Use the high-level dispatcher wrappers

Author: jmarshall

devtools/emulate-tools.py

@@ -5,71 +5,67 @@
 behaviour by using pysam's facilities.
 """
 
+import argparse
 import gzip
 import os
 import sys
 import tempfile
 
 import pysam
+import pysam.samtools
+import pysam.bcftools
 
-cmd = os.path.basename(sys.argv[0])
-print(f"emulate-tools.py: {cmd}", file=sys.stderr)
+command = os.path.basename(sys.argv[0])
 
-if cmd == 'samtools' or cmd == 'bcftools':
-    if len(sys.argv) > 1:
-        print(f"emulate-tools.py: {cmd} {sys.argv[1]}", file=sys.stderr)
-        tool = pysam.utils.PysamDispatcher(cmd, sys.argv[1], ())
-        print(f"emulate-tools.py: => {tool}", file=sys.stderr)
-        args = sys.argv[2:]
-        try:
-            if '-?' in args:
-                print(tool.usage())
-            elif '-o' in args or '-bo' in args or '-Co' in args:
-                print("emulate-tools.py: pre for -o", file=sys.stderr)
-                tool(*args, catch_stdout=False)
-                print("emulate-tools.py: post for -o", file=sys.stderr)
-            else:
-                print("emulate-tools.py: pre for default", file=sys.stderr)
-                output = tool(*args)
-                print("emulate-tools.py: post for default", file=sys.stderr)
-                if isinstance(output, str):
-                    sys.stdout.write(output)
-                elif isinstance(output, bytes):
-                    sys.stdout.buffer.write(output)
-
-        except pysam.utils.SamtoolsError as e:
-            sys.exit('emulate-tools.py: {}'.format(e))
+if command in ("samtools", "bcftools"):
+    command = f"{command} {sys.argv[1]}"
+    args = sys.argv[2:]
 
+    if command == "samtools view":
+        pysam.samtools.view(*args)
+    elif command == "samtools index":
+        pysam.samtools.index(*args)
+    elif command == "samtools faidx":
+        pysam.samtools.faidx(*args)
+    elif command == "samtools calmd":
+        pysam.samtools.calmd(*args)
+    elif command == "bcftools view":
+        pysam.bcftools.view(*args)
+    elif command == "bcftools index":
+        pysam.bcftools.index(*args)
     else:
-        if cmd == 'samtools':
-            v = pysam.version.__samtools_version__
-        else:
-            v = pysam.version.__bcftools_version__
-        print('Program: {}\nVersion: {}'.format(cmd, v), file=sys.stderr)
+        sys.exit(f"emulate-tools.py: unknown subcommand {command!r}")
 
-elif cmd == 'bgzip':
-    if len(sys.argv) == 1:
-        f = tempfile.NamedTemporaryFile(delete=False)
-        f.write(sys.stdin.buffer.read())
-        f.close()
-        pysam.tabix_compress(f.name, '-', force=True)
-        os.remove(f.name)
+else:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-c", action="store_false", dest="decompress")
+    parser.add_argument("-d", action="store_true", dest="decompress")
+    parser.add_argument("-f", action="store_true", dest="force")
+    parser.add_argument("-p", dest="preset")
+    parser.add_argument("input_file", nargs="?")
+    opt = parser.parse_args()
 
-    elif len(sys.argv) == 2 and sys.argv[1] == '-d':
-        with gzip.open(sys.stdin.buffer, 'rb') as f:
-            sys.stdout.buffer.write(f.read())
+    if command == "bgzip":
+        if opt.decompress:
+            print("gunzip from stdin", file=sys.stderr)
+            with gzip.open(sys.stdin.buffer, 'rb') as f:
+                sys.stdout.buffer.write(f.read())
 
-    elif len(sys.argv) == 3 and sys.argv[1] == '-c':
-        pysam.tabix_compress(sys.argv[2], '-', force=True)
+        elif opt.input_file:
+            print(f"bgzip {opt.input_file!r}", file=sys.stderr)
+            pysam.tabix_compress(opt.input_file, "-", force=True)
 
-    else:
-        sys.exit('emulate-tools.py: unrecognised bgzip command')
+        else:
+            print("bgzip from stdin", file=sys.stderr)
+            f = tempfile.NamedTemporaryFile(delete=False)
+            f.write(sys.stdin.buffer.read())
+            f.close()
+            pysam.tabix_compress(f.name, "-", force=True)
+            os.remove(f.name)
 
-elif cmd == 'tabix':
-    if len(sys.argv) == 5 and sys.argv[1] == '-f' and sys.argv[2] == '-p':
-        pysam.tabix_index(sys.argv[4], preset=sys.argv[3])
-    else:
-        sys.exit('emulate-tools.py: unrecognised tabix command')
+    elif command == "tabix":
+        print(f"pysam.tabix_index({opt.input_file!r}, preset={opt.preset!r})", file=sys.stderr)
+        pysam.tabix_index(opt.input_file, preset=opt.preset)
 
-else:
-    sys.exit('emulate-tools.py: unknown command "{}"'.format(cmd))
+    else:
+        sys.exit(f"emulate-tools.py: unknown command {command!r}")