Fixing tests to use 1/-1 strand numbering

biopython · Feb 26, 2015 · 39cf674 · 39cf674
1 parent 0d7bd47
commit 39cf674
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Showing 4 changed files with 16 additions and 14 deletions.
diff --git a/Bio/AlignIO/FastaIO.py b/Bio/AlignIO/FastaIO.py
@@ -140,7 +140,7 @@ def build_hsp():
         alignment = MultipleSeqAlignment([], alphabet)
 
         #TODO - Introduce an annotated alignment class?
-        #See also Bio/AlignIO/MafIO.py for same requirement.        
+        #See also Bio/AlignIO/MafIO.py for same requirement.
         #For now, store the annotation a new private property:
         alignment._annotations = {}
 

diff --git a/Bio/AlignIO/MafIO.py b/Bio/AlignIO/MafIO.py
@@ -423,7 +423,7 @@ def search(self, starts, ends):
 
                 yield fetched
 
-    def get_spliced(self, starts, ends, strand = "+1"):
+    def get_spliced(self, starts, ends, strand = 1):
         """Returns a multiple alignment of the exact sequence range provided.
 
         Accepts two lists of start and end positions on target_seqname, representing

diff --git a/Tests/output/test_SeqIO b/Tests/output/test_SeqIO
@@ -1741,6 +1741,7 @@ Testing reading uniprot-xml format file SwissProt/H2CNN8.xml
  Checking can write/read as 'sff' format
  Failed: Missing SFF flow information
  Checking can write/read as 'tab' format
+ Checking can write/read as 'maf' format
  Checking can write/read as 'nexus' format
  Checking can write/read as 'phylip-sequential' format
 Testing reading swiss format file SwissProt/H2CNN8.txt
@@ -1768,6 +1769,7 @@ Testing reading swiss format file SwissProt/H2CNN8.txt
  Checking can write/read as 'sff' format
  Failed: Missing SFF flow information
  Checking can write/read as 'tab' format
+ Checking can write/read as 'maf' format
  Checking can write/read as 'nexus' format
  Checking can write/read as 'phylip-sequential' format
 Testing reading genbank format file GenBank/noref.gb

diff --git a/Tests/test_MafIO_index.py b/Tests/test_MafIO_index.py
@@ -171,7 +171,7 @@ def test_records_begin(self):
                                 description="",
                                 annotations={"start": 3009319,
                                              "srcSize": 129993255,
-                                             "strand": "+1", 
+                                             "strand": 1,
                                              "size": 162})
 
             recs[1] = SeqRecord(Seq("TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
@@ -183,7 +183,7 @@ def test_records_begin(self):
                                 description="",
                                 annotations={"start": 11087,
                                              "srcSize": 13221,
-                                             "strand": "+1",
+                                             "strand": 1,
                                              "size": 164})
 
             fetched_recs = self.idx._get_record(34)
@@ -200,7 +200,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 3021494,
                                              "srcSize": 129993255,
-                                             "strand": "+1", 
+                                             "strand": 1,
                                              "size": 42})
 
             recs[1] = SeqRecord(Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
@@ -209,7 +209,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 16173516,
                                              "srcSize": 174210431,
-                                             "strand": "-1",
+                                             "strand": -1,
                                              "size": 46})
 
             recs[2] = SeqRecord(Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
@@ -218,7 +218,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 16393864,
                                              "srcSize": 173908612,
-                                             "strand": "-1",
+                                             "strand": -1,
                                              "size": 46})
 
             recs[3] = SeqRecord(Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
@@ -227,7 +227,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 15875298,
                                              "srcSize": 170899992,
-                                             "strand": "-1",
+                                             "strand": -1,
                                              "size": 46})
 
             recs[4] = SeqRecord(Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
@@ -236,7 +236,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 78072287,
                                              "srcSize": 125616256,
-                                             "strand": "-1",
+                                             "strand": -1,
                                              "size": 46})
 
             recs[5] = SeqRecord(Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
@@ -245,7 +245,7 @@ def test_records_end(self):
                                 description="",
                                 annotations={"start": 14757144,
                                              "srcSize": 54797317,
-                                             "strand": "-1",
+                                             "strand": -1,
                                              "size": 36})
 
             fetched_recs = self.idx._get_record(99228)
@@ -347,7 +347,7 @@ def test_invalid_strand(self):
                               (0, 1000), (500, 1500), ".")
 
         def test_no_alignment(self):
-            result = self.idx.get_spliced((0, 1000), (500, 1500), "+1")
+            result = self.idx.get_spliced((0, 1000), (500, 1500), 1)
 
             self.assertEqual(len(result), 1)
             self.assertEqual(len(result[0].seq), 1000)
@@ -367,7 +367,7 @@ def test_correct_retrieval_1(self):
                                           (3134909, 3185897, 3192258, 3193677,
                                            3203580, 3206222, 3208186, 3211493,
                                            3212019, 3217518, 3219906, 3220446,
-                                           3227479), "+1")
+                                           3227479), 1)
 
             cnksr3 = str(SeqIO.read("MAF/cnksr3.fa", "fasta").seq).upper()
             mm9_seq = "".join([str(x.seq) for x in result if x.id.startswith("mm9")]).replace("-", "")
@@ -384,12 +384,12 @@ def setUp(self):
         def test_inconsistent_strand(self):
             self.assertRaises(ValueError,
                               self.idx.get_spliced,
-                              (0, 3021421), (1000, 3022000), "+1")
+                              (0, 3021421), (1000, 3022000), 1)
 
         def test_bundle_without_target(self):
             self.assertRaises(ValueError,
                               self.idx.get_spliced,
-                              (3009319,), (3009900,), "+1")
+                              (3009319,), (3009900,), 1)
 
 if __name__ == "__main__":
     runner = unittest.TextTestRunner(verbosity=2)