update dev from patches

CHANGELOG.md

@@ -7,6 +7,16 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.1] - 2024-12-19
+
+### Fixed
+- Added missing `-n` arg to `end-motifs`.
+- Fixed incorrect `ValueError` regarding the `negative_strand` arg.
+- Incorrect function name for `wps` leading to errors when called from CLI.
+
+### Added
+- Additional tests for the CLI lazy loading implementation
+
 ## [0.10.0] - 2024-12-18
 
 ### Changed

README.md

@@ -8,6 +8,7 @@
     <ul>
       <li><a href="#functionality">Functionality</a></li>
       <li><a href="#documentation">Documentation</a></li>
+      <li><a href="#wiki">Wiki/Tutorials</a></li>
       <li><a href="#compatible-file-formats">Compatible File Formats</a></li>
       <li><a href="#using-fragment-files">Using Fragment Files</a></li>
     </ul>
@@ -53,12 +54,14 @@ FinaleToolkit has support for the following cell-free DNA fragmentation features
 ### Documentation
 Documentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/finaletoolkit-docs/).
 
+### Wiki/Tutorials
+The wiki and tutorial page for FinaleToolkit can be found [here](https://github.com/epifluidlab/FinaleToolkit/wiki).
+
 ### Compatible File Formats
 
 FinaleToolkit is compatible with almost any paired-end sequence data:
 
 - Binary Alignment Map (`.bam`) files with an associated index file (`.bam.bai`).
-- Sequence Alignment Map (`.sam`) files.
 - Compressed Reference-oriented Alignment Map (`.cram`) files.
 - Fragment (`.frag.gz`) files with an associated tabix index file (`.frag.gz.tbi`).
 
@@ -74,4 +77,4 @@ We encourage you to use our comprehensive database, FinaleDB, to access relevant
 - Yaping Liu: yaping@northwestern.edu
 
 ## License
-This project falls under an MIT license. See the included `LICENSE` file for details.
+This project falls under an MIT license. See the included `LICENSE` file for details.

src/finaletoolkit/cli/main_cli.py

@@ -104,7 +104,7 @@ def main_cli_parser():
         action='store_true',
         help='Enable verbose mode to display detailed processing information.')
     cli_coverage.set_defaults(
-        module='..frag._coverage', func='coverage')
+        module='finaletoolkit.frag._coverage', func='coverage')
 
     # frag-length-bins
     cli_frag_length_bins = subparsers.add_parser(
@@ -186,7 +186,7 @@ def main_cli_parser():
         default=0,
         help='Enable verbose mode to display detailed processing '
         'information.')
-    cli_frag_length_bins.set_defaults(module='..frag._frag_length', func='frag_length_bins')
+    cli_frag_length_bins.set_defaults(module='finaletoolkit.frag._frag_length', func='frag_length_bins')
 
     # frag-length-intervals
     cli_frag_length_intervals = subparsers.add_parser(
@@ -250,7 +250,7 @@ def main_cli_parser():
         action='count',
         help='Enable verbose mode to display detailed processing '
         'information.')
-    cli_frag_length_intervals.set_defaults(module='..frag._frag_length', func='frag_length_intervals')
+    cli_frag_length_intervals.set_defaults(module='finaletoolkit.frag._frag_length', func='frag_length_intervals')
 
     # cleavage-profile
     cli_cleavage_profile = subparsers.add_parser(
@@ -337,7 +337,7 @@ def main_cli_parser():
         default=0,
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_cleavage_profile.set_defaults(module='..frag._cleavage_profile', func='multi_cleavage_profile')
+    cli_cleavage_profile.set_defaults(module='finaletoolkit.frag._cleavage_profile', func='multi_cleavage_profile')
 
     # wps
     cli_wps = subparsers.add_parser(
@@ -426,7 +426,7 @@ def main_cli_parser():
         action='count',
         default=0,
         help='Enable verbose mode to display detailed processing information.')
-    cli_wps.set_defaults(module='..frag', func='_multi_wps')
+    cli_wps.set_defaults(module='finaletoolkit.frag', func='multi_wps')
 
