Merge pull request #24 from phac-nml/fix/seq-id-str

Fix up issue when sequence id was a number

CHANGELOG.md

@@ -1,3 +1,7 @@
+# Version 0.2.2
+
+* Fix issue where `staramr` crashes if an input contig id is a number.
+
 # Version 0.2.1
 
 * Minor

staramr/blast/results/BlastResultsParser.py

@@ -4,6 +4,7 @@
 
 import Bio.SeqIO
 import pandas as pd
+import numpy as np
 
 from staramr.blast.BlastHandler import BlastHandler
 from staramr.blast.results.BlastHitPartitions import BlastHitPartitions
@@ -82,7 +83,8 @@ def _get_out_file_name(self, in_file):
         pass
 
     def _handle_blast_hit(self, in_file, database_name, blast_file, results, hit_seq_records):
-        blast_table = pd.read_table(blast_file, header=None, names=BlastHandler.BLAST_COLUMNS, index_col=False)
+        blast_table = pd.read_table(blast_file, header=None, names=BlastHandler.BLAST_COLUMNS, index_col=False).astype(
+            dtype={'qseqid': np.unicode_, 'sseqid': np.unicode_})
         partitions = BlastHitPartitions()
 
         blast_table['plength'] = (blast_table.length / blast_table.qlen) * 100.0

staramr/tests/integration/data/test-seq-id.fsa

@@ -0,0 +1,9 @@
+>1
+ATGGACATCAGGCAAATGAACAGAACCCATCTGGATCACTGGCGCGGATTGCGAAAACAG
+CTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCC
+GATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCC
+TCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGT
+ATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTG
+CAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAAT
+ACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTC
+TACCGAAAGCGTTGTTGA

staramr/tests/integration/detection/test_AMRDetection.py

@@ -62,6 +62,17 @@ def testResfinderAminoglycosideNameSuccess(self):
         self.assertAlmostEqual(result['%Overlap'].iloc[0], 100.00, places=2, msg='Wrong overlap')
         self.assertEqual(result['Accession'].iloc[0], 'NC_003197', msg='Wrong accession')
 
+    def testNumericalSequenceID(self):
+        file = path.join(self.test_data_dir, "test-seq-id.fsa")
+        files = [file]
+        self.amr_detection.run_amr_detection(files, 99, 90, 90)
+
+        resfinder_results = self.amr_detection.get_resfinder_results()
+        self.assertEqual(len(resfinder_results.index), 1, 'Wrong number of rows in result')
+
+        result = resfinder_results[resfinder_results['Gene'] == "aac(6')-Iaa"]
+        self.assertEqual(result['Contig'].iloc[0], "1", "Incorrect contig id")
+
     def testResfinderBetaLactam2MutationsSuccess(self):
         file = path.join(self.test_data_dir, "beta-lactam-blaIMP-42-mut-2.fsa")
         files = [file]