[MRG] allow gzipped gather csv inputs to tax (#2339)

src/sourmash/tax/tax_utils.py

@@ -85,17 +85,15 @@ def collect_gather_csvs(cmdline_gather_input, *, from_file=None):
     return gather_csvs
 
 
-def load_gather_results(gather_csv, *, delimiter=',',
-                        essential_colnames=EssentialGatherColnames,
+def load_gather_results(gather_csv, *, essential_colnames=EssentialGatherColnames,
                         seen_queries=None, force=False):
     "Load a single gather csv"
     if not seen_queries:
         seen_queries=set()
     header = []
     gather_results = []
     gather_queries = set()
-    with open(gather_csv, 'rt') as fp:
-        r = csv.DictReader(fp, delimiter=delimiter)
+    with sourmash_args.FileInputCSV(gather_csv) as r:
         header = r.fieldnames
         # check for empty file
         if not header:

tests/test_tax.py

@@ -2010,6 +2010,40 @@ def test_annotate_0(runtmp):
     assert "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri" in lin_gather_results[4]
 
 
+def test_annotate_gzipped_gather(runtmp):
+    # test annotate basics
+    c = runtmp
+
+    g_csv = utils.get_test_data('tax/test1.gather.csv')
+    # rewrite gather_csv as gzipped csv
+    gz_gather = runtmp.output('test1.gather.csv.gz')
+    with open(g_csv, 'rb') as f_in, gzip.open(gz_gather, 'wb') as f_out:
+        f_out.writelines(f_in)
+
+    tax = utils.get_test_data('tax/test.taxonomy.csv')
+    csvout = runtmp.output("test1.gather.with-lineages.csv")
+    out_dir = os.path.dirname(csvout)
+
+    c.run_sourmash('tax', 'annotate', '--gather-csv', gz_gather, '--taxonomy-csv', tax, '-o', out_dir)
+
+    print(c.last_result.status)
+    print(c.last_result.out)
+    print(c.last_result.err)
+
+    assert c.last_result.status == 0
+    assert os.path.exists(csvout)
+
+    lin_gather_results = [x.rstrip() for x in open(csvout)]
+    print("\n".join(lin_gather_results))
+    assert f"saving 'annotate' output to '{csvout}'" in runtmp.last_result.err
+
+    assert "lineage" in lin_gather_results[0]
+    assert "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli" in lin_gather_results[1]
+    assert "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri" in lin_gather_results[2]
+    assert "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola vulgatus" in lin_gather_results[3]
+    assert "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri" in lin_gather_results[4]
+
+
 def test_annotate_gather_argparse(runtmp):
     # test annotate with two gather CSVs, second one empty, and --force.
     # this tests argparse handling w/extend.

tests/test_tax_utils.py

@@ -156,6 +156,17 @@ def test_load_gather_results():
     assert len(gather_results) == 4
 
 
+def test_load_gather_results_gzipped(runtmp):
+    gather_csv = utils.get_test_data('tax/test1.gather.csv')
+
+    # rewrite gather_csv as gzipped csv
+    gz_gather = runtmp.output('g.csv.gz')
+    with open(gather_csv, 'rb') as f_in, gzip.open(gz_gather, 'wb') as f_out:
+        f_out.writelines(f_in)
+    gather_results, header, seen_queries = load_gather_results(gz_gather)
+    assert len(gather_results) == 4
+
+
 def test_load_gather_results_bad_header(runtmp):
     g_csv = utils.get_test_data('tax/test1.gather.csv')