format code

docs/conf.py

@@ -220,7 +220,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "pyensembl.tex", "pyensembl Documentation", "Hammer Lab", "manual"),
+    (
+        master_doc,
+        "pyensembl.tex",
+        "pyensembl Documentation",
+        "Hammer Lab",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

pyensembl/__init__.py

@@ -19,12 +19,18 @@
 from .genome import Genome
 from .locus import Locus
 from .reference_name import (  # ensembl_grch36,; ensembl_grch37,; ensembl_grch38,
-    find_species_by_reference, genome_for_reference_name,
-    normalize_reference_name, which_reference)
+    find_species_by_reference,
+    genome_for_reference_name,
+    normalize_reference_name,
+    which_reference,
+)
 from .search import find_nearest_locus
 from .sequence_data import SequenceData
-from .species import (check_species_object, find_species_by_name,
-                      normalize_species_name)
+from .species import (
+    check_species_object,
+    find_species_by_name,
+    normalize_species_name,
+)
 from .transcript import Transcript
 from .version import __version__
 

pyensembl/download_cache.py

@@ -151,7 +151,10 @@ def _fields(self):
         )
 
     def __eq__(self, other):
-        return other.__class__ is DownloadCache and self._fields() == other._fields()
+        return (
+            other.__class__ is DownloadCache
+            and self._fields() == other._fields()
+        )
 
     def __hash__(self):
         return hash(self._fields())
@@ -213,10 +216,14 @@ def cached_path(self, path_or_url):
         # if we expect the download function to decompress this file then
         # we should use its name without the compression extension
         if self.decompress_on_download:
-            local_filename = self._remove_compression_suffix_if_present(local_filename)
+            local_filename = self._remove_compression_suffix_if_present(
+                local_filename
+            )
 
         if len(local_filename) == 0:
-            raise ValueError("Can't determine local filename for %s" % (path_or_url,))
+            raise ValueError(
+                "Can't determine local filename for %s" % (path_or_url,)
+            )
 
         return join(self.cache_directory_path, local_filename)
 
@@ -319,9 +326,9 @@ def delete_cached_files(self, prefixes=[], suffixes=[]):
         """
         if isdir(self.cache_directory_path):
             for filename in listdir():
-                delete = any([filename.endswith(ext) for ext in suffixes]) or any(
-                    [filename.startswith(pre) for pre in prefixes]
-                )
+                delete = any(
+                    [filename.endswith(ext) for ext in suffixes]
+                ) or any([filename.startswith(pre) for pre in prefixes])
                 if delete:
                     path = join(self.cache_directory_path, filename)
                     logger.info("Deleting %s", path)

pyensembl/ensembl_release_versions.py

@@ -10,16 +10,24 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .config import (MAX_ENSEMBL_RELEASE, MAX_ENSEMBLGENOME_RELEASE,
-                     MIN_ENSEMBL_RELEASE, MIN_ENSEMBLGENOME_RELEASE)
+from .config import (
+    MAX_ENSEMBL_RELEASE,
+    MAX_ENSEMBLGENOME_RELEASE,
+    MIN_ENSEMBL_RELEASE,
+    MIN_ENSEMBLGENOME_RELEASE,
+)
 
 
 def check_release_number(release, database=None):
     """
     Check to make sure a release is in the valid range of Ensembl releases.
     """
     if release is None:
-        return MAX_ENSEMBL_RELEASE if database is None else MAX_ENSEMBLGENOME_RELEASE
+        return (
+            MAX_ENSEMBL_RELEASE
+            if database is None
+            else MAX_ENSEMBLGENOME_RELEASE
+        )
     try:
         release = int(release)
     except ValueError:

pyensembl/exon.py

@@ -15,7 +15,9 @@
 
 
 class Exon(Locus):
-    def __init__(self, exon_id, contig, start, end, strand, gene_name, gene_id):
+    def __init__(
+        self, exon_id, contig, start, end, strand, gene_name, gene_id
+    ):
         Locus.__init__(self, contig, start, end, strand)
         self.exon_id = exon_id
         self.gene_name = gene_name

pyensembl/fasta.py

@@ -32,7 +32,8 @@ def _parse_header_id(line):
     """
     if type(line) is not bytes:
         raise TypeError(
-            "Expected header line to be of type %s but got %s" % (bytes, type(line))
+            "Expected header line to be of type %s but got %s"
+            % (bytes, type(line))
         )
 
     if len(line) <= 1:

pyensembl/gene.py

@@ -17,7 +17,9 @@
 
 
 class Gene(LocusWithGenome):
-    def __init__(self, gene_id, gene_name, contig, start, end, strand, biotype, genome):
+    def __init__(
+        self, gene_id, gene_name, contig, start, end, strand, biotype, genome
+    ):
         LocusWithGenome.__init__(
             self,
             contig=contig,
@@ -98,7 +100,8 @@ def transcripts(self):
         # its particular information, might be more efficient if we
         # just get all the columns here, but how do we keep that modular?
         return [
-            self.genome.transcript_by_id(result[0]) for result in transcript_id_results
+            self.genome.transcript_by_id(result[0])
+            for result in transcript_id_results
         ]
 
     @memoized_property