Fix code style issues with Black

Clinical-Genomics · Jul 1, 2024 · b0e7f8d · b0e7f8d
1 parent 8635189
commit b0e7f8d
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Showing 14 changed files with 436 additions and 290 deletions.
diff --git a/scripts/check_expansions.py b/scripts/check_expansions.py
@@ -7,9 +7,12 @@
 from stranger.resources import repeats_path
 from stranger.utils import parse_repeat_file, get_repeat_info
 
+
 @click.command()
-@click.option('-f', '--repeats-file',
-    type = click.Path(exists=True),
+@click.option(
+    "-f",
+    "--repeats-file",
+    type=click.Path(exists=True),
     help="Path to a file with repeat definitions. See README for explanation",
     default=repeats_path,
     show_default=True,
@@ -19,33 +22,66 @@ def cli(context, repeats_file):
     """Table print repeat info"""
 
     repeat_information = {}
-    with open(repeats_file, 'r') as file_handle:
-        repeat_information = parse_repeat_file(file_handle, repeats_file_type='json')
+    with open(repeats_file, "r") as file_handle:
+        repeat_information = parse_repeat_file(file_handle, repeats_file_type="json")
 
     if not repeat_information:
         LOG.warning("Could not find any repeat info")
         context.abort()
 
-    header = ["HGNCId", "LocusId", "DisplayRU", "InheritanceMode", "normal_max", "pathologic_min", "Disease", "SourceDisplay", "SourceId"]
+    header = [
+        "HGNCId",
+        "LocusId",
+        "DisplayRU",
+        "InheritanceMode",
+        "normal_max",
+        "pathologic_min",
+        "Disease",
+        "SourceDisplay",
+        "SourceId",
+    ]
     table_line = "| {0} | {1} | {2} | {3} | {4} | {5} | {6} | {7} | {8} |"
-    click.echo(table_line.format(
-        header[0], header[1], header[2], header[3], header[4], header[5], header[6], header[7], header[8]
-    ))
-    click.echo(table_line.format('-------', '-------', '-------', '-------', '-------',
-                                 '-------', '-------', '-------', '-------' ))
+    click.echo(
+        table_line.format(
+            header[0],
+            header[1],
+            header[2],
+            header[3],
+            header[4],
+            header[5],
+            header[6],
+            header[7],
+            header[8],
+        )
+    )
+    click.echo(
+        table_line.format(
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+            "-------",
+        )
+    )
     for entry in repeat_information:
-        click.echo(table_line.format(
-            repeat_information[entry][header[0]],
-            entry,
-            repeat_information[entry][header[2]],
-            repeat_information[entry][header[3]],
-            repeat_information[entry][header[4]],
-            repeat_information[entry][header[5]],
-            repeat_information[entry][header[6]],
-            repeat_information[entry][header[7]],
-            repeat_information[entry][header[8]],
-        ))
-
-
-if __name__=='__main__':
+        click.echo(
+            table_line.format(
+                repeat_information[entry][header[0]],
+                entry,
+                repeat_information[entry][header[2]],
+                repeat_information[entry][header[3]],
+                repeat_information[entry][header[4]],
+                repeat_information[entry][header[5]],
+                repeat_information[entry][header[6]],
+                repeat_information[entry][header[7]],
+                repeat_information[entry][header[8]],
+            )
+        )
+
+
+if __name__ == "__main__":
     cli()
diff --git a/scripts/check_hgnc_id.py b/scripts/check_hgnc_id.py
@@ -3,29 +3,36 @@
 import requests
 
 LOG = logging.getLogger(__name__)
-LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
 import click
 
 from stranger.resources import repeats_path
 from stranger.utils import parse_repeat_file, get_repeat_info
 
+
 @click.command()
-@click.option('-f', '--repeats-file',
-    type = click.Path(exists=True),
+@click.option(
+    "-f",
+    "--repeats-file",
+    type=click.Path(exists=True),
     help="Path to a file with repeat definitions. See README for explanation",
     default=repeats_path,
     show_default=True,
 )
-@click.option('--loglevel', default='INFO', type=click.Choice(LOG_LEVELS),
-              help="Set the level of log output.", show_default=True)
+@click.option(
+    "--loglevel",
+    default="INFO",
+    type=click.Choice(LOG_LEVELS),
+    help="Set the level of log output.",
+    show_default=True,
+)
 @click.pass_context
 def cli(context, repeats_file, loglevel):
     """Table print repeat info"""
     coloredlogs.install(level=loglevel)
-    with open(repeats_file, 'r') as file_handle:
-        repeat_information = parse_repeat_file(file_handle, repeats_file_type='json')
-
+    with open(repeats_file, "r") as file_handle:
+        repeat_information = parse_repeat_file(file_handle, repeats_file_type="json")
 
