Updated Readme

thoughtworks · Mar 24, 2024 · 51ff252 · 51ff252
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diff --git a/README.md b/README.md
@@ -112,20 +112,21 @@ The starting cell population and terminal cell population cluster IDs to be ener
 
     Eg: cmi run grn_inference --artefacts ./artefacts/temp --params ./data/terminal.csv
 
-- <u>stage</u>: functional analysis (Uniprot)  
+- <u>stage</u>: trrust analysis (TRRUST)  
 
-    cmi run functional_analysis --artefacts ./artefacts/[directory_name] transync_genes.csv signet_unique_gene_list.csv  
+    cmi run trrust_analysis --artefacts ./artefacts/[directory_name] --params ./data/trrust_rawdata_human.tsv
+
+    Eg: cmi run trrust_analysis --artefacts ./artefacts/temp --params ./data/trrust_rawdata_human.tsv 
 
-    Eg: cmi run functional_analysis --artefacts ./artefacts/temp transync_genes.csv signet_unique_gene_list.csv
 
 - <u>stage</u>: gene network (Cytoscape)  
 
     cmi run create_network --artefacts ./artefacts/[directory_name] --params ./artefacts/[directory_name]/Trrust_Analysis/trrust_analysis.csv
 
     Eg: cmi run create_network --artefacts ./artefacts/temp --params ./artefacts/temp/Trrust_Analysis/trrust_analysis.csv 
 
-- <u>stage</u>: trrust analysis (TRRUST)  
+- <u>stage</u>: functional analysis (Uniprot)  
 
-    cmi run trrust_analysis --artefacts ./artefacts/[directory_name] --params ./data/trrust_rawdata_human.tsv
+    cmi run functional_analysis --artefacts ./artefacts/[directory_name] transync_genes.csv signet_unique_gene_list.csv  
 
-    Eg: cmi run trrust_analysis --artefacts ./artefacts/temp --params ./data/trrust_rawdata_human.tsv 
+    Eg: cmi run functional_analysis --artefacts ./artefacts/temp transync_genes.csv signet_unique_gene_list.csv
diff --git a/cmi/stages/functional_analysis.py b/cmi/stages/functional_analysis.py
@@ -47,8 +47,8 @@ def uniprot(artefacts_path, file):
     logger.info(f"Functional analysis started using: {artefacts_path, file}")
     file_path = artefacts_path + file
     file_name = str(file)
-    file_name = file_name.split("/")
-    file_name =file_name[2] or file
+    # file_name = file_name.split("/")
+    # file_name =file_name[2] or file
 
     genes = pd.read_csv(file_path)['Gene']
     jobs_ids = (get_jobs_ids(genes))