BugFixes: #100 and #51.

aertslab · Oct 9, 2019 · 8974d39 · 8974d39
1 parent 275615b
commit 8974d39
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Showing 3 changed files with 20 additions and 3 deletions.
diff --git a/scripts/cli_test_script.sh b/scripts/cli_test_script.sh
@@ -48,6 +48,23 @@ pyscenic ctx "${DATA_FOLDER}/GSE103322.modules.sample.dat" \
        --output "${DATA_FOLDER}/motifs.csv" \
        --num_workers ${CORES}
 
+pyscenic ctx "${DATA_FOLDER}/GSE103322.modules.sample.dat" \
+       "${DB_FOLDER}/hg19-500bp-upstream-10species.mc9nr.feather" \
+       "${DB_FOLDER}/hg19-500bp-upstream-7species.mc9nr.feather" \
+       --annotations_fname "${RESOURCES_FOLDER}/motifs-v9-nr.hgnc-m0.001-o0.0.tbl" \
+       --mode "dask_multiprocessing" \
+       --chunk_size 1 \
+       --output "${DATA_FOLDER}/regulons.dat" \
+       --num_workers ${CORES}
+
+pyscenic ctx "${DATA_FOLDER}/GSE103322.modules.sample.dat" \
+       "${DB_FOLDER}/hg19-500bp-upstream-10species.mc9nr.feather" \
+       --annotations_fname "${RESOURCES_FOLDER}/motifs-v9-nr.hgnc-m0.001-o0.0.tbl" \
+       --mode "dask_multiprocessing" \
+       --chunk_size 1 \
+       --output "${DATA_FOLDER}/regulons.gmt" \
+       --num_workers ${CORES}
+
 ###############
 # TEST AUCELL #
 ###############

diff --git a/src/pyscenic/cli/utils.py b/src/pyscenic/cli/utils.py
@@ -172,7 +172,8 @@ def save_enriched_motifs(df, fname:str) -> None:
             with open(fname, 'w') as f:
                 f.write(json.dumps(name2targets))
         elif extension == '.dat':
-            pickle.dump(regulons, fname)
+            with open(fname, 'wb') as f:
+                pickle.dump(regulons, f)
         elif extension == '.gmt':
             GeneSignature.to_gmt(fname, regulons)
         elif extension in {'.yaml', '.yml'}:

diff --git a/src/pyscenic/genesig.py b/src/pyscenic/genesig.py
@@ -87,7 +87,7 @@ def to_gmt(cls, fname: str, signatures: List[Type['GeneSignature']], field_separ
         :param gene_separator: The separator that separates the genes.
         """
         #assert not os.path.exists(fname), "{} already exists.".format(fname)
-        with open(fname, "w") as file:
+        with open(fname, "wt") as file:
             for signature in signatures:
                 genes = gene_separator.join(signature.genes)
                 file.write("{}{}{}{}{}\n".format(signature.name, field_separator,
@@ -340,7 +340,6 @@ def non_empty(self, attribute, value):
         if len(value) == 0:
             raise ValueError("A regulon must have a transcription factor.")
 
-    @property
     def metadata(self, field_separator: str = ',') -> str:
         return "tf={}{}score={}".format(self.transcription_factor, field_separator, self.score)