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Update cli names
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ddomingof committed Apr 25, 2019
1 parent da4115d commit c68d0bf
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions src/pathme/cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -308,7 +308,7 @@ def statistics(connection, verbose, only_canonical, export):
@click.option('-r', '--reactome_path', help='Reactome BEL folder.', default=REACTOME_BEL, show_default=True)
@click.option('-w', '--wikipathways_path', help='WikiPathways BEL folder', default=WIKIPATHWAYS_BEL, show_default=True)
@click.option('-o', '--output', help='Output directory', default=SPIA_DIR, show_default=True)
def export_to_spia(kegg_path, reactome_path, wikipathways_path, output):
def spia(kegg_path, reactome_path, wikipathways_path, output):
"""Export BEL Pickles to SPIA Excel."""
click.echo(f'Results will be exported to {output}')

Expand Down Expand Up @@ -362,8 +362,8 @@ def export_to_spia(kegg_path, reactome_path, wikipathways_path, output):
@click.option('-o', '--output', help='Output directory', default=UNIVERSE_DIR, show_default=True)
@click.option('--no-flatten', is_flag=True, help='Do not flatten complex/reactions nodes')
@click.option('--no-normalize-names', is_flag=True, help='Do not normalize names')
def export_harmonized_universe(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no_normalize_names):
"""Return harmonized universe BELGraph of all the databases included in PathMe."""
def universe(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no_normalize_names):
"""Export harmonized PathMe universe."""
logging.basicConfig(level=logging.info, format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
logger.setLevel(logging.INFO)

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