Fixed some deprecated BioPython warnings.

bin/trim-primers.py

@@ -5,7 +5,6 @@
 import sys
 from Bio import SeqIO
 from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
 from dark.sequence import findPrimerBidiLimits
 
 
@@ -53,5 +52,4 @@ def trimPrimers(primer, verbose):
 
     args = parser.parse_args()
 
-    trimPrimers(Seq(args.primer.upper(), IUPAC.unambiguous_dna),
-                args.verbose)
+    trimPrimers(Seq(args.primer.upper()), args.verbose)

test/test_dna.py

@@ -1,13 +1,17 @@
 import six
 from unittest import TestCase
 
-from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
-
 from dark.dna import (
     AMBIGUOUS, BASES_TO_AMBIGUOUS, compareDNAReads, matchToString,
     findKozakConsensus, FloatBaseCounts, sequenceToRegex)
 from dark.reads import Read, DNARead, DNAKozakRead
 
+# The following are the letters that used to be on
+# from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
+# IUPACAmbiguousDNA.letters
+# But Bio.Alphabet is now deprecated and will be removed.
+AMBIGUOUS_DNA_LETTERS = 'GATCRYWSMKHBVDN'
+
 
 class TestAmbiguousLetters(TestCase):
     """
@@ -17,7 +21,7 @@ def testExpectedAmbiguousLetters(self):
         """
         The ambiguous DNA letters must match those given by IUPAC.
         """
-        self.assertEqual(sorted(IUPACAmbiguousDNA.letters), sorted(AMBIGUOUS))
+        self.assertEqual(sorted(AMBIGUOUS_DNA_LETTERS), sorted(AMBIGUOUS))
 
     def testExpectedLengthOne(self):
         """
@@ -31,7 +35,7 @@ def testExpectedLengthsGreaterThanOne(self):
         The ambiguous DNA letters must be in sets of size greater than one
         and less than 5.
         """
-        for base in set(IUPACAmbiguousDNA.letters) - set('ACGT'):
+        for base in set(AMBIGUOUS_DNA_LETTERS) - set('ACGT'):
             self.assertTrue(5 > len(AMBIGUOUS[base]) > 1)
 
     def testAmbiguousLettersAreAllACGT(self):

test/test_sequence.py

@@ -1,7 +1,6 @@
 from unittest import TestCase
 from dark.sequence import findPrimer, findPrimerBidi, findPrimerBidiLimits
 from Bio.Seq import Seq
-from Bio.Alphabet import IUPAC
 
 
 class TestFindPrimer(TestCase):
@@ -13,39 +12,39 @@ def testNotFound(self):
         """
         If a primer is not found, the empty list must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual([], findPrimer('BLAH', seq))
 
     def testFoundAtStart(self):
         """
         If a primer is found at the start of a sequence, a list containing 0
         must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual([0], findPrimer('AC', seq))
 
     def testFoundAtEnd(self):
         """
         If a primer is found at the end of a sequence, the correct value
         must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual([2], findPrimer('GT', seq))
 
     def testFoundMultiple(self):
         """
         If a primer is found multiple times, the correct value
         must be returned.
         """
-        seq = Seq('ACGTACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGTACGT')
         self.assertEqual([0, 4], findPrimer('ACG', seq))
 
     def testOverlapping(self):
         """
         If a primer is present twice but is overlapping, only the first
         instance should be returned.
         """
-        seq = Seq('GAAA', IUPAC.unambiguous_dna)
+        seq = Seq('GAAA')
         self.assertEqual([1], findPrimer('AA', seq))
 
 
@@ -58,7 +57,7 @@ def testNotFound(self):
         """
         If a primer is not found, empty lists must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual(([], []), findPrimerBidi('BLAH', seq))
 
     def testFoundStartEnd(self):
@@ -67,7 +66,7 @@ def testFoundStartEnd(self):
         the forward sequence, end of the reverse complement), the
         correct value must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual(([0], [2]), findPrimerBidi('AC', seq))
 
     def testFoundEndStart(self):
@@ -76,31 +75,31 @@ def testFoundEndStart(self):
         the forward sequence, start of the reverse complement), the
         correct value must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual(([2], [0]), findPrimerBidi('GT', seq))
 
     def testFoundMultiple(self):
         """
         If a primer is found multiple times, the correct value
         must be returned.
         """
-        seq = Seq('ACGTACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGTACGT')
         self.assertEqual(([0, 4], [1, 5]), findPrimerBidi('ACG', seq))
 
     def testOverlappingForwards(self):
         """
         If a primer is present twice forwards but is overlapping, only
         the first instance should be returned.
         """
-        seq = Seq('GAAA', IUPAC.unambiguous_dna)
+        seq = Seq('GAAA')
         self.assertEqual(([1], []), findPrimerBidi('AA', seq))
 
     def testOverlappingBackwards(self):
         """
         If a primer is present twice backwards but is overlapping, only
         the first instance should be returned.
         """
-        seq = Seq('GTTT', IUPAC.unambiguous_dna)
+        seq = Seq('GTTT')
         self.assertEqual(([], [1]), findPrimerBidi('AA', seq))
 
 
@@ -114,7 +113,7 @@ def testNotFound(self):
         If a primer is not found, the returned offsets must include
         the whole sequence.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual((0, 4), findPrimerBidiLimits('BLAH', seq))
 
     def testFoundStartEnd(self):
@@ -123,7 +122,7 @@ def testFoundStartEnd(self):
         the forward sequence, end of the reverse complement), the
         correct value must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual((2, 2), findPrimerBidiLimits('AC', seq))
 
     def testFoundEndStart(self):
@@ -132,31 +131,31 @@ def testFoundEndStart(self):
         the forward sequence, start of the reverse complement), the
         correct value must be returned.
         """
-        seq = Seq('ACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGT')
         self.assertEqual((4, 4), findPrimerBidiLimits('GT', seq))
 
     def testFoundMultiple(self):
         """
         If a primer is found multiple times, the correct value
         must be returned.
         """
-        seq = Seq('ACGTACGT', IUPAC.unambiguous_dna)
+        seq = Seq('ACGTACGT')
         self.assertEqual((7, 8), findPrimerBidiLimits('ACG', seq))
 
     def testOverlappingForwards(self):
         """
         If a primer is present twice forwards but is overlapping, only
         the first instance should be returned.
         """
-        seq = Seq('GAAA', IUPAC.unambiguous_dna)
+        seq = Seq('GAAA')
         self.assertEqual((3, 4), findPrimerBidiLimits('AA', seq))
 
     def testOverlappingBackwards(self):
         """
         If a primer is present twice backwards but is overlapping, only
         the first instance should be returned.
         """
-        seq = Seq('GTTT', IUPAC.unambiguous_dna)
+        seq = Seq('GTTT')
         self.assertEqual((0, 1), findPrimerBidiLimits('AA', seq))
 
     def testLonger(self):
@@ -166,6 +165,5 @@ def testLonger(self):
         seq = Seq('AAAAAAAAAA'
                   'GGGGGGGGGG'
                   'AAAAAAAAAA'
-                  'AAAAAAAAAA',
-                  IUPAC.unambiguous_dna)
+                  'AAAAAAAAAA')
         self.assertEqual((20, 40), findPrimerBidiLimits('GGGGGGGGGG', seq))