formatting

Author: danlu1

genie_registry/bed.py

@@ -562,7 +562,6 @@ def _process(self, beddf, seq_assay_id, newpath, parentid, create_panel=True):
         final_bed = add_feature_type(temp_bed_path, exon_gtf_path, gene_gtf_path)
         final_bed["CENTER"] = self.center
         final_bed["Chromosome"] = final_bed["Chromosome"].astype(str)
-        import pdb; pdb.set_trace()
         if create_panel:
             self.create_gene_panel(final_bed, seq_assay_id, gene_panel_path, parentid)
         return final_bed
@@ -601,11 +600,9 @@ def process_steps(
         Returns:
             str: Path to new bed file
         """
-        import pdb; pdb.set_trace()
         final_beddf = self._process(
             beddf=beddf, seq_assay_id=seq_assay_id, newpath=newPath, parentid=parentId
         )
-        import pdb; pdb.set_trace()
         load.update_table(
             syn=self.syn,
             databaseSynId=databaseSynId,
@@ -694,9 +691,7 @@ def _validate(self, beddf):
                 gene_positiondf = gene_position_table.convert_dtypes()
                 # The apply function of a DataFrame is called twice on the first row (known
                 # pandas behavior)
-                import pdb; pdb.set_trace()
                 beddf = beddf.apply(lambda x: remap_symbols(x, gene_positiondf), axis=1)
-                import pdb; pdb.set_trace()
                 if any(beddf["Hugo_Symbol"].isnull()):
                     warning += (
                         "BED file: "

genie_registry/clinical.py

@@ -14,6 +14,7 @@
 from genie.database_to_staging import redact_phi
 from genie.example_filetype_format import FileTypeFormat
 from synapseclient.models import query
+
 logger = logging.getLogger(__name__)
 
 

genie_registry/mutationsInCis.py

@@ -6,6 +6,7 @@
 from genie.example_filetype_format import FileTypeFormat
 from genie import load, process_functions
 from synapseclient.models import query
+
 logger = logging.getLogger(__name__)
 
 # def updateMutationInCisData(syn, databaseSynId, newData, center, col, toDelete=False):