Text case from Kamil Slowikowski for Nexus bug just fixed

biopython · Mar 20, 2012 · 475de4d · 475de4d
1 parent 541f2b5
commit 475de4d
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diff --git a/Tests/Nexus/codonposset.nex b/Tests/Nexus/codonposset.nex
@@ -0,0 +1,25 @@
+#NEXUS
+[MacClade 4.05 registered to Computational Biologist, University]
+
+
+BEGIN DATA;
+       DIMENSIONS  NTAX=2 NCHAR=22;
+       FORMAT DATATYPE=DNA  MISSING=? GAP=- ;
+MATRIX
+[                           10        20 ]
+[                           .         .  ]
+
+Aegotheles         AAAAAGGCATTGTGGTGGGAAT   [22]
+Aerodramus         ?????????TTGTGGTGGGAAT   [13]
+;
+END;
+
+
+BEGIN CODONS;
+       CODONPOSSET * CodonPositions =
+               N: 1-10,
+               1: 11-22\3,
+               2: 12-22\3,
+               3: 13-22\3;
+       CODESET  * UNTITLED = Universal: all ;
+END;
diff --git a/Tests/output/test_AlignIO b/Tests/output/test_AlignIO
@@ -135,6 +135,18 @@ Testing reading nexus format file Nexus/test_Nexus_input.nex with 1 alignments
  Checking can write/read as 'stockholm' format
  Checking can write/read as 'fasta' format
  Checking can write/read as 'tab' format
+Testing reading nexus format file Nexus/codonposset.nex with 1 alignments
+ Alignment 0, with 2 sequences of length 22
+  AAAAAGGCATTGTGGTGGGAAT Aegotheles
+  ?????????TTGTGGTGGGAAT Aerodramus
+ Checking can write/read as 'clustal' format
+ Checking can write/read as 'nexus' format
+ Checking can write/read as 'phylip' format
+ Checking can write/read as 'phylip-relaxed' format
+ Checking can write/read as 'phylip-sequential' format
+ Checking can write/read as 'stockholm' format
+ Checking can write/read as 'fasta' format
+ Checking can write/read as 'tab' format
 Testing reading stockholm format file Stockholm/simple.sth with 1 alignments
  Alignment 0, with 2 sequences of length 104
   UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCA...UGU AP001509.1

diff --git a/Tests/test_AlignIO.py b/Tests/test_AlignIO.py
@@ -36,6 +36,7 @@
     ("fasta", 3, 1, 'GFF/multi.fna'), #Trivial nucleotide alignment
 #Following example is also used in test_Nexus.py
     ("nexus", 9, 1, 'Nexus/test_Nexus_input.nex'),
+    ("nexus", 2, 1, 'Nexus/codonposset.nex'),
     ("stockholm", 2, 1, 'Stockholm/simple.sth'),
     ("stockholm", 6, 1, 'Stockholm/funny.sth'),
     ("phylip", 6, 1, 'Phylip/reference_dna.phy'),