Better outfile handling in CLI

Author: standage

microhapulator/cli/diff.py

@@ -11,7 +11,7 @@
 # -------------------------------------------------------------------------------------------------
 
 
-from microhapulator import open
+from microhapulator import open as mhopen
 import microhapulator.api as mhapi
 from microhapulator.profile import Profile
 
@@ -32,7 +32,7 @@ def subparser(subparsers):
 
 def main(args):
     differ = mhapi.diff(Profile(fromfile=args.profile1), Profile(fromfile=args.profile2))
-    with open(args.out, "w") as fh:
+    with mhopen(args.out, "w") as fh:
         for marker, diff1, diff2 in differ:
             print(marker, file=fh)
             if len(diff1) > 0:

microhapulator/cli/dist.py

@@ -12,6 +12,7 @@
 
 
 import json
+from microhapulator import open as mhopen
 import microhapulator.api as mhapi
 from microhapulator.profile import Profile
 
@@ -35,5 +36,5 @@ def main(args):
     data = {
         "hamming_distance": d,
     }
-    with open(args.out, "w") as fh:
+    with mhopen(args.out, "w") as fh:
         json.dump(data, fh, indent=4)

microhapulator/cli/getrefr.py

@@ -54,7 +54,7 @@ def download_is_needed(url, filepath, checksum):
 
 def subparser(subparsers):
     desc = "Download and index a GRCh38 assembly file suitable as a whole-genome mapping reference"
-    cli = subparsers.add_parser("getrefr", description=desc)
+    subparsers.add_parser("getrefr", description=desc)
 
 
 def main(args):

microhapulator/cli/sim.py

@@ -10,7 +10,7 @@
 # Development Center.
 # -------------------------------------------------------------------------------------------------
 
-
+from microhapulator import open as mhopen
 from microhapulator import load_marker_frequencies
 import microhapulator.api as mhapi
 from microhapulator.marker import MicrohapIndex
@@ -57,7 +57,7 @@ def subparser(subparsers):
 def main(args):
     frequencies = load_marker_frequencies(args.freq)
     profile = mhapi.sim(frequencies, seed=args.seed)
-    with open(args.out, "w") as fh:
+    with mhopen(args.out, "w") as fh:
         profile.dump(fh)
         message = "profile JSON written to {:s}".format(fh.name)
         print("[MicroHapulator::sim]", message, file=sys.stderr)

microhapulator/cli/unite.py

@@ -12,6 +12,7 @@
 
 
 import numpy.random
+from microhapulator import open as mhopen
 from microhapulator.profile import Profile
 
 
@@ -44,5 +45,5 @@ def main(args):
         Profile(fromfile=args.mom),
         Profile(fromfile=args.dad),
     )
-    with open(args.out, "w") as fh:
+    with mhopen(args.out, "w") as fh:
         profile.dump(fh)