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peteryin21 / py-merp

A Python Package for Mendelian Randomization Analysis
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IVFs not being generated #2

Open demingy opened 9 years ago

demingy commented 9 years ago

I tried running MeRP and can't get it to generate the IVFs. I'm using Python 2.7.8 (default, April 15 2015, 09:26:43) [GCC 4.9.2 20150212 (Red Hat 4.9.2-6)] on linux2.

When I initially used m.pull() I received an error about no such file or directory: './data/finalgwas.txt' so I created a /data directory in my home directory and used m.pull() again. This time there was no error but this is what displayed on the screen: Generating IVFs for all traits in NHGRI GWAS catalog . . . 0 IVFs generated in /traitFiles

I looked in the /data directory and there is a finalgwas.txt with 19603 lines that appear to be complete. There's a /traitFiles directory but it is empty. My home directory also has an index file but it is empty.

peteryin21 commented 9 years ago

Hi @demingy. Thanks for the message.

  1. The package should include a /data/ directory. Are you running the python env from the py-merp directory?
  2. I fixed a bug in the pull() function that arose while cleaning up code in the past couple weeks. Also updated some file handling steps in case that was causing a problem in linux.

I've updated the package and tested it out on my mac--downloading virtualbox now to test on linux also.

In mean time, can you see if these changes fixed your problem? Let me know how the rest of the pipeline goes. Also, would love to learn about your uses for Merp and how I could improve it-- if you have a minute feel free to shoot me an email at py.peteryin@gmail.com.