Fix code style issues with Black

Clinical-Genomics · Nov 5, 2024 · ed2a26d · ed2a26d
1 parent 7684077
commit ed2a26d
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Showing 4 changed files with 17 additions and 46 deletions.
diff --git a/scripts/check_hgnc_id.py b/scripts/check_hgnc_id.py
@@ -60,19 +60,15 @@ def cli(context, repeats_file, loglevel):
 
         if len(response_rest["docs"]) > 1:
             LOG.warning(
-                "Entry {} got {} hgnc responses - using first".format(
-                    entry, len(response_rest)
-                )
+                "Entry {} got {} hgnc responses - using first".format(entry, len(response_rest))
             )
 
         symbol_from_id = response_rest["docs"][0]["symbol"]
 
         if symbol_from_id == locus_symbol:
             LOG.info("OK locus %s symbol %s", entry, locus_symbol)
         elif symbol_from_id.lower() == locus_symbol.lower():
-            LOG.warning(
-                "OK locus %s symbol %s but differs in case", entry, locus_symbol
-            )
+            LOG.warning("OK locus %s symbol %s but differs in case", entry, locus_symbol)
         else:
             LOG.error(
                 "OOOPS locus_symbol %s and symbol %s from HGNC id %i do not match",

diff --git a/scripts/compare_locus_values_json.py b/scripts/compare_locus_values_json.py
@@ -43,9 +43,7 @@ def cli(context, repeats_file, alt_repeats_file, loglevel):
         repeat_information = parse_repeat_file(file_handle, repeats_file_type="json")
 
     with open(alt_repeats_file, "r") as file_handle:
-        other_repeat_information = parse_repeat_file(
-            file_handle, repeats_file_type="json"
-        )
+        other_repeat_information = parse_repeat_file(file_handle, repeats_file_type="json")
 
     if not repeat_information or not other_repeat_information:
         LOG.warning("Could not find any repeat info")

diff --git a/stranger/cli.py b/stranger/cli.py
@@ -43,9 +43,7 @@ def print_version(ctx, param, value):
 )
 @click.option("-i", "--family_id", default="1")
 @click.option("-t", "--trgt", is_flag=True, help="File was produced with TRGT")
-@click.option(
-    "--version", is_flag=True, callback=print_version, expose_value=False, is_eager=True
-)
+@click.option("--version", is_flag=True, callback=print_version, expose_value=False, is_eager=True)
 @click.option(
     "--loglevel",
     default="INFO",
@@ -184,29 +182,22 @@ def cli(context, vcf, family_id, repeats_file, loglevel, trgt):
             individual_index = get_individual_index(header_info)
             variant_info["format_dicts"] = get_format_dicts(
                 variant_info["FORMAT"],
-                [
-                    variant_info[individual]
-                    for individual in header_info[individual_index:]
-                ],
+                [variant_info[individual] for individual in header_info[individual_index:]],
             )
 
             if len(variant_info["alts"]) > 1:
                 variant_infos = decompose_var(variant_info)
 
             for variant_info in variant_infos:
-                update_decomposed_variant_format_fields(
-                    variant_info, header_info, individual_index
-                )
+                update_decomposed_variant_format_fields(variant_info, header_info, individual_index)
 
         for variant_info in variant_infos:
             repeat_data = get_repeat_info(variant_info, repeat_information)
 
             if repeat_data:
                 variant_info["info_dict"]["STR_STATUS"] = repeat_data["repeat_strings"]
                 variant_info["info_dict"]["STR_NORMAL_MAX"] = str(repeat_data["lower"])
-                variant_info["info_dict"]["STR_PATHOLOGIC_MIN"] = str(
-                    repeat_data["upper"]
-                )
+                variant_info["info_dict"]["STR_PATHOLOGIC_MIN"] = str(repeat_data["upper"])
                 variant_info["info_dict"]["RankScore"] = ":".join(
                     [str(family_id), str(repeat_data["rank_score"])]
                 )

diff --git a/stranger/utils.py b/stranger/utils.py
@@ -72,18 +72,14 @@ def parse_json(file_handle):
             normal_max = repeat_unit["NormalMax"]
         except KeyError as err:
             LOG.warning(
-                "Repeat number {0} ({1}) is missing 'NormalMax'. Skipping..".format(
-                    i, repid
-                )
+                "Repeat number {0} ({1}) is missing 'NormalMax'. Skipping..".format(i, repid)
             )
             continue
         try:
             pathologic_min = repeat_unit["PathologicMin"]
         except KeyError as err:
             LOG.warning(
-                "Repeat number {0} ({1}) is missing 'PathologicMin'. Skipping..".format(
-                    i, repid
-                )
+                "Repeat number {0} ({1}) is missing 'PathologicMin'. Skipping..".format(i, repid)
             )
             continue
 
@@ -101,9 +97,7 @@ def parse_json(file_handle):
             # TRGT uses TRID instead of REPID
             trid = repeat_unit["TRID"]
 
-            repeat_info[trid] = dict(
-                normal_max=normal_max, pathologic_min=pathologic_min
-            )
+            repeat_info[trid] = dict(normal_max=normal_max, pathologic_min=pathologic_min)
 
             for annotated_key in ANNOTATE_REPEAT_KEYS:
                 if repeat_unit.get(annotated_key):
@@ -117,9 +111,7 @@ def parse_json(file_handle):
             reference_region = repeat_unit["ReferenceRegion"]
         except KeyError as err:
             LOG.warning(
-                "Repeat number {0} ({1}) is missing 'ReferenceRegion'. Skipping..".format(
-                    i, repid
-                )
+                "Repeat number {0} ({1}) is missing 'ReferenceRegion'. Skipping..".format(i, repid)
             )
             continue
         if "PathologicRegion" in repeat_unit:
@@ -255,9 +247,7 @@ def get_repeat_info(variant_info, repeat_info):
 
     for annotate_repeat_key in ANNOTATE_REPEAT_KEYS:
         if repeat_info[repeat_id].get(annotate_repeat_key):
-            repeat_data[annotate_repeat_key] = str(
-                repeat_info[repeat_id][annotate_repeat_key]
-            )
+            repeat_data[annotate_repeat_key] = str(repeat_info[repeat_id][annotate_repeat_key])
 
     return repeat_data
 
@@ -291,9 +281,7 @@ def get_trgt_repeat_res(variant_info, repeat_info):
                     continue
 
                 if len(mcs) > 1:
-                    pathologic_mcs = repeat_info[repeat_id].get(
-                        "pathologic_struc", range(len(mcs))
-                    )
+                    pathologic_mcs = repeat_info[repeat_id].get("pathologic_struc", range(len(mcs)))
 
                     for index, count in enumerate(mcs):
                         if index in pathologic_mcs:
@@ -389,9 +377,7 @@ def get_individual_index(header_info):
     return individual_index
 
 
-def update_decomposed_variant_format_fields(
-    variant_info, header_info, individual_index
-):
+def update_decomposed_variant_format_fields(variant_info, header_info, individual_index):
     """
     Update variant_info individual FORMAT fields with information found in the now up to date
     format_dicts.
@@ -454,8 +440,8 @@ def decompose_var(variant_info):
                 if field in ["GT"]:
                     continue
                 variant_component_value = individual_value.split(",")[variant_component]
-                result_variants[index]["format_dicts"][individual_index][field] = (
-                    variant_component_value
-                )
+                result_variants[index]["format_dicts"][individual_index][
+                    field
+                ] = variant_component_value
 
     return result_variants