Merge pull request #90 from Edinburgh-Genome-Foundry/zulko/fix-missing-bio

Zulko/fix missing bio

Author: veghp

dnachisel/SequencePattern/MotifPssmPattern.py

@@ -1,6 +1,5 @@
 from Bio.Seq import Seq
 from Bio import motifs
-from Bio.Align.AlignInfo import PSSM
 from .SequencePattern import SequencePattern
 import numpy as np
 
@@ -29,10 +28,8 @@ class MotifPssmPattern(SequencePattern):
       sequence(s) with the absolute highest possible score".
     """
 
-    def __init__(
-        self, pssm, threshold=None, relative_threshold=None,
-    ):
-        if not isinstance(pssm, Bio.motifs.Motif):
+    def __init__(self, pssm, threshold=None, relative_threshold=None):
+        if not isinstance(pssm, motifs.Motif):
             raise ValueError(
                 f"Expected PSSM type of `Bio.motifs.Motif`, but {type(pssm)} was passed"
             )
@@ -70,7 +67,7 @@ def find_matches_in_string(self, sequence):
         #     sequence, threshold=self.threshold, both=False
         # )
         indices = find_pssm_matches_with_numpy(
-            pssm_matrix=self.pssm_matrix, sequence=sequence, threshold=self.threshold,
+            pssm_matrix=self.pssm_matrix, sequence=sequence, threshold=self.threshold
         )
         return [(i, i + self.size, 1) for i in indices]
 
@@ -115,7 +112,7 @@ def from_sequences(
         motif.name = name
         pssm = motif
         return MotifPssmPattern(
-            pssm=pssm, threshold=threshold, relative_threshold=relative_threshold,
+            pssm=pssm, threshold=threshold, relative_threshold=relative_threshold
         )
 
     @classmethod
@@ -164,7 +161,7 @@ def list_from_file(
 
         return [
             MotifPssmPattern(
-                pssm, threshold=threshold, relative_threshold=relative_threshold,
+                pssm, threshold=threshold, relative_threshold=relative_threshold
             )
             for pssm in motifs_list
         ]