CLI: More comprehensive set of tests.

aertslab · Dec 20, 2018 · 8678f35 · 8678f35
1 parent 2629f6b
commit 8678f35
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 0 deletions.
diff --git a/scripts/cli_test_script.sh b/scripts/cli_test_script.sh
@@ -30,6 +30,16 @@ pyscenic ctx "${DATA_FOLDER}/GSE103322.modules.sample.dat" \
        --output "${DATA_FOLDER}/motifs.csv" \
        --num_workers ${CORES}
 
+pyscenic ctx "${DATA_FOLDER}/GSE103322.sample.net.csv" \
+       "${DB_FOLDER}/hg19-500bp-upstream-10species.mc9nr.feather" \
+       "${DB_FOLDER}/hg19-500bp-upstream-7species.mc9nr.feather" \
+       --annotations_fname "${RESOURCES_FOLDER}/motifs-v9-nr.hgnc-m0.001-o0.0.tbl" \
+       --expression_mtx_fname "${DATA_FOLDER}/GSE103322.em.hgnc.sample.loom" \
+       --mode "dask_multiprocessing" \
+       --chunk_size 1 \
+       --output "${DATA_FOLDER}/motifs.csv" \
+       --num_workers ${CORES}
+
 pyscenic ctx "${DATA_FOLDER}/GSE103322.modules.sample.dat" \
        "${DB_FOLDER}/hg19-500bp-upstream-10species.mc9nr.feather" \
        "${DB_FOLDER}/hg19-500bp-upstream-7species.mc9nr.feather" \

diff --git a/src/pyscenic/cli/pyscenic.py b/src/pyscenic/cli/pyscenic.py
@@ -120,6 +120,9 @@ def prune_targets_command(args):
     # The alternative for which was opted in the end is binary pickling.
     extension = os.path.splitext(args.module_fname.name)[1].lower()
     if extension in {'.csv', '.tsv'}:
+        if args.expression_mtx_fname is None:
+            LOGGER.error("No expression matrix is supplied.")
+            sys.exit(0)
         LOGGER.info("Creating modules.")
         modules = adjacencies2modules(args)
     else: