From 047171c4d3f1a6e6b0a7cb86907130d298f19717 Mon Sep 17 00:00:00 2001 From: REDA Clemence Date: Fri, 14 Apr 2023 10:42:48 +0200 Subject: [PATCH] fix omnipath --- src/NORDic/UTILS/utils_network.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/NORDic/UTILS/utils_network.py b/src/NORDic/UTILS/utils_network.py index dda1dea..3e71129 100644 --- a/src/NORDic/UTILS/utils_network.py +++ b/src/NORDic/UTILS/utils_network.py @@ -111,7 +111,7 @@ def merge_network_PPI(network, PPI, quiet=True): ## https://workflows.omnipathdb.org/tissue-hpa.pdf ## https://workflows.omnipathdb.org/networks-r.html -def get_network_from_OmniPath(gene_list=None, disease_name=None, species="human", sources_int=None, domains_int=None, types_int=None, min_curation_effort=-1, domains_annot='HPA_tissue', quiet=False): +def get_network_from_OmniPath(gene_list=None, disease_name=None, species="human", sources_int="OMNIPATH", domains_int=None, types_int=None, min_curation_effort=-1, domains_annot='HPA_tissue', quiet=False): ''' Retrieve a network from OmniPath @param\tgene_list\tPython character string[default=None]: List of genes to consider (or do not filter the interactions from Omnipath if =None) @@ -129,7 +129,7 @@ def get_network_from_OmniPath(gene_list=None, disease_name=None, species="human" assert species in ['human', 'mouse', 'rat'] assert types_int in [None, "post_translational", "transcriptional", "post_transcriptional", "mirna_transcriptional"] assert sources_int in [None]+list(op.interactions.AllInteractions.resources()) - assert domains_int in [None, "DOROTHEA", "KINASE_EXTRA", "LIGREC_EXTRA", "LNCRNA_MRNA", "MIRNA_TARGET","OMNIPATH", + assert domains_int in ["DOROTHEA", "KINASE_EXTRA", "LIGREC_EXTRA", "LNCRNA_MRNA", "MIRNA_TARGET","OMNIPATH", "PATHWAY_EXTRA", "SMALL_MOLECULE", "TF_MIRNA", "TF_REGULONS", "TF_TARGET"] assert domains_annot in [None]+list(op.requests.Annotations.resources()) assert (gene_list is not None) or (disease_name is not None)