     # adjust wps
     cli_adjust_wps = subparsers.add_parser(
@@ -508,7 +508,7 @@ def main_cli_parser():
         '--verbose',
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_adjust_wps.set_defaults(module='..frag._adjust_wps', func='adjust_wps')
+    cli_adjust_wps.set_defaults(module='finaletoolkit.frag._adjust_wps', func='adjust_wps')
 
     # delfi
     cli_delfi = subparsers.add_parser(
@@ -599,7 +599,7 @@ def main_cli_parser():
         action='count',
         default=0,
         help='Enable verbose mode to display detailed processing information.')
-    cli_delfi.set_defaults(module='..frag._delfi', func='delfi')
+    cli_delfi.set_defaults(module='finaletoolkit.frag._delfi', func='delfi')
 
     # delfi-gc-correct
     cli_delfi_gc = subparsers.add_parser(
@@ -630,7 +630,7 @@ def main_cli_parser():
         '--verbose',
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_delfi_gc.set_defaults(module='..frag._delfi_gc_correct', func='cli_delfi_gc_correct')
+    cli_delfi_gc.set_defaults(module='finaletoolkit.frag._delfi_gc_correct', func='cli_delfi_gc_correct')
 
     # end-motifs
     cli_motifs = subparsers.add_parser(
@@ -670,6 +670,13 @@ def main_cli_parser():
         dest="both_strands",
         help="Set flag to only consider one strand for end-motifs."
     )
+    cli_motifs.add_argument(
+        '-n',
+        '--negative-strand',
+        action="store_true",
+        help="Set flag in conjunction with -B to only consider 5' end motifs "
+        "on the negative strand."
+    )
     cli_motifs.add_argument(
         '-o',
         '--output-file',
@@ -693,7 +700,7 @@ def main_cli_parser():
         default=0,
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_motifs.set_defaults(module='..frag._end_motifs', func='end_motifs')
+    cli_motifs.set_defaults(module='finaletoolkit.frag._end_motifs', func='end_motifs')
 
     # interval-end-motifs
     cli_interval_motifs = subparsers.add_parser(
@@ -782,7 +789,7 @@ def main_cli_parser():
         default=0,
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_interval_motifs.set_defaults(module='..frag._end_motifs', func='interval_end_motifs')
+    cli_interval_motifs.set_defaults(module='finaletoolkit.frag._end_motifs', func='interval_end_motifs')
 
     # mds
     cli_mds = subparsers.add_parser(
@@ -807,7 +814,7 @@ def main_cli_parser():
         default=0,
         type=int,
         help='Number of header rows to ignore. Default is 0')
-    cli_mds.set_defaults(module='..frag._end_motifs', func='_cli_mds')
+    cli_mds.set_defaults(module='finaletoolkit.frag._end_motifs', func='_cli_mds')
 
     # interval-mds
     cli_interval_mds = subparsers.add_parser(
@@ -837,7 +844,7 @@ def main_cli_parser():
         default=0,
         type=int,
         help='Number of header rows to ignore. Default is 0')
-    cli_interval_mds.set_defaults(module='..frag._end_motifs', func='_cli_interval_mds')
+    cli_interval_mds.set_defaults(module='finaletoolkit.frag._end_motifs', func='_cli_interval_mds')
 
     # filter-bam
     cli_filter_bam = subparsers.add_parser(
@@ -904,7 +911,7 @@ def main_cli_parser():
         '--verbose',
         action='count',
         help='Enable verbose mode to display detailed processing information.')
-    cli_filter_bam.set_defaults(module='..utils', func='filter_bam')
+    cli_filter_bam.set_defaults(module='finaletoolkit.utils', func='filter_bam')
 
