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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
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ENSEMBL IDs #3

Closed chrarnold closed 4 years ago

chrarnold commented 4 years ago

Hi, a quick question: Is it possible to support also ENSEMBL IDs as input?

bgyori commented 4 years ago

It is currently not supported but we'll look into adding support for that. Thanks!

chrarnold commented 4 years ago

Hi, I tried to use Ensembl IDs but this is what I got:

`$ genewalk --project cll_test --genes cll_ENSEMBL_IDs_activator_repressor --id_type ensembl_id

INFO: [2019-09-23 16:12:38] gensim.summarization.textcleaner - 'pattern' package not found; tag filters are not available for English

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] genewalk: error: argument --id_type: invalid choice: 'ensembl_id' (choose from 'hgnc_symbol', 'hgnc_id', 'mgi_id') `

Before, I updated genewalk as described: pip install git+https://github.com/churchmanlab/genewalk.git

Also, the missing package warning should not be there, right?

Thanks for your input!

bgyori commented 4 years ago

I confirmed that this is working on the latest Github master so I think your pip installation didn't work for some reason. Try making sure that pip forces an update using:

pip install -U git+https://github.com/churchmanlab/genewalk.git
chrarnold commented 4 years ago

You are right, that was it! It looked like it downloaded, but without the -U it nevertheless did not work correctly. Thanks!