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Fix SPIA names
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Daniel Domingo-Fernandez committed Mar 6, 2019
1 parent d4a5d7e commit 54136ea
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions src/pathme/cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@
from pybel.struct.mutation import collapse_to_genes, collapse_all_variants
from tqdm import tqdm

from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel

logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -306,13 +308,13 @@ def statistics(connection, verbose, only_canonical, export):
@click.option('-o', '--output', help='Output directory', default=SPIA_DIR, show_default=True)
def export_to_spia(kegg_path, reactome_path, wikipathways_path, output):
"""Export BEL Pickles to SPIA Excel."""
from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel
click.echo(f'Results will be exported to {output}')

kegg_pickles, reactome_pickles, wp_pickles = get_all_pickles(kegg_path, reactome_path, wikipathways_path)

all_pickles = kegg_pickles + reactome_pickles + wp_pickles

logger.info(f'A total of {len(all_pickles)} will be exported')
click.echo(f'A total of {len(all_pickles)} will be exported')

iterator = tqdm(all_pickles, desc='Exporting SPIA excel files')

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