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churchmanlab / genewalk

GeneWalk identifies relevant gene functions for a biological context using network representation learning
https://churchman.med.harvard.edu/genewalk
BSD 2-Clause "Simplified" License
127 stars 14 forks source link

ensembl_id #17

Closed marttine closed 4 years ago

marttine commented 4 years ago

The documentation shows that genewalk supports ensembl_id. However, after simple installation (pip install genewalk) and a test run, it reports an error that ensembl_id is not supported.

usage: genewalk [-h] --project PROJECT --genes GENES --id_type {hgnc_symbol,hgnc_id,mgi_id} [--stage {all,node_vectors,null_distribution,statistics}] [--base_folder BASE_FOLDER] [--network_source {pc,indra,edge_list,sif}] [--network_file NETWORK_FILE] [--nproc NPROC] [--nreps_graph NREPS_GRAPH] [--nreps_null NREPS_NULL] [--alpha_fdr ALPHA_FDR] [--save_dw SAVE_DW] [--random_seed RANDOM_SEED]

ri23 commented 4 years ago

Hi @marttine The github repo is currently ahead of the python package in terms of support for ensembl ids. If you install genewalk using pip install git+https://github.com/churchmanlab/genewalk.git it should work. We will release an updated Python package in the near future to reflect these updates.