bugfix: gtf file writing

picea/dag.py

@@ -1,4 +1,5 @@
 """Direct Acyclic Graphs"""
+
 from collections import defaultdict
 from copy import deepcopy
 from typing import Callable, DefaultDict, Dict, Hashable, Iterable, List, Optional
@@ -9,6 +10,7 @@ class DAGElement:
     """
     Element in a DAG, intended to be used as BaseClass
     """
+
     def __init__(
         self,
         ID: str,
@@ -100,7 +102,8 @@ def _traverse(
 
 
 class DirectedAcyclicGraph:
-    """"Base DAG class"""
+    """Base DAG class"""
+
     def __init__(self) -> None:
         self._elements: Dict[Hashable, DAGElement] = dict()
 
@@ -142,10 +145,7 @@ def add(self, element: DAGElement) -> None:
     def pop(self, ID: Hashable) -> DAGElement:
         return self._elements.pop(ID)
 
-    def groupby(
-        self,
-        group_func: Callable[[DAGElement], Hashable]
-    ) -> DefaultDict[Hashable, "DirectedAcyclicGraph"]:
+    def groupby(self, group_func: Callable[[DAGElement], Hashable]) -> DefaultDict[Hashable, "DirectedAcyclicGraph"]:
         """
         Group elements in the current collection by calling 'group_func' and using \
         the results as a dictionary key
@@ -165,10 +165,7 @@ def groupby(
             element._container = self
         return grouped
 
-    def filter(
-        self,
-        filter_func: Callable[[DAGElement], bool]
-    ) -> "DirectedAcyclicGraph":
+    def filter(self, filter_func: Callable[[DAGElement], bool]) -> "DirectedAcyclicGraph":
         """
         Filter elements in the current collection based on the output of filter_func
 

picea/ontology.py

@@ -29,29 +29,19 @@ def __getitem__(self, ID) -> OntologyTerm:
         if not term._children and not term._parents and term.__dict__.get("alt_id"):
             alt_id = term.__dict__.get("alt_id")[0]
             term = self._elements[alt_id]
-            warnings.warn(
-                f"Accessed GO term by alt ID {ID}, "
-                f"returning main GO term with ID {alt_id}"
-            )
+            warnings.warn(f"Accessed GO term by alt ID {ID}, " f"returning main GO term with ID {alt_id}")
         return term
 
     @classmethod
-    def from_obo(
-        cls, filename: str = None, string: str = None, skip_obsolete=True
-    ) -> "Ontology":
+    def from_obo(cls, filename: str = None, string: str = None, skip_obsolete=True) -> "Ontology":
         assert filename or string
         assert not (filename and string)
         ontology = cls()
         if filename:
             with open(filename) as filehandle:
                 string = filehandle.read()
 
-        obo_iter = (
-            el
-            for _, el in groupby(
-                string.strip().split("\n"), lambda line: line[:1] == "["
-            )
-        )
+        obo_iter = (el for _, el in groupby(string.strip().split("\n"), lambda line: line[:1] == "["))
 
         ontology._header = list(next(obo_iter))