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nadavbra / pwas

Proteome-Wide Association Study
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example request #2

Closed ruxi closed 3 years ago

ruxi commented 3 years ago

Hi @nadavbra

Is there an formatting example for the genotyping_spec.csv for plink-format?

So far my csv file looks like this:

name,format,bed_file_path,bim_file_path,fam_file_path
mydata,plink,file.bed,file.bim,file.fam

When I try to run list_all_variants it return an pandas error for the genotyping_manager

IndexError: single positional indexer is out-of-bounds

Thanks

nadavbra commented 3 years ago

Hi,

Of course!

Here you can find examples for the UK Biobank (in our filesystem): ftp://ftp.cs.huji.ac.il/users/nadavb/ukbb_genotyping_specs/ These files were generated by ukbb_parser.

If you write this file manually, make sure that all files are referenced by full path.

If you are still facing errors and need help, please copy-paste the full stack traces you receive.

Good luck, Nadav

ruxi commented 3 years ago

Thanks for the quick reply @nadavbra.

I found the issue: my famfile was tab delimited the script only recognizes spaces.

Made a pull request so that it recognizes both: https://github.com/nadavbra/pwas/pull/3

nadavbra commented 3 years ago

Thank you @ruxi for making the effort to debug it and fix the code. I merged your pull request.