     # agg-bw
     cli_agg_bw = subparsers.add_parser(
@@ -945,7 +952,7 @@ def main_cli_parser():
         action='count',
         help='Enable verbose mode to display detailed processing '
         'information.')
-    cli_agg_bw.set_defaults(module='..utils._agg_bw', func='agg_bw')
+    cli_agg_bw.set_defaults(module='finaletoolkit.utils._agg_bw', func='agg_bw')
 
     # gap-bed
     cli_gap_bed = subparsers.add_parser(
@@ -965,7 +972,7 @@ def main_cli_parser():
     cli_gap_bed.add_argument(
         'output_file',
         help='Path to write BED file to. If "-" used, writes to stdout.')
-    cli_gap_bed.set_defaults(module='..genome.gaps', func='_cli_gap_bed')
+    cli_gap_bed.set_defaults(module='finaletoolkit.genome.gaps', func='_cli_gap_bed')
 
     return parser
 
@@ -984,7 +991,7 @@ def main_cli():
             func_module = funcargs.pop('module')
             func_name = funcargs.pop('func')
 
-            module = importlib.import_module(func_module, 'finaletoolkit.cli')
+            module = importlib.import_module(func_module)
             function = getattr(module, func_name)
 
             function(**funcargs)

src/finaletoolkit/frag/_end_motifs.py

@@ -571,9 +571,9 @@ def region_end_motifs(
     if verbose:
         start_time = time()
 
-    if not both_strands and negative_strand:
+    if both_strands and negative_strand:
         raise ValueError(
-            'Cannot have both both_strands=False and negative_strand=True.')
+            'Cannot have both both_strands and negative_strand.')
 
     # iterable of fragments
     frag_ends = frag_generator(

src/finaletoolkit/utils/utils.py

@@ -355,6 +355,7 @@ def frag_generator(
                     "input_file is does not follow Fragmentation file format "
                     "accepted by FinaleToolkit. Attempting to read as a BED6 "
                     "file.",
+                    UserWarning
                     )
                 bed_format = True
             else:

src/finaletoolkit/version.py

@@ -2,4 +2,4 @@
 Single-source module for the package version number.
 """
 
-__version__ = "0.9.1"
+__version__ = "0.10.1"

tests/test_cli.py

@@ -3,6 +3,7 @@
 """
 import os
 from inspect import getfullargspec
+import importlib
 
 import pytest
 
@@ -17,6 +18,17 @@ class TestCLIArgs:
     """
     Test if provided commandline flags match args in associated function.
     """
+    @pytest.mark.parametrize("name,subparser", subcommands.items())
+    def test_lazy_import(self, name, subparser):
+        # getting module and func
+        module = subparser._defaults['module']
+        func = subparser._defaults['func']
+
+        # try to see module spec
+        module = importlib.import_module(module)
+        function = getattr(module, func)
+        assert callable(function), f'The {func} is not a callable in {module}.'
+
     @pytest.mark.skip(reason="Currently does not work with the lazy loading implementation")
     @pytest.mark.skipif(
         IN_GITHUB_ACTIONS,

tests/test_frag_io.py

@@ -6,6 +6,7 @@
 """
 
 import numpy as np
+import pytest
 
 from finaletoolkit.utils.utils import frag_generator, frag_array, overlaps
 
@@ -58,10 +59,11 @@ def test_bed_gz(self, request):
         right number of reads
         """
         path = request.path.parent / 'data' / '12.3444.b37.frag.bed.gz'
-        frag_gen = frag_generator(
-            path, "12", quality_threshold=0, min_length=0, max_length=9999
-        )
-        frags = [frag for frag in frag_gen]
+        with pytest.warns(UserWarning):
+            frag_gen = frag_generator(
+                path, "12", quality_threshold=0, min_length=0, max_length=9999
+            )
+            frags = [frag for frag in frag_gen]
 
         chroms = np.array([chrom for chrom, *_ in frags])
         starts = np.array([start for _, start, *_ in frags])