ENSEMBL IDs about genewalk HOT 4 CLOSED

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

from genewalk.

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!

from genewalk.

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

from genewalk.

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

from genewalk.