Merge branch 'release/0.3.4' into master

msk-access · Apr 28, 2021 · cb50a0e · cb50a0e
2 parents 039275e + 62432b1
commit cb50a0e
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Showing 5 changed files with 10 additions and 25 deletions.
diff --git a/genotype_variants/__init__.py b/genotype_variants/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Ronak Shah"""
 __email__ = 'rons.shah@gmail.com'
-__version__ = '0.3.3'
+__version__ = '0.3.4'
diff --git a/genotype_variants/commands/__init__.py b/genotype_variants/commands/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Ronak Shah"""
 __email__ = 'rons.shah@gmail.com'
-__version__ = '0.3.3'
+__version__ = '0.3.4'
diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py
@@ -21,8 +21,7 @@
 def create_all_maf_dataframe(
     original_dataframe, standard_dataframe, simplex_duplex_dataframe
 ):
-    """Code to merge all the data frames generated from MAF files into one data frame
-    """
+    """Code to merge all the data frames generated from MAF files into one data frame"""
     np.seterr(divide="ignore", invalid="ignore")
     mutation_key = [
         "Chromosome",
@@ -95,31 +94,17 @@ def create_all_maf_dataframe(
             )
             exit(1)
 
-        try:
-            df_s["Tumor_Seq_Allele2"] = df_s["Tumor_Seq_Allele1"]
-            logger.debug(
-                "genotype:variants:small_variants::create_duplex_simplex_dataframe:: Successfully generated Tumor_Seq_Allele2 column"
-            )
-        except:
-            e = sys.exc_info()[0]
-            logger.error(
-                "genotype:variants:small_variants::create_duplex_simplex_dataframe:: Could not generate Tumor_Seq_Allele2 column due to error, %s",
-                e,
-            )
-            exit(1)
-
         if df_s.shape[0] > 0:
             try:
                 df_s["t_alt_count_reverse_standard"] = (
-                    df_s["t_alt_count_standard"]
-                    - df_s["t_alt_count_forward_standard"]
+                    df_s["t_alt_count_standard"] - df_s["t_alt_count_forward_standard"]
                 )
                 df_s["t_ref_count_reverse_standard"] = (
-                    df_s["t_ref_count_standard"]
-                    - df_s["t_ref_count_forward_standard"]
+                    df_s["t_ref_count_standard"] - df_s["t_ref_count_forward_standard"]
                 )
                 df_s["t_total_count_reverse_standard"] = (
-                    df_s["t_total_count_standard"] - df_s["t_total_count_forward_standard"]
+                    df_s["t_total_count_standard"]
+                    - df_s["t_total_count_forward_standard"]
                 )
                 logger.debug(
                     "genotype:variants:small_variants::create_all_maf_dataframe:: Successfully generated reverse count columns in standard data frame"
@@ -128,7 +113,7 @@ def create_all_maf_dataframe(
                 e = sys.exc_info()[0]
                 logger.error(
                     "genotype:variants:small_variants::create_all_maf_dataframe:: Could not generate reverse count columns in standard data frame due to error, %s",
-                    e
+                    e,
                 )
                 exit(1)
         else:

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.3
+current_version = 0.3.4
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -48,6 +48,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/msk-access/genotype_variants',
-    version='0.3.3',
+    version='0.3.4',
     zip_safe=False,
 )