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Separating the old and new Motif code, and adding automatic pwm, pssm…

… calculation to the new Motif class
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mdehoon
mdehoon committed Jan 11, 2013
1 parent 57ae89c commit d1a3efb2e937ed15118cd257890648b2418164d1
Showing with 2,239 additions and 1,327 deletions.
  1. +1 −1 Bio/Motif/AlignAce.py
  2. +1 −1 Bio/Motif/Jaspar.py
  3. +1 −1 Bio/Motif/MEME.py
  4. +483 −0 Bio/Motif/Matrix.py
  5. +240 −1,201 Bio/Motif/_Motif.py
  6. +500 −7 Bio/Motif/__init__.py
  7. +3 −22 Doc/Tutorial.tex
  8. +1,010 −94 Tests/test_Motif.py
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@@ -6,7 +6,7 @@
"""Parsing AlignACE output files
"""
-from Bio.Motif import Motif
+from Bio.Motif import NewMotif as Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
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@@ -1,4 +1,4 @@
-from Bio.Motif import Motif
+from Bio.Motif import NewMotif as Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
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@@ -6,7 +6,7 @@
from Bio.Alphabet import IUPAC
from Bio import Seq
-from Bio.Motif import Motif as BaseMotif
+from Bio.Motif import NewMotif as BaseMotif
def read(handle):
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