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tanghaibao / goatools

Python library to handle Gene Ontology (GO) terms
BSD 2-Clause "Simplified" License
749 stars 212 forks source link

Issues Generating Background GeneSet #224

Open TTCooper-PhD opened 2 years ago

TTCooper-PhD commented 2 years ago

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.

dvklopfenstein commented 2 years ago

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.