issue biocommons#606 - reformat code

kyuhas · Dec 23, 2020 · a84ba97 · a84ba97
1 parent 5d579a8
commit a84ba97
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Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/hgvs/variantmapper.py b/hgvs/variantmapper.py
@@ -21,7 +21,7 @@
 import hgvs.sequencevariant
 import hgvs.validator
 
-from hgvs.exceptions import HGVSDataNotAvailableError, HGVSUnsupportedOperationError, HGVSInvalidVariantError, \
+from hgvs.exceptions import HGVSUnsupportedOperationError, HGVSInvalidVariantError, \
     HGVSInvalidIntervalError
 from hgvs.decorators.lru_cache import lru_cache
 from hgvs.enums import PrevalidationLevel
@@ -162,7 +162,8 @@ def g_to_n(self, var_g, tx_ac, alt_aln_method=hgvs.global_config.mapping.alt_aln
                                              alt_ac=var_g.ac,
                                              alt_aln_method=alt_aln_method)
 
-        if (mapper.strand == -1 and not hgvs.global_config.mapping.strict_bounds
+        if (mapper.strand == -1
+                and not hgvs.global_config.mapping.strict_bounds
                 and not mapper.g_interval_is_inbounds(var_g.posedit.pos)):
             _logger.info("Renormalizing out-of-bounds minus strand variant on genomic sequence")
             var_g = self.left_normalizer.normalize(var_g)
@@ -184,7 +185,8 @@ def g_to_n(self, var_g, tx_ac, alt_aln_method=hgvs.global_config.mapping.alt_aln
         var_n = hgvs.sequencevariant.SequenceVariant(ac=tx_ac,
                                                      type="n",
                                                      posedit=hgvs.posedit.PosEdit(pos_n, edit_n))
-        if (self.replace_reference and var_n.posedit.pos.start.base >= 0
+        if (self.replace_reference
+                and var_n.posedit.pos.start.base >= 0
                 and var_n.posedit.pos.end.base < mapper.tgt_len):
             self._replace_reference(var_n)
         if self.add_gene_symbol:

diff --git a/tests/issues/test_606.py b/tests/issues/test_606.py
@@ -6,25 +6,26 @@
 
 class TestIssue606(unittest.TestCase):
     def test_606(self):
-        """https://github.com/biocommons/hgvs/issues/606"""
-
-        from hgvs.easy import am37, parser
         """
+            https://github.com/biocommons/hgvs/issues/606
+
             Occasionally, an IndexError is thrown by the _get_altered_sequence method. This seems to occur
             when there is either inconsistent data for a transcript in UTA or an invalid variant input.
-            There could be other root causes, but these are two that we have observed and are illustrated in the 
+            There could be other root causes, but these are two that we have observed and are illustrated in the
             examples below.
-            
+
             Example 1 (NC_000001.10:g.16890441C>G):
-            Transcript NM_017940.4 has inconsistent data. 25 exons in the 'transcript' alignment to itself, 
-            but 28 exons in the 'splign' alignment to the reference sequence.  
+            Transcript NM_017940.4 has inconsistent data. 25 exons in the 'transcript' alignment to itself,
+            but 28 exons in the 'splign' alignment to the reference sequence.
             Ends up with an index error in _get_altered_sequence.
-    
+
             Example 2 (NM_001291722.1:c.283-3C>T):
             This is invalid input -- according to the transcript in UTA, exon 5 starts at position 286 of the transcript,
             not position 283. Ends up with an index error in _get_altered_sequence.
         """
 
+        from hgvs.easy import am37, parser
+
         # Example 1
         hgvs.global_config.mapping.strict_bounds = False
         hgvs_g = 'NC_000001.10:g.16890441C>G'