Compare sequence objects for equality.

str(record) is the string representation of the entire record and
comparing the string representations compares more than the sequences.

augur/align.py

@@ -129,13 +129,12 @@ def read_sequences(*fnames):
     try:
         for fname in fnames:
             for record in SeqIO.parse(fname, 'fasta'):
-                if record.name in seqs:
-                    if str(record) != str(seqs[record.name]):
-                        raise AlignmentError("Detected duplicate input strains \"%s\" but the sequences are different."%record.name)
+                if record.name in seqs and record.seq != seqs[record.name].seq:
+                    raise AlignmentError("Detected duplicate input strains \"%s\" but the sequences are different." % record.name)
                     # if the same sequence then we can proceed (and we only take one)
                 seqs[record.name] = record
     except FileNotFoundError:
-        raise AlignmentError("\nCannot read sequences -- make sure the file %s exists and contains sequences in fasta format"%fname)
+        raise AlignmentError("\nCannot read sequences -- make sure the file %s exists and contains sequences in fasta format" % fname)
     except ValueError as error:
         raise AlignmentError("\nERROR: Problem reading in {}: {}".format(fname, str(error)))
     return seqs

tests/data/align/aa-seq_h3n2_ha_2y_HA1_dup.fasta

@@ -0,0 +1,28 @@
+>A/Victoria/361/2011
+QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILD
+GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF
+NNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIW
+GVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPG
+DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRI
+TYGACPRYVKQSTLKLATGMRNVPEKQTR
+>A/Hawaii/22/2012
+QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD
+GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF
+NNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHSNFKYPALNVTMPNNEQFDKLYIW
+GVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPG
+DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
+TYGACPRYVKQSTLKLATGMRNVPEKQTR
+>A/Texas/50/2012
+QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD
+GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF
+NNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIW
+GVHHPGTDKDQIFLYAQPSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPG
+DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
+TYGACPRYVKQSTLKLATGMRNVPEKQTR
+>A/Texas/50/2012
+QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD
+GENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEF
+NNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIW
+GVHHPGTDKDQIFLYAQPSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPG
+DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
+TYGACPRYATQSTLKLATGMRNVPEKQTR

tests/test_align.py

@@ -3,11 +3,11 @@
 from Bio.SeqRecord import SeqRecord
 
 from shlex import quote
-import pathlib
 
 from augur import align
 
 import pytest
+import pathlib
 
 
 class TestAlign:
@@ -76,7 +76,7 @@ def test_check_duplicates_MSA_and_string_with_duplicates(self):
         )
         with pytest.raises(align.AlignmentError):
             assert align.check_duplicates(alignment, "seq3")
-            
+
     def test_prune_seqs_matching_alignment(self):
         sequence = {
             "seq1": SeqRecord(Seq("GTAC"), name="seq1"),
@@ -139,5 +139,8 @@ def test_read_sequences(self):
         data_file = pathlib.Path('tests/data/align/test_aligned_sequences.fasta')
         result = align.read_sequences(data_file)
         assert len(result.keys()) == 3
-
-
+
+    def test_read_seq_compare(self):
+        data_file = pathlib.Path("tests/data/align/aa-seq_h3n2_ha_2y_2HA1_dup.fasta")
+        with pytest.raises(align.AlignmentError):
+            assert align.read_sequences(data_file)