     if not repeat_information:
         LOG.warning("Could not find any repeat info")
@@ -37,10 +44,10 @@ def cli(context, repeats_file, loglevel):
 
     for entry in repeat_information:
         hgnc_id = repeat_information[entry]["HGNCId"]
-        locus_symbol = entry.split('_')[0]
+        locus_symbol = entry.split("_")[0]
 
         url = "https://rest.genenames.org/search/hgnc_id/" + str(hgnc_id)
-        response = requests.get(url, headers= {"Accept":"application/json"})
+        response = requests.get(url, headers={"Accept": "application/json"})
 
         if not response:
             LOG.warning("Entry {} not found".format(entry))
@@ -52,17 +59,24 @@ def cli(context, repeats_file, loglevel):
             LOG.warning("Entry {} not found".format(entry))
 
         if len(response_rest["docs"]) > 1:
-            LOG.warning("Entry {} got {} hgnc responses - using first".format(entry,len(response_rest)))
+            LOG.warning(
+                "Entry {} got {} hgnc responses - using first".format(entry, len(response_rest))
+            )
 
-        symbol_from_id = response_rest['docs'][0]['symbol']
+        symbol_from_id = response_rest["docs"][0]["symbol"]
 
-        if symbol_from_id == locus_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)
         else:
-            LOG.error("OOOPS locus_symbol %s and symbol %s from HGNC id %i do not match", locus_symbol, symbol_from_id, hgnc_id)
+            LOG.error(
+                "OOOPS locus_symbol %s and symbol %s from HGNC id %i do not match",
+                locus_symbol,
+                symbol_from_id,
+                hgnc_id,
+            )
 
 
-if __name__=='__main__':
+if __name__ == "__main__":
     cli()
diff --git a/scripts/compare_locus_values_json.py b/scripts/compare_locus_values_json.py
@@ -3,37 +3,47 @@
 import requests
 
 LOG = logging.getLogger(__name__)
-LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
 import click
 
 from stranger.resources import repeats_path
 from stranger.utils import parse_repeat_file, get_repeat_info
 
+
 @click.command()
-@click.option('-f', '--repeats-file',
-    type = click.Path(exists=True),
+@click.option(
+    "-f",
+    "--repeats-file",
+    type=click.Path(exists=True),
     help="Path to a file with repeat definitions. See README for explanation",
     default=repeats_path,
     show_default=True,
 )
-@click.option('-x', '--alt-repeats-file',
-    type = click.Path(exists=True),
+@click.option(
+    "-x",
+    "--alt-repeats-file",
+    type=click.Path(exists=True),
     help="Path to a second file with repeat definitions. See README for explanation",
     default=repeats_path,
     show_default=True,
 )
-@click.option('--loglevel', default='INFO', type=click.Choice(LOG_LEVELS),
-              help="Set the level of log output.", show_default=True)
+@click.option(
+    "--loglevel",
+    default="INFO",
+    type=click.Choice(LOG_LEVELS),
+    help="Set the level of log output.",
+    show_default=True,
+)
 @click.pass_context
 def cli(context, repeats_file, alt_repeats_file, loglevel):
     """Test if values differ between loci for variant catalog jsons"""
     coloredlogs.install(level=loglevel)
-    with open(repeats_file, 'r') as file_handle:
-        repeat_information = parse_repeat_file(file_handle, repeats_file_type='json')
+    with open(repeats_file, "r") as file_handle:
+        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')
+    with open(alt_repeats_file, "r") as file_handle:
+        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")
@@ -48,8 +58,14 @@ def cli(context, repeats_file, alt_repeats_file, loglevel):
                 LOG.warning("Entry %s field %s missing in alt file entry.", entry, key)
                 continue
             if other_repeat_information[entry][key] != repeat_information[entry][key]:
-                LOG.error("Entry %s field %s differs between file: %s and alt: %s",entry, key, repeat_information[entry][key], other_repeat_information[entry][key])
+                LOG.error(
+                    "Entry %s field %s differs between file: %s and alt: %s",
+                    entry,
+                    key,
+                    repeat_information[entry][key],
+                    other_repeat_information[entry][key],
+                )
 
 
-if __name__=='__main__':
+if __name__ == "__main__":
     cli()