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Add test of Ancestry code by shunting output to 23&Me conversion function #37

Closed taltman closed 6 years ago

taltman commented 6 years ago

Create a test function in MAMBA that uses your code to generate a 23 & Me text file, and then puts that file as input for the 23 & Me -> VCF function that I've written.

This will require you to use the Docker framework to auto-install the dependencies that are external to Python.

Thank you!

mxscott commented 6 years ago

Hey Tomer, I think the way I have been naming my converted 23andMe files (converted23andme.txt) is causing some issues when your code tries to convert one of my files because of the name. Is there a standard naming practice I should follow?

Edit: I think I found a generic filename that works in the parser.

mxscott commented 6 years ago

In the makefile, the file you try to get with: "wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gzi" Does not show up anymore and it is preventing the tests from running correctly. wget gives a no such file error. Is there a replacement that I could substitute in?

taltman commented 6 years ago

Hi Max, I've committed a series of changes to dev. You should pull those changes from the dev branch to your feature branch, so that you'll work past that build issue in the Makefile. Thanks!

taltman commented 6 years ago

Hi @mxscott, regarding the filename issue, probably best to create a separate issue and assign it to me if you are hitting a problem working with the code. Please include an example of where a file name leads to breakage. Thanks!