Fix denominator

src/jcvi/projects/sugarcane.py

@@ -40,6 +40,7 @@
     savefig,
 )
 from ..graphics.chromosome import Chromosome as ChromosomePlot
+from ..utils.cbook import short_float
 
 SoColor = "#7436a4"  # Purple
 SsColor = "#5a8340"  # Green
@@ -356,23 +357,25 @@ def summary(self) -> List[Tuple[str, int, int, int]]:
             group_chrom_count = group_count / len(chromosomes[0])
             group_so_size = group_count if subgenome == "SO" else 0
             group_ss_size = group_count if subgenome == "SS" else 0
+            group_size = group_so_size + group_ss_size
             ans.append(
                 (
                     subgenome,
                     group_chrom_count,
-                    group_so_size / SO_GENE_COUNT,
-                    group_ss_size / SS_GENE_COUNT,
+                    group_so_size / group_size,
+                    group_ss_size / group_size,
                 )
             )
             total_chrom_count += group_chrom_count
             total_so_size += group_so_size
             total_ss_size += group_ss_size
+        total_size = total_so_size + total_ss_size
         ans.append(
             (
                 "Total",
                 total_chrom_count,
-                total_so_size / SO_GENE_COUNT,
-                total_ss_size / SS_GENE_COUNT,
+                total_so_size / total_size,
+                total_ss_size / total_size,
             )
         )
         return ans
@@ -409,11 +412,11 @@ def _percent_summary(self, a, tag, precision=1):
             round(np.min(a), precision),
             round(np.max(a), precision),
         )
-        s = f"*{tag}*%: {mean:.1f}%"
+        s = f"*{tag}*%: {short_float(mean, precision)}%"
         print(s)
         if mn == mean and mx == mean:
             return s
-        return s + f" ({mn:.1f}-{mx:.1f}%)"
+        return s + f" ({short_float(mn, precision)}-{short_float(mx, precision)}%)"
 
     @property
     def percent_SO_summary(self):

src/jcvi/utils/cbook.py

@@ -199,6 +199,22 @@ def percentage(a, b, precision=1, mode: Optional[int] = 0):
     return pct
 
 
+def short_float(f, precision=1, trim_zeros=True):
+    """
+    Format a float to a string with a fixed precision, and optionally trim
+    trailing zeros.
+
+    >>> short_float(3.1415926)
+    '3.1'
+    >>> short_float(3.002)
+    '3'
+    """
+    f = f"{f:.{precision}f}"
+    if trim_zeros:
+        f = f.rstrip("0").rstrip(".")
+    return f
+
+
 def thousands(x):
     """
     >>> thousands(12345)

tests/utils/test_cbook.py

@@ -2,7 +2,7 @@
 import pytest
 
 from jcvi.apps.base import cleanup
-from jcvi.utils.cbook import autoscale, depends, gene_name, seqid_parse
+from jcvi.utils.cbook import autoscale, depends, gene_name, seqid_parse, short_float
 
 
 @pytest.mark.parametrize(
@@ -52,3 +52,16 @@ def func1(infile="a", outfile="b"):
     func1(infile="a", outfile="b")
     assert op.exists("b")
     cleanup("a", "b")
+
+
+@pytest.mark.parametrize(
+    "f,precision,trim_zeros,output",
+    [
+        (0.123456, 3, True, "0.123"),
+        (0.0000, 2, True, "0"),
+        (3.1000, 2, False, "3.10"),
+        (3.0, 2, True, "3"),
+    ],
+)
+def test_short_float(f, precision, trim_zeros, output):
+    assert short_float(f, precision, trim_zeros) == output