Rename python modules to their equivalent commands

Author: EricR86

README.md

@@ -16,9 +16,11 @@ Newmap requires a CPU that supports the AVX2 instruction set.
 
 OpenMP is required for parallel processing.
 
-## Documentation / Read The Docs
+## Documentation
 The latest for Newmap is available on [Read the Docs](https://newmap.readthedocs.io).
 
+All commands have a `--help` option to provide additional usage information.
+
 ## Quick start
 
 ### Installation

newmap/generate_index.py newmap/index.pynewmap/generate_index.py renamed to newmap/index.py

@@ -2,9 +2,9 @@
 from importlib.metadata import version
 import sys
 
-from newmap import generate_index, unique_counts, unique_counts_conversion
+from newmap import index, search, track
 from newmap.util import DEFAULT_MAPPABILITY_READ_LENGTH, INDEX_EXTENSION
-from newmap.unique_counts_conversion import STDOUT_FILENAME
+from newmap.track import STDOUT_FILENAME
 
 # Will throw PackageNotFoundError if package is not installed
 __version__ = version("newmap")
@@ -46,7 +46,7 @@ def parse_subcommands():
     generate_index_parser = subparsers.add_parser(
                             INDEX_SUBCOMMAND,
                             help="Create an FM index from sequences")
-    generate_index_parser.set_defaults(func=generate_index.main)
+    generate_index_parser.set_defaults(func=index.main)
 
     # TODO: Consider changing to -i and -o for input and output
     generate_index_parser.add_argument(
@@ -89,7 +89,7 @@ def parse_subcommands():
                             help="Find the shortest unique sequence length "
                                  "at each position in sequences.")
 
-    unique_length_parser.set_defaults(func=unique_counts.main)
+    unique_length_parser.set_defaults(func=search.main)
 
     unique_length_parser.add_argument(
         "fasta_file",
@@ -184,7 +184,7 @@ def parse_subcommands():
            "unique sequence lengths.")
 
     generate_mappability_parser.set_defaults(
-        func=unique_counts_conversion.main)
+        func=track.main)
 
     generate_mappability_parser.add_argument(
         "read_length",

newmap/main.py

@@ -6,7 +6,7 @@
 from newmap._c_newmap_count_kmers import count_kmers, count_kmers_from_sequence
 from newmap.main import (DEFAULT_COMPRESSION_RATIO,
                          DEFAULT_SEED_LENGTH)
-from newmap.generate_index import generate_fm_index
+from newmap.index import generate_fm_index
 
 
 class TestCountKmers(unittest.TestCase):

newmap/unique_counts.py newmap/search.pynewmap/unique_counts.py renamed to newmap/search.py

@@ -8,8 +8,8 @@
 
 from newmap.main import (DEFAULT_COMPRESSION_RATIO,
                          DEFAULT_SEED_LENGTH)
-from newmap.generate_index import generate_fm_index
-from newmap.unique_counts import write_unique_counts
+from newmap.index import generate_fm_index
+from newmap.search import write_unique_counts
 
 # Expected minimum unique lengths at each position
 # NB: In order to manually count correctly, it is important to remember to
@@ -36,6 +36,7 @@ def setUpClass(cls):
 
     @classmethod
     def tearDownClass(cls):
+        # TODO: Clean up unique files created during the test
         cls.genome_index_file.close()
 
     def test_binary_search(self):

newmap/unique_counts_conversion.py newmap/track.pynewmap/unique_counts_conversion.py renamed to newmap/track.py

@@ -6,9 +6,9 @@
 
 from newmap.main import (DEFAULT_COMPRESSION_RATIO,
                          DEFAULT_SEED_LENGTH)
-from newmap.generate_index import generate_fm_index
-from newmap.unique_counts import write_unique_counts
-from newmap.unique_counts_conversion import write_mappability_files
+from newmap.index import generate_fm_index
+from newmap.search import write_unique_counts
+from newmap.track import write_mappability_files
 
 
 class TestCountKmers(unittest.TestCase):

tests/test_count_kmers.py

@@ -3,7 +3,7 @@
 import numpy as np
 from numpy import testing as npt
 
-from newmap.unique_counts import update_upper_search_bound
+from newmap.search import update_upper_search_bound
 
 
 class TestUpperBoundChange(unittest.TestCase):