upgrade bam2fasta and use new pysam version

sourmash-bio · Feb 15, 2021 · 9c6a58a · 9c6a58a
1 parent bad70dd
commit 9c6a58a
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/setup.py b/setup.py
@@ -80,7 +80,7 @@ def build_native(spec):
         'doc' : ['sphinx', 'myst-parser[sphinx]', 'alabaster',
                  "sphinxcontrib-napoleon", "nbsphinx",
                  "ipython"],
-        '10x': ['bam2fasta==1.0.4'],
+        '10x': ['bam2fasta==1.0.8', 'pysam>=0.16.0'],
         'storage': ["ipfshttpclient>=0.4.13", "redis"]
     },
     "include_package_data": True,

diff --git a/tests/test_sourmash_compute.py b/tests/test_sourmash_compute.py
@@ -274,14 +274,15 @@ def test_do_sourmash_compute_10x_filter_umis():
         barcodes = [filename.replace(".fasta", "") for filename in fasta_files]
         assert len(barcodes) == 1
         assert len(fasta_files) == 1
-        assert barcodes[0] == 'lung_epithelial_cell|AAATGCCCAAACTGCT-1'
+        print((barcodes[0],))
+        assert barcodes[0].startswith('lung_epithelial_cell_AAATGCCCAAACTGCT-1')
         count = 0
         fasta_file_name = os.path.join(fastas_dir, fasta_files[0])
         for record in screed.open(fasta_file_name):
             name = record.name
             sequence = record.sequence
             count += 1
-            assert name.startswith('lung_epithelial_cell|AAATGCCCAAACTGCT-1')
+            assert name.startswith('lung_epithelial_cell_AAATGCCCAAACTGCT-1')
             assert sequence.count(">") == 0
             assert sequence.count("X") == 0