Merge pull request #63 from AlexsLemonade/wvauclain/quant_sf_only

Add `quant_sf_only` to the hlf.download_dataset args
AlexsLemonade · Jul 15, 2021 · 6a16ef9 · 6a16ef9
2 parents 1509821 + 512b18c
commit 6a16ef9
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diff --git a/pyrefinebio/high_level_functions.py b/pyrefinebio/high_level_functions.py
@@ -51,6 +51,7 @@ def download_dataset(
     aggregation="EXPERIMENT",
     transformation="NONE",
     skip_quantile_normalization=False,
+    quant_sf_only=False,
     timeout=None,
     extract=False,
     prompt=True,
@@ -94,6 +95,8 @@ def download_dataset(
         skip_quantile_normalization (bool): control whether or not the dataset should skip quantile
                                             normalization for RNA-seq Samples
 
+        quant_sf_only (bool): include only quant.sf files in the generated dataset.
+
         timeout (datetime.timedelta): if specified the function will return None after timeout is reached.
 
         extract (bool): if true, the downloaded zip file will be automatically extracted
@@ -115,6 +118,7 @@ def download_dataset(
         email_address=email_address,
         aggregate_by=aggregation,
         quantile_normalize=(not skip_quantile_normalization),
+        quant_sf_only=quant_sf_only,
         notify_me=notify_me,
     )
 

diff --git a/tests/test_high_level_functions.py b/tests/test_high_level_functions.py
@@ -32,6 +32,7 @@ def test_download_dataset_dataset_dict(self, mock_post, mock_get, mock_download)
                 "email_address": "foo@test.com",
                 "start": True,
                 "quantile_normalize": True,
+                "quant_sf_only": False,
                 "notify_me": False,
             },
         )
@@ -63,6 +64,7 @@ def test_download_dataset_notify_me(self, mock_post, mock_get, mock_download):
                 "email_address": "foo@test.com",
                 "start": True,
                 "quantile_normalize": True,
+                "quant_sf_only": False,
                 "notify_me": True,
             },
         )
@@ -94,6 +96,7 @@ def test_download_dataset_experiments(self, mock_post, mock_get, mock_download):
                 "email_address": "foo@test.com",
                 "start": True,
                 "quantile_normalize": True,
+                "quant_sf_only": False,
                 "notify_me": False,
             },
         )