From 51ff252c8aabf81a251013a7cdd251c8347aa434 Mon Sep 17 00:00:00 2001 From: Avani7 Date: Mon, 25 Mar 2024 05:11:38 +0530 Subject: [PATCH] Updated Readme --- README.md | 13 +++++++------ cmi/stages/functional_analysis.py | 4 ++-- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index be740ac..09571e4 100644 --- a/README.md +++ b/README.md @@ -112,11 +112,12 @@ 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 -- stage: functional analysis (Uniprot) +- stage: 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 - stage: gene network (Cytoscape) @@ -124,8 +125,8 @@ The starting cell population and terminal cell population cluster IDs to be ener Eg: cmi run create_network --artefacts ./artefacts/temp --params ./artefacts/temp/Trrust_Analysis/trrust_analysis.csv -- stage: trrust analysis (TRRUST) +- stage: 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 index b6a051b..ba0979d 100644 --- 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))