reformatted with black and isort

biocommons · Sep 11, 2023 · 21e6106 · 21e6106
1 parent 1073d1f
commit 21e6106
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Showing 63 changed files with 1,857 additions and 1,622 deletions.
diff --git a/src/hgvs/__init__.py b/src/hgvs/__init__.py
@@ -49,8 +49,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import logging
 import re

diff --git a/src/hgvs/alignmentmapper.py b/src/hgvs/alignmentmapper.py
@@ -27,17 +27,20 @@
 #
 
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 from bioutils.coordinates import strand_int_to_pm
 from six.moves import range
 
 import hgvs.location
 from hgvs import global_config
 from hgvs.enums import Datum
-from hgvs.exceptions import (HGVSDataNotAvailableError, HGVSError,
-                             HGVSInvalidIntervalError, HGVSUsageError)
+from hgvs.exceptions import (
+    HGVSDataNotAvailableError,
+    HGVSError,
+    HGVSInvalidIntervalError,
+    HGVSUsageError,
+)
 from hgvs.utils import build_tx_cigar
 from hgvs.utils.cigarmapper import CIGARMapper
 
@@ -88,7 +91,6 @@ def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
         self.alt_aln_method = alt_aln_method
 
         if self.alt_aln_method != "transcript":
-
             tx_info = hdp.get_tx_info(self.tx_ac, self.alt_ac, self.alt_aln_method)
             if tx_info is None:
                 raise HGVSDataNotAvailableError(
@@ -126,7 +128,6 @@ def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
             self.tgt_len = self.cigarmapper.tgt_len
 
         else:
-
             # this covers the identity cases n <-> c
             tx_identity_info = hdp.get_tx_identity_info(self.tx_ac)
             if tx_identity_info is None:

diff --git a/src/hgvs/assemblymapper.py b/src/hgvs/assemblymapper.py
@@ -1,15 +1,17 @@
 # -*- coding: utf-8 -*-
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import logging
 
 import hgvs
 import hgvs.normalizer
-from hgvs.exceptions import (HGVSDataNotAvailableError, HGVSError,
-                             HGVSInvalidVariantError,
-                             HGVSUnsupportedOperationError)
+from hgvs.exceptions import (
+    HGVSDataNotAvailableError,
+    HGVSError,
+    HGVSInvalidVariantError,
+    HGVSUnsupportedOperationError,
+)
 from hgvs.variantmapper import VariantMapper
 
 _logger = logging.getLogger(__name__)
@@ -57,7 +59,7 @@ def __init__(
         replace_reference=hgvs.global_config.mapping.replace_reference,
         add_gene_symbol=hgvs.global_config.mapping.add_gene_symbol,
         *args,
-        **kwargs
+        **kwargs,
     ):
         """
         :param object hdp: instance of hgvs.dataprovider subclass
@@ -78,7 +80,7 @@ def __init__(
             prevalidation_level=prevalidation_level,
             add_gene_symbol=add_gene_symbol,
             *args,
-            **kwargs
+            **kwargs,
         )
         self.assembly_name = assembly_name
         self.alt_aln_method = alt_aln_method

diff --git a/src/hgvs/config.py b/src/hgvs/config.py
@@ -27,8 +27,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import logging
 import re

diff --git a/src/hgvs/dataproviders/interface.py b/src/hgvs/dataproviders/interface.py
@@ -3,8 +3,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import abc
 import os

diff --git a/src/hgvs/dataproviders/ncbi.py b/src/hgvs/dataproviders/ncbi.py
@@ -311,7 +311,6 @@ def _get_cursor(self, n_retries=1):
         n_tries_rem = n_retries + 1
         while n_tries_rem > 0:
             try:
-
                 conn = self._pool.getconn() if self.pooling else self._conn
 
                 # autocommit=True obviates closing explicitly
@@ -330,7 +329,6 @@ def _get_cursor(self, n_retries=1):
                 break
 
             except psycopg2.OperationalError:
-
                 _logger.warning("Lost connection to {url}; attempting reconnect".format(url=self.url))
                 if self.pooling:
                     self._pool.closeall()
@@ -340,7 +338,6 @@ def _get_cursor(self, n_retries=1):
             n_tries_rem -= 1
 
         else:
-
             # N.B. Probably never reached
             raise HGVSError("Permanently lost connection to {url} ({n} retries)".format(url=self.url, n=n_retries))
 

diff --git a/src/hgvs/dataproviders/seqfetcher.py b/src/hgvs/dataproviders/seqfetcher.py
@@ -3,8 +3,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import logging
 import os

diff --git a/src/hgvs/dataproviders/uta.py b/src/hgvs/dataproviders/uta.py
@@ -4,8 +4,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import contextlib
 import inspect
@@ -580,7 +579,6 @@ def _get_cursor(self, n_retries=1):
         n_tries_rem = n_retries + 1
         while n_tries_rem > 0:
             try:
-
                 conn = self._pool.getconn() if self.pooling else self._conn
 
