[MRG] update lca summarize output to output total counts (#1838)

* update lca summarize output

* add a check where counts != total_counts for lca summarize

src/sourmash/lca/command_summarize.py

@@ -116,21 +116,22 @@ def output_results(lineage_counts, total_counts, filename=None, sig=None):
 
         print_results('{:5} {:>5}   {}   {}:{} {}'.format(p, count, lineage, filename, sig.md5sum()[:8], sig))
 
-def output_csv(lineage_counts, csv_fp, filename, sig, write_header=True):
+def output_csv(lineage_counts, total_counts, csv_fp, filename, sig,
+               write_header=True):
     """\
     Output results in CSV.
     """
 
     w = csv.writer(csv_fp)
     if write_header:
         headers = ['count'] + list(lca_utils.taxlist())
-        headers += ['filename', 'sig_name', 'sig_md5']
+        headers += ['filename', 'sig_name', 'sig_md5', 'total_counts']
         w.writerow(headers)
 
     for (lineage, count) in lineage_counts.items():
         debug('lineage:', lineage)
         row = [count] + lca_utils.zip_lineage(lineage, truncate_empty=False)
-        row += [filename, sig.name, sig.md5sum()]
+        row += [filename, sig.name, sig.md5sum(), total_counts]
         w.writerow(row)
 
 
@@ -198,7 +199,7 @@ def summarize_main(args):
                            filename=filename, sig=sig)
 
             if csv_fp:
-                output_csv(lineage_counts, csv_fp, filename, sig,
+                output_csv(lineage_counts, total, csv_fp, filename, sig,
                            write_header=write_header)
                 write_header = False
     finally:

tests/test_lca.py

@@ -1693,10 +1693,47 @@ def test_single_summarize_to_output_check_filename(runtmp):
     outdata = open(runtmp.output('output.txt'), 'rt').read()
 
     assert 'loaded 1 signatures from 1 files total.' in runtmp.last_result.err
-    assert 'count,superkingdom,phylum,class,order,family,genus,species,strain,filename,sig_name,sig_md5\n' in outdata
-    assert '200,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii,,'+os.path.join(in_dir, 'q.sig')+',TARA_ASE_MAG_00031,5b438c6c858cdaf9e9b05a207fa3f9f0' in outdata
+    assert 'count,superkingdom,phylum,class,order,family,genus,species,strain,filename,sig_name,sig_md5,total_counts\n' in outdata
+    assert '200,Bacteria,Proteobacteria,Gammaproteobacteria,Alteromonadales,Alteromonadaceae,Alteromonas,Alteromonas_macleodii,,'+os.path.join(in_dir, 'q.sig')+',TARA_ASE_MAG_00031,5b438c6c858cdaf9e9b05a207fa3f9f0,200.0\n' in outdata
+    print(outdata)
 
 
+def test_summarize_unknown_hashes_to_output_check_total_counts(runtmp):
+    taxcsv = utils.get_test_data('lca-root/tax.csv')
+    input_sig1 = utils.get_test_data('lca-root/TARA_MED_MAG_00029.fa.sig')
+    input_sig2 = utils.get_test_data('lca-root/TOBG_MED-875.fna.gz.sig')
+    lca_db = runtmp.output('lca-root.lca.json')
+
+    cmd = ['lca', 'index', taxcsv, lca_db, input_sig2]
+    runtmp.sourmash(*cmd)
+
+    print(cmd)
+    print(runtmp.last_result.out)
+    print(runtmp.last_result.err)
+
+    assert os.path.exists(lca_db)
+
+    assert '1 identifiers used out of 2 distinct identifiers in spreadsheet.' in runtmp.last_result.err
+
+    cmd = ['lca', 'summarize', '--db', lca_db, '--query', input_sig1,
+           '-o', 'out.csv']
+    runtmp.sourmash(*cmd)
+
+    print(cmd)
+    print(runtmp.last_result.out)
+    print(runtmp.last_result.err)
+
+    assert '(root)' not in runtmp.last_result.out
+    assert '11.5%    27   Archaea;Euryarcheoata;unassigned;unassigned;novelFamily_I' in runtmp.last_result.out
+
+    with open(runtmp.output('out.csv'), newline="") as fp:
+        r = csv.DictReader(fp)
+        rows = list(r)
+        pairs = [ (row['count'], row['total_counts']) for row in rows ]
+        pairs = [ (float(x), float(y)) for x, y in pairs ]
+        pairs = set(pairs)
+
+        assert pairs == { (27.0, 234.0) }
 
 
 def test_single_summarize_scaled(runtmp):