Fix similar qid and sid names

psa.py

@@ -16,7 +16,7 @@
 import shutil
 import random
 
-__version__ = '1.0.2'
+__version__ = '1.0.3'
 
 # Check whether needle is on PATH and marked as executable.
 assert shutil.which('needle'), "needle not found (is emboss installed?)"
@@ -373,11 +373,11 @@ def emboss_parse(handle: Iterable[str]) -> namedtuple:
                 score = float(cols[2])
         # Parse alignment
         else:
-            if line.startswith(qid):
+            if line.startswith(f'{qid} '):
                 qaln.append(cols[2])
                 qpos.append(int(cols[1]))
                 qpos.append(int(cols[3]))
-            elif line.startswith(sid):
+            elif line.startswith(f'{sid} '):
                 saln.append(cols[2])
                 spos.append(int(cols[1]))
                 spos.append(int(cols[3]))

test.py

@@ -42,7 +42,7 @@ def test_stretcher_protein(self):
         self.assertEqual(len(aln.qaln), len(aln.saln))
         self.assertEqual(len(aln.qaln), aln.length)
 
-    def test_needle_dna_qid_sid(self):
+    def test_needle_dna_qid_sid_1(self):
         qid = 'dna1'
         sid = 'dna2'
         qseq = 'ATGCTAGATA'
@@ -53,6 +53,17 @@ def test_needle_dna_qid_sid(self):
         self.assertEqual(aln.qid, qid)
         self.assertEqual(aln.sid, sid)
 
+    def test_needle_dna_qid_sid_2(self):
+        qid = 'query1'
+        sid = 'query10'
+        qseq = 'ATGCTAGATA'
+        sseq = 'ATGCTAGTTA'
+        aln = psa.needle(moltype='nucl', qseq=qseq, sseq=sseq, qid=qid, sid=sid)
+        self.assertEqual(len(aln.qaln), len(aln.saln))
+        self.assertEqual(len(aln.qaln), aln.length)
+        self.assertEqual(aln.qid, qid)
+        self.assertEqual(aln.sid, sid)
+
 
 class TestPairwiseAlignment(unittest.TestCase):