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kordk / torch-ecpg

(GPU accelerated) eCpG mapper
BSD 3-Clause "New" or "Revised" License
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Download annotation files for GTP #25

Closed liamgd closed 1 year ago

liamgd commented 1 year ago

The tecpg data gtp -y downloads GTP methylation, expression, and covariate matrices from https://ftp.ncbi.nlm.nih.gov. However, annotation files are not downloaded. What should the tecpg data gtp -y command do?

  1. Prompt the user to manually copy the GTP annotation files into the annot directory
  2. Find the tecpg python package directory and copy the files from the demo directory into the annot directory
  3. Programmatically generate the annotation files, implemented in gtp.py
  4. Upload GTP annotation files to a cloud service (or a public github repository) and download them upon each tecpg data gtp -y
kordk commented 1 year ago

The GTP dataset is primarily for evaluation. So, lets do (1) Prompt the user to manually copy the GTP annotation files into the annot directory

liamgd commented 1 year ago

Added a small warning to add annotation files manually in dcb8866.