Commit 85c94842 authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

Yapf

parent b7fcd69c

deepchem/metrics/genomic_metrics.py

+1 −2
Original line number Diff line number Diff line
@@ -37,8 +37,7 @@ def get_motif_scores(encoded_sequences, 
        [[1 - GC_fraction, GC_fraction, GC_fraction, 1 - GC_fraction]] * len(

            pwm[0])).T

    gc_log_pwm = np.log(gc_pwm)

    log_scores = get_pssm_scores(encoded_sequences,

                                      log_pwm)

    log_scores = get_pssm_scores(encoded_sequences, log_pwm)

    gc_log_scores = get_pssm_scores(encoded_sequences, gc_log_pwm)

    scores[:, j, :] = log_scores - gc_log_scores

  if max_scores is not None:

deepchem/metrics/tests/test_genomics.py

+2 −2
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ LETTERS = "ACGT" 
from deepchem.metrics.genomic_metrics import get_motif_scores

from deepchem.metrics.genomic_metrics import get_pssm_scores





class TestGenomicMetrics(unittest.TestCase):

  """

  Tests that genomic metrics work as expected.
@@ -32,7 +33,6 @@ class TestGenomicMetrics(unittest.TestCase): 
    motif_scores = get_motif_scores(sequences, [motif_name])

    self.assertEqual(motif_scores.shape, (3, 1, 5))





  def test_get_pssm_scores(self):

    """Test get_pssm_scores returns correct shape."""

    motif_name = "TAL1_known4"

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