update test

schneebergerlab · Oct 28, 2024 · 422abd5 · 422abd5
1 parent 751c419
commit 422abd5
Showing 1 changed file with 15 additions and 26 deletions.
diff --git a/test/pytest.py b/test/pytest.py
@@ -8,23 +8,7 @@ def test_cli(self):
         p = Popen('syri -h'.split(), stdout=PIPE, stderr=PIPE)
         out = p.communicate()
         assert 'error' not in out[1].decode()
-
-    # def test_coords_input(self):
-    #     from subprocess import Popen, PIPE
-    #     from glob import glob
-    #     coords = "out.filtered.coords"
-    #     delta = "out.filtered.delta"
-    #     ref = "tair10_chr4.fa.gz"
-    #     qry = "ler_chr4.fa.gz"
-    #     cdir = os.getcwd()
-    #     os.chdir('test/test_data/')
-    #     command = f'syri -c {coords} -d {delta} -r {ref} -q {qry} -k -F T --prefix test_coords'.split()
-    #     p = Popen(command, stdout=PIPE, stderr=PIPE)
-    #     out = p.communicate()
-    #     print(out)
-    #     assert all([f in glob("test_coords*") for f in ["test_coordssyri.out", "test_coordssyri.vcf", "test_coordssyri.summary"]])
-    #
-    # # END
+    # END
 
     def test_bam_input(self):
         from subprocess import Popen, PIPE
@@ -33,14 +17,17 @@ def test_bam_input(self):
         bam = 'out.bam'
         ref = "tair10_chr4.fa.gz"
         qry = "ler_chr4.fa.gz"
-        # cdir = os.getcwd()
-        # os.chdir('test/test_data/')
-        command = f'syri -c {bam} -r {ref} -q {qry}  -F B --prefix test_bam'.split()
+        prefix = "test_bam"
+        for f in glob(f"{prefix}*"):
+            try:
+                os.remove(f)
+            except OSError as e:
+                pass
+        command = f'syri -c {bam} -r {ref} -q {qry}  -F B --prefix {prefix}'.split()
         p = Popen(command, stdout=PIPE, stderr=PIPE)
         out = p.communicate()
-        print(out)
-        assert all([f in glob("test_bam*") for f in ["test_bamsyri.out", "test_bamsyri.vcf", "test_bamsyri.summary"]])
-        for f in glob("test_bam*"):
+        assert all([f"{prefix}{f}" in glob(f"{prefix}*") for f in ["syri.out", "syri.vcf", "syri.summary"]])
+        for f in glob(f"{prefix}*"):
             try:
                 os.remove(f)
             except OSError as e:
@@ -55,12 +42,14 @@ def test_paf_input(self):
         ref = "tair10_chr4.fa.gz"
         qry = "ler_chr4.fa.gz"
         prefix = "test_paf"
-        # cdir = os.getcwd()
-        # os.chdir('test/test_data/')
+        for f in glob(f"{prefix}*"):
+            try:
+                os.remove(f)
+            except OSError:
+                pass
         command = f'syri -c {paf} -r {ref} -q {qry}  -F P --prefix {prefix}'.split()
         p = Popen(command, stdout=PIPE, stderr=PIPE)
         out = p.communicate()
-        print(out)
         assert all([f"{prefix}{f}" in glob(f"{prefix}*") for f in ["syri.out", "syri.vcf", "syri.summary"]])
         for f in glob(f"{prefix}*"):
             try: