diff --git a/src/bin/pwy_enrichment_reactome.py b/src/bin/pwy_enrichment_reactome.py index 6294849..dbc21b1 100755 --- a/src/bin/pwy_enrichment_reactome.py +++ b/src/bin/pwy_enrichment_reactome.py @@ -13,8 +13,6 @@ --excludeDisease Exclude disease pathways --pdf Write pathway report into pathway_enrichment.pdf --pdfname=PDF Specify pathway report name - --xlsx=XLSX Write enrichment analysis into a xlsx file [default: enrichment.xlsx] - --tsv=TSV Write enrichment analysis into a tsv file --csv=CSV Write pathway enrichment analysis into a csv file [default: pathway_enrichment.csv] --ids0=NF Write list of identifiers that were not found [default: ids_mapping.csv] --ids1=F Write list of identifiers that were found [default: ids_notfound.csv] @@ -26,8 +24,6 @@ __copyright__ = "Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved." __author__ = "DV Klopfenstein" -# import os -# import sys from docopt import docopt from reactomepy.code.rest.service_analysis import AnalysisService from reactomepy.code.rest.token_mgr import TokenManager @@ -39,7 +35,6 @@ def main(): """Run Reactome's Pathway Enrichment Analysis UniProt example.""" - #### args = get_args(__doc__, {'token', 'pdf', 'csv', 'data', 'sample_name'}) docargs = docopt(__doc__) args = clean_args(docargs) ana = AnalysisService(args['tokenlog'])