                 # autocommit=True obviates closing explicitly
@@ -604,7 +602,6 @@ def _get_cursor(self, n_retries=1):
                 break
 
             except psycopg2.OperationalError:
-
                 _logger.warning("Lost connection to {url}; attempting reconnect".format(url=self.url))
                 if self.pooling:
                     self._pool.putconn(conn)
@@ -616,7 +613,6 @@ def _get_cursor(self, n_retries=1):
             n_tries_rem -= 1
 
         else:
-
             # N.B. Probably never reached
             raise HGVSError("Permanently lost connection to {url} ({n} retries)".format(url=self.url, n=n_retries))
 

diff --git a/src/hgvs/decorators/deprecated.py b/src/hgvs/decorators/deprecated.py
@@ -4,8 +4,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import collections
 import warnings

diff --git a/src/hgvs/decorators/lru_cache.py b/src/hgvs/decorators/lru_cache.py
@@ -11,8 +11,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 from collections import namedtuple
 from functools import update_wrapper

diff --git a/src/hgvs/edit.py b/src/hgvs/edit.py
@@ -9,8 +9,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import attr
 import six

diff --git a/src/hgvs/exceptions.py b/src/hgvs/exceptions.py
@@ -3,8 +3,7 @@
 
 """
 
-from __future__ import (absolute_import, division, print_function,
-                        unicode_literals)
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 
 class HGVSError(Exception):

diff --git a/src/hgvs/extras/babelfish.py b/src/hgvs/extras/babelfish.py
@@ -1,10 +1,11 @@
 """translate between HGVS and other formats"""
 import os
 
-import hgvs
-import hgvs.normalizer
 from bioutils.assemblies import make_ac_name_map, make_name_ac_map
 from bioutils.sequences import reverse_complement
+
+import hgvs
+import hgvs.normalizer
 from hgvs.edit import NARefAlt
 from hgvs.location import Interval, SimplePosition
 from hgvs.normalizer import Normalizer
@@ -54,20 +55,20 @@ def hgvs_to_vcf(self, var_g):
             start_i -= 1
             alt = self.hdp.seqfetcher.fetch_seq(vleft.ac, start_i, end_i)
             ref = alt[0]
-        elif typ == 'inv':
+        elif typ == "inv":
             ref = vleft.posedit.edit.ref
             alt = reverse_complement(ref)
         else:
             alt = vleft.posedit.edit.alt or ""
 
-            if typ in ('del', 'ins'):  # Left anchored
+            if typ in ("del", "ins"):  # Left anchored
                 start_i -= 1
                 ref = self.hdp.seqfetcher.fetch_seq(vleft.ac, start_i, end_i)
                 alt = ref[0] + alt
             else:
                 ref = vleft.posedit.edit.ref
                 if ref == alt:
-                    alt = '.'
+                    alt = "."
         return chrom, start_i + 1, ref, alt, typ
 
     def vcf_to_g_hgvs(self, chrom, position, ref, alt):
@@ -82,25 +83,25 @@ def vcf_to_g_hgvs(self, chrom, position, ref, alt):
                 alt = alt[lp:]
                 position += lp
 
-        if ref == '':  # Insert
+        if ref == "":  # Insert
             # Insert uses coordinates around the insert point.
             start = position - 1
             end = position
         else:
             start = position
             end = position + len(ref) - 1
 
-        if alt == '.':
+        if alt == ".":
             alt = ref
 
-        var_g = SequenceVariant(ac=ac,
-                                type='g',
-                                posedit=PosEdit(Interval(start=SimplePosition(start),
-                                                         end=SimplePosition(end),
-                                                         uncertain=False),
-                                                NARefAlt(ref=ref or None,
-                                                         alt=alt or None,
-                                                         uncertain=False)))
+        var_g = SequenceVariant(
+            ac=ac,
+            type="g",
+            posedit=PosEdit(
+                Interval(start=SimplePosition(start), end=SimplePosition(end), uncertain=False),
+                NARefAlt(ref=ref or None, alt=alt or None, uncertain=False),
+            ),
+        )
         n = Normalizer(self.hdp)
         return n.normalize(var_g)