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Clinical-Genomics · Nov 28, 2024 · 6caa609 · 6caa609
1 parent 7f7563e
commit 6caa609
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Showing 7 changed files with 14 additions and 8 deletions.
diff --git a/genmod/annotate_models/genetic_models.py b/genmod/annotate_models/genetic_models.py
@@ -71,9 +71,9 @@
     check_X_dominant,
     check_X_recessive,
 )
-
 from .models.compound_model import check_compounds
 
+
 def check_genetic_models(variant_batch, families, phased=False, strict=False):
     """
     Check and annotate which genetic models that are followed for the variants

diff --git a/genmod/annotate_models/models/__init__.py b/genmod/annotate_models/models/__init__.py
@@ -6,4 +6,10 @@
 from .recessive_model import check_recessive
 from .x_models import check_X_dominant, check_X_recessive
 
-__all__ = ['check_dominant','check_compounds', 'check_recessive', 'check_X_dominant', 'check_X_recessive']
+__all__ = [
+    "check_dominant",
+    "check_compounds",
+    "check_recessive",
+    "check_X_dominant",
+    "check_X_recessive",
+]
diff --git a/genmod/annotate_models/variant_annotator.py b/genmod/annotate_models/variant_annotator.py
@@ -18,9 +18,9 @@
 
 from genmod.vcf_tools import get_genotypes
 
-from .make_haploblocks import get_haploblocks
-from .genetic_models import check_genetic_models
 from .fix_variant import make_print_version
+from .genetic_models import check_genetic_models
+from .make_haploblocks import get_haploblocks
 
 
 class VariantAnnotator(Process):

diff --git a/genmod/utils/get_batches.py b/genmod/utils/get_batches.py
@@ -161,7 +161,8 @@ def get_batches(
 
     logger.info(
         "Chromosome {0} parsed. Time to parse" " chromosome: {0}".format(
-            current_chrom, )
+            current_chrom,
+        )
     )
 
     if len(batch) > 0:

diff --git a/genmod/utils/get_priority.py b/genmod/utils/get_priority.py
@@ -1,4 +1,3 @@
-
 from genmod.score_variants import RANK_SCORE_TYPE_NAMES
 
 

diff --git a/tests/functionality/test_annotate_variant.py b/tests/functionality/test_annotate_variant.py
@@ -1,7 +1,6 @@
 from click.testing import CliRunner
-from genmod.commands.base import cli
-
 from genmod import logger
+from genmod.commands.base import cli
 from genmod.log import init_log
 
 VCF_FILE = "tests/fixtures/test_vcf_regions.vcf"

diff --git a/tests/variant_annotation/test_get_haploblocks.py b/tests/variant_annotation/test_get_haploblocks.py
@@ -1,5 +1,6 @@
 from genmod.annotate_models.make_haploblocks import get_haploblocks
 
+
 def get_variant(**kwargs):
     """
     Construct a variant and return it
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,3 @@

		from genmod.score_variants import RANK_SCORE_TYPE_NAMES


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