NaN supports are allowed in pileup with warning, no crash. Cache for test data download fixed. metavariable TRACK_PATH for call-compartments added.

Author: agalitsyna

cooltools/cli/call_compartments.py

@@ -19,6 +19,7 @@
     "--reference-track",
     help="Reference track for orienting and ranking eigenvectors",
     type=TabularFilePath(exists=True, default_column_index=3),
+    metavar="TRACK_PATH"
 )
 @click.option(
     "--contact-type",

cooltools/lib/common.py

@@ -119,13 +119,15 @@ def download_file(url, local_filename=None):
 
     data_home = get_data_home(data_home)
 
-    assert len(keys)>0 # Checking that test data file is parsed sucessfully
+    assert len(keys)>0 # Checking that test data file is parsed successfully
+    downloaded = '' # Empty string that will be returned if the request was empty
     for key, url, local_filename in available_datasets:
         if not key in keys:
             continue
 
         file_path = os.path.join(data_home, local_filename)
         if cache and os.path.exists(file_path):
+            downloaded = file_path
             continue
         elif cache:
             print("Test dataset {} (file {}) is not in the cache directory {}".format(key, local_filename, data_home))

cooltools/snipping.py

@@ -140,9 +140,9 @@ def _pileup(data_select, data_snip, arg):
     support, feature_group = arg
     # check if support region is on- or off-diagonal
     if len(support) == 2:
-        region1, region2 = map(bioframe.parse_region_string, support)
+        region1, region2 = map(bioframe.region.parse_region_string, support)
     else:
-        region1 = region2 = bioframe.parse_region_string(support)
+        region1 = region2 = bioframe.region.parse_region_string(support)
 
     # check if features are on- or off-diagonal
     if "start" in feature_group:
@@ -184,9 +184,7 @@ def pileup(features, data_select, data_snip, map=map):
 
     """
     if features.region.isnull().any():
-        raise ValueError(
-            "Drop features with no region assignment before calling pileup!"
-        )
+        print("Some features do not have regions assigned! Some snips will be empty.")
 
     features = features.copy()
     features["_rank"] = range(len(features))