Test synteny as well

jcvi/graphics/synteny.py

@@ -18,9 +18,11 @@
 """
 
 import sys
-from typing import Optional
+
+from typing import List, Optional
 
 import numpy as np
+
 from matplotlib import transforms
 from matplotlib.path import Path
 
@@ -626,7 +628,7 @@ def draw_gene_legend(
         ax.text(xr, ytop + d / 2, "repeat", ha="center")
 
 
-def main():
+def main(args: List[str]):
     p = OptionParser(__doc__)
     p.add_argument("--switch", help="Rename the seqid with two-column file")
     p.add_argument("--tree", help="Display trees on the bottom of the figure")
@@ -684,7 +686,7 @@ def main():
         action="store_true",
         help="If set, do not exclude small features from annotation track (<1%% of region)",
     )
-    opts, args, iopts = p.set_image_options(figsize="8x7")
+    opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 3:
         sys.exit(not p.print_help())
@@ -728,6 +730,8 @@ def main():
     image_name = pf + "." + iopts.format
     savefig(image_name, dpi=iopts.dpi, iopts=iopts)
 
+    return image_name
+
 
 if __name__ == "__main__":
-    main()
+    main(sys.argv[1:])

tests/graphics/data/blocks

@@ -0,0 +1,50 @@
+GSVIVT01012261001	.
+GSVIVT01012259001	.
+GSVIVT01012258001	.
+GSVIVT01012257001	.
+GSVIVT01012255001	Prupe.1G290900.1
+GSVIVT01012253001	Prupe.1G290800.2
+GSVIVT01012252001	Prupe.1G290700.1
+GSVIVT01012250001	Prupe.1G290600.1
+GSVIVT01012249001	Prupe.1G290500.1
+GSVIVT01012248001	Prupe.1G290400.1
+GSVIVT01012247001	Prupe.1G290200.2
+GSVIVT01012246001	Prupe.1G290100.3
+GSVIVT01012245001	Prupe.1G290000.1
+GSVIVT01012244001	Prupe.1G289800.1
+GSVIVT01012243001	.
+GSVIVT01012242001	.
+GSVIVT01012241001	.
+GSVIVT01012240001	.
+GSVIVT01012239001	Prupe.1G289700.1
+GSVIVT01012238001	.
+GSVIVT01012237001	Prupe.1G289300.1
+GSVIVT01012236001	Prupe.1G289200.2
+GSVIVT01012235001	.
+GSVIVT01012234001	Prupe.1G289100.1
+GSVIVT01012233001	Prupe.1G289000.1
+GSVIVT01012232001	.
+GSVIVT01012231001	Prupe.1G288900.1
+GSVIVT01012230001	Prupe.1G288700.1
+GSVIVT01012229001	.
+GSVIVT01012228001	Prupe.1G288300.1
+GSVIVT01012227001	Prupe.1G288100.3
+GSVIVT01012226001	.
+GSVIVT01012225001	Prupe.1G288000.1
+GSVIVT01012224001	Prupe.1G287800.1
+GSVIVT01012223001	Prupe.1G287500.1
+GSVIVT01012222001	Prupe.1G287300.2
+GSVIVT01012221001	Prupe.1G287300.1
+GSVIVT01012220001	Prupe.1G287200.1
+GSVIVT01012219001	Prupe.1G286800.1
+GSVIVT01012218001	Prupe.1G286700.2
+GSVIVT01012217001	.
+GSVIVT01012216001	Prupe.1G285700.1
+GSVIVT01012215001	Prupe.1G286600.2
+GSVIVT01012214001	Prupe.1G286500.1
+GSVIVT01012213001	Prupe.1G286400.1
+GSVIVT01012212001	Prupe.1G286200.1
+GSVIVT01012211001	Prupe.1G286100.1
+GSVIVT01012210001	Prupe.1G286000.1
+GSVIVT01012209001	Prupe.1G286000.1
+GSVIVT01012208001	Prupe.1G285900.1

tests/graphics/data/blocks.layout

@@ -0,0 +1,5 @@
+# x,   y, rotation,   ha,     va,   color, ratio,            label
+0.5, 0.6,        0, left, center,       m,     1,       grape Chr1
+0.5, 0.4,        0, left, center, #fc8d62,     1, peach scaffold_1
+# edges
+e, 0, 1

tests/graphics/test_karyotype.py

@@ -5,6 +5,7 @@
 import os.path as op
 import pytest
 
+from jcvi.apps.base import cleanup
 from jcvi.graphics.karyotype import main as karyotype_main, make_circle_name
 
 
@@ -27,6 +28,7 @@ def test_make_circle_name(sid, rev, expected):
 def test_main():
     cwd = os.getcwd()
     os.chdir(op.join(op.dirname(__file__), "data"))
+    cleanup("karyotype.pdf")
     image_name = karyotype_main(["seqids", "layout"])
     assert op.exists(image_name)
     os.chdir(cwd)

tests/graphics/test_synteny.py

@@ -1,10 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: UTF-8 -*-
 
+import os
+import os.path as op
 import pytest
 
+from jcvi.apps.base import cleanup
+from jcvi.formats.bed import merge
+from jcvi.graphics.synteny import LayoutLine, main as synteny_main
 from jcvi.utils.validator import ValidationError
-from jcvi.graphics.synteny import LayoutLine
 
 
 @pytest.mark.parametrize(
@@ -43,3 +47,13 @@ def test_valid_layoutline(row, delimiter):
 def test_invalid_layoutline(row, delimiter, error):
     with pytest.raises(error):
         _ = LayoutLine(row, delimiter)
+
+
+def test_main():
+    cwd = os.getcwd()
+    os.chdir(op.join(op.dirname(__file__), "data"))
+    cleanup("grape_peach.bed", "blocks.pdf")
+    merge(["grape.bed", "peach.bed", "-o", "grape_peach.bed"])
+    image_name = synteny_main(["blocks", "grape_peach.bed", "blocks.layout"])
+    assert op.exists(image_name)
+    os.chdir(cwd)