This program is for people who want to run miptools wrangler on a subset of probes from several different probesets. It takes (or excludes) a subset of probes of interest from several different mip_arms files, and produces a new project folder containing a merged mip_arms file and mipsets.csv file that have only the probes you want. This new merged folder can then serve as a project folder for running miptools wrangler. For each merger, you'll need to provide (in the merge_probe_sets.yaml file):
- a list of mip_arms files you'd like to merge
- a list of probes of interest (to include or exclude for your merger)
Install conda (if you don't already have it) with: https://github.com/conda-forge/miniforge#mambaforge
Install snakemake in an environment called snakemake with:
mamba create -c conda-forge -c bioconda -n snakemake snakemake- Download the contents of this git repo to a folder on your machine and cd into that folder (so that "ls" shows merge_probe_sets.smk).
- Open the merge_probe_sets.yaml file and enter the name of the new project folder you'd like to create in the "output_folder" variable (this can be a relative or absolute path). Use a text editor that outputs unix line endings (e.g. vscode, notepad++, gedit, micro, emacs, vim, vi, etc.).
- list locations of arms files you want to use under the "mip_arms_files" variable
- tell the program if you'd like to "include" or "exclude" a list of probes with the "include/exclude" variable
- tell the program where your list of probes of interest is located with the variable "probe_names_file" (an example is provided here, in input_files/mip_ids.txt)
- Activate snakemake with:
conda activate snakemake- Run snakemake with:
snakemake -s merge_probe_sets.smk --cores 4