Add test_allmaps.test_path()

tests/assembly/allmaps.py/inputs/JM-2.chain

@@ -1,66 +1,66 @@
-chain	1000	scaffold_158	1026459	+	0	1026459	chr23	15272643	+	0	1026459	1
-1026459
-
-chain	1000	scaffold_1006	98986	+	0	98986	chr23	15272643	+	1026559	1125545	2
-98986
+chain	1000	scaffold_821	137336	+	0	137336	chr23	15272643	+	0	137336	1
+137336
 
-chain	1000	scaffold_382	404603	+	0	404603	chr23	15272643	-	13742395	14146998	3
-404603
+chain	1000	scaffold_792	147429	+	0	147429	chr23	15272643	+	137436	284865	2
+147429
 
-chain	1000	scaffold_648	201681	+	0	201681	chr23	15272643	+	1530348	1732029	4
-201681
+chain	1000	scaffold_866	127595	+	0	127595	chr23	15272643	+	284965	412560	3
+127595
 
-chain	1000	scaffold_829	131171	+	0	131171	chr23	15272643	+	1732129	1863300	5
-131171
+chain	1000	scaffold_1189	71547	+	0	71547	chr23	15272643	-	14788436	14859983	4
+71547
 
-chain	1000	scaffold_642	203512	+	0	203512	chr23	15272643	+	1863400	2066912	6
-203512
+chain	1000	scaffold_375	406785	+	0	406785	chr23	15272643	-	14381551	14788336	5
+406785
 
-chain	1000	scaffold_513	263302	+	0	263302	chr23	15272643	+	2067012	2330314	7
-263302
+chain	1000	scaffold_310	502147	+	0	502147	chr23	15272643	-	13879304	14381451	6
+502147
 
-chain	1000	scaffold_331	470372	+	0	470372	chr23	15272643	+	2330414	2800786	8
-470372
+chain	1000	scaffold_95	1588924	+	0	1588924	chr23	15272643	+	1393439	2982363	7
+1588924
 
-chain	1000	scaffold_150	1083458	+	0	1083458	chr23	15272643	+	2800886	3884344	9
-1083458
+chain	1000	scaffold_148	1097854	+	0	1097854	chr23	15272643	-	11192326	12290180	8
+1097854
 
-chain	1000	scaffold_80	1825797	+	0	1825797	chr23	15272643	+	3884444	5710241	10
-1825797
+chain	1000	scaffold_225	700647	+	0	700647	chr23	15272643	+	4080417	4781064	9
+700647
 
-chain	1000	scaffold_43	2563023	+	0	2563023	chr23	15272643	+	5710341	8273364	11
-2563023
+chain	1000	scaffold_164	979419	+	0	979419	chr23	15272643	-	9512060	10491479	10
+979419
 
-chain	1000	scaffold_129	1238496	+	0	1238496	chr23	15272643	-	5760683	6999179	12
+chain	1000	scaffold_129	1238496	+	0	1238496	chr23	15272643	+	5760683	6999179	11
 1238496
 
-chain	1000	scaffold_164	979419	+	0	979419	chr23	15272643	+	9512060	10491479	13
-979419
+chain	1000	scaffold_43	2563023	+	0	2563023	chr23	15272643	-	5710341	8273364	12
+2563023
 
-chain	1000	scaffold_225	700647	+	0	700647	chr23	15272643	+	10491579	11192226	14
-700647
+chain	1000	scaffold_80	1825797	+	0	1825797	chr23	15272643	-	3884444	5710241	13
+1825797
 
-chain	1000	scaffold_148	1097854	+	0	1097854	chr23	15272643	+	11192326	12290180	15
-1097854
+chain	1000	scaffold_150	1083458	+	0	1083458	chr23	15272643	-	2800886	3884344	14
+1083458
 
-chain	1000	scaffold_95	1588924	+	0	1588924	chr23	15272643	+	12290280	13879204	16
-1588924
+chain	1000	scaffold_331	470372	+	0	470372	chr23	15272643	+	12471857	12942229	15
+470372
 
-chain	1000	scaffold_310	502147	+	0	502147	chr23	15272643	+	13879304	14381451	17
-502147
+chain	1000	scaffold_642	203512	+	0	203512	chr23	15272643	+	12942329	13145841	16
+203512
 
-chain	1000	scaffold_375	406785	+	0	406785	chr23	15272643	+	14381551	14788336	18
-406785
+chain	1000	scaffold_829	131171	+	0	131171	chr23	15272643	-	1995531	2126702	17
+131171
 
-chain	1000	scaffold_792	147429	+	0	147429	chr23	15272643	+	14788436	14935865	19
-147429
+chain	1000	scaffold_513	263302	+	0	263302	chr23	15272643	-	1732129	1995431	18
+263302
 
-chain	1000	scaffold_1189	71547	+	0	71547	chr23	15272643	+	14935965	15007512	20
-71547
+chain	1000	scaffold_648	201681	+	0	201681	chr23	15272643	+	13540614	13742295	19
+201681
 
-chain	1000	scaffold_866	127595	+	0	127595	chr23	15272643	+	15007612	15135207	21
-127595
+chain	1000	scaffold_382	404603	+	0	404603	chr23	15272643	+	13742395	14146998	20
+404603
 
-chain	1000	scaffold_821	137336	+	0	137336	chr23	15272643	+	15135307	15272643	22
-137336
+chain	1000	scaffold_1006	98986	+	0	98986	chr23	15272643	+	14147098	14246084	21
+98986
+
+chain	1000	scaffold_158	1026459	+	0	1026459	chr23	15272643	+	14246184	15272643	22
+1026459
 

tests/assembly/test_allmaps.py

@@ -1,5 +1,8 @@
 import os.path as op
 
+from jcvi.apps.base import cleanup
+from jcvi.assembly.allmaps import path
+
 
 def datafile(path: str) -> str:
     """Returns the path to a file in the designated test directory."""
@@ -29,3 +32,20 @@ def test_liftover():
     liftover(chainfile, bedfile, liftedbedfile, unmapfile="unmapped", cstyle="l")
     compare_line_by_line(liftedbedfile, expected)
     cleanup(liftedbedfile, "unmapped")
+
+
+def test_path():
+    bedfile = datafile("inputs/JM-2.bed")
+    fastafile = datafile("inputs/scaffolds.fasta.gz")
+    weightsfile = datafile("inputs/weights.txt")
+    output_image = "chr23.pdf"
+    cleanup(output_image)
+    path(
+        [
+            bedfile,
+            fastafile,
+            "-w",
+            weightsfile,
+        ]
+    )
+    assert op.exists(output_image)