Issues Generating Background GeneSet
TTCooper-PhD opened this issue · comments
I am trying to generate a background geneset for homo sapiens. I am currently trying to run GOATOOLS from jupyter notebook, but I am running into issues with the instructions from the "background_genes_ncbi.py" notebook.
Specifically, I cannot get understand how to execute this ( $ scripts/ncbi_gene_results_to_python.py gene_result.txt -o genes_ncbi_10090_proteincoding.py
gene_result.txt genes_ncbi_10090_proteincoding.py
26058 lines READ: gene_result.txt
26033 geneids WROTE: genes_ncbi_10090_proteincoding.py ) in the command prompt within anadaconda.
The documentation should consider additional information or screenshots to improve the clarity of this package.
Thank you for your interest in GOA Tools and for taking the time to write. I was busy completing my PhD (now done) and so had been delayed for your issue.
Please take a look at the updated notebook and comment if there is anything else that you would specifically like to see.
Thank you so much again for taking your time to alert us to this issue. Addressing your ideas certainly will improve GOA Tools for a multitude of researchers.