window size. Otherwise, there will be no way for pixy to know the intervals over which to calculate your summary stats. So, if you want a window size of 1, you should specify --window_size 1 (as you did!).

So then on to the next problem, your pandas error. I can't reproduce that on my end, can you post your chr4_gene_locations.txt? That error might also be from your populations.txt file. Have a look at those two files, make sure they are valid tab-separated files etc. (or post them here). You could also try rerunning with the --debug flag to get a traceback of the pandas error.

Let me know how it goes!

from pixy.

Hi,

I checked the populations file and sites_file and verified that they were tab delimited. I'm including them here at this link: https://drive.google.com/drive/folders/1ex8zMsylNyIfuIHuX3Uuq0ORUnxI8Oj7?usp=sharing . Thanks for your help!

from pixy.

Hi Jesse,

Thanks for sending me your data! Interestingly, I wasn't able to reproduce your error. The calculations were slow (single-site mode is still very slow), but they did complete (let me know if you'd like the output file). While I was at it, I added some new optimizations that will speed this type of analysis up in the future.

Re: your error, a few questions:

1. What OS are you running pixy on?
2. There is an extra tab at the end of the second line of your populations.txt file. It didn't seem to affect anything for me, but I wonder if this might be connected to the problem.
3. Can you re-run your analysis with the --debug flag? and paste the output here?

from pixy.

Just following up here, once your input file issue is resolved, it would probably be worth updating to the new version 1.2.5.beta1 on conda. The single sites + sites file combination you are doing is much faster in the new version.

from pixy.

Updating my pixy to the latest on conda seemed to fix everything! I can now use the sites_file argument.

from pixy.