Merge pull request #102 from Kudostoy0u/main

Add test for coverage function, fixed return value

.gitignore

@@ -8,3 +8,5 @@ pip-wheel-metadata
 build/*
 tests/tmp/*
 .coverage*
+test.py 
+test2.py

CHANGELOG.md

@@ -6,6 +6,15 @@ The format is based on
 [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [0.7.3] - 2024-08-20
+
+### Changed
+ - Used "not" instead of "~" in an if statement
+ - Added a test for the coverage function
+
+### Fixed
+ - Ensured that the coverage value returns the expected value (previously returned an empty generator)
+
 ## [0.7.2] - 2024-08-17
 
 ### Changed

src/finaletoolkit/frag/coverage.py

@@ -160,6 +160,7 @@ def coverage(
     coverages : Iterable[tuple[str, int, int, str, float]]
         Fragment coverages over intervals.
     """
+    returnVal = []
     if (verbose):
         start_time = time.time()
         sys.stderr.write(
@@ -209,7 +210,6 @@ def coverage(
             ) if verbose else intervals,
             min(len(intervals) // 2 // workers + 1, 40)
         )
-
         if verbose:
             tqdm.write('Retrieving total coverage for file\n')
         total_coverage = total_coverage_results.get()
@@ -244,13 +244,15 @@ def coverage(
                             f'{contig}\t{start}\t{stop}\t'
                             f'{coverage/total_coverage[4]*scale_factor}\n'
                         )
+                        returnVal.append((contig,start,stop,name,coverage/total_coverage[4]*scale_factor))
                 else:
                     for contig, start, stop, name, coverage in coverages:
                         output.write(
                             f'{contig}\t{start}\t{stop}\t'
                             f'{name}\t'
                             f'{coverage/total_coverage[4]*scale_factor}\n'
                         )
+                        returnVal.append((contig,start,stop,name,coverage/total_coverage[4]*scale_factor))
             finally:
                 if output_is_file:
                     output.close()
@@ -262,6 +264,5 @@ def coverage(
         sys.stderr.write(
             f'coverage took {end_time - start_time} s to complete\n'
         )
-
-    return coverages
+    return returnVal
 

src/finaletoolkit/utils/utils.py

@@ -515,7 +515,7 @@ def _get_intervals(
 
     with open(interval_file) as bed:
         for line in bed:
-            if ~line.startswith('#'):
+            if not line.startswith('#'):
                 if line != '':
                     contig, start, stop, *name = line.split()
                     start = int(start)

src/finaletoolkit/version.py

@@ -2,4 +2,4 @@
 Single-source module for the package version number.
 """
 
-__version__ = "0.7.2"
+__version__ = "0.7.3"

tests/data/intervals.bed

@@ -0,0 +1,2 @@
+12	34443118	34443538
+12	34444968	34446115

tests/test_coverage.py

@@ -41,5 +41,21 @@ def test_coverage_interval_midpoints(self, request):
         assert cov == pytest.approx(2)
 
 class TestCoverage:
-    def coverage(self, request):
-        pass
+    def test_coverage(self, request):
+        input_file = request.path.parent / 'data' / '12.3444.b37.frag.gz'
+        intervals = request.path.parent / 'data' / 'intervals.bed'
+        results = coverage(input_file,intervals,"-")
+        for i in range(2):
+            chrom, start, stop, name, cov = results[i]
+            if i == 0:  
+                assert chrom == '12'
+                assert start == 34443118
+                assert stop == 34443538
+                assert name == '.'
+                assert cov == pytest.approx(312500.0)
+            elif i == 1:
+                assert chrom == '12'
+                assert start == 34444968
+                assert stop == 34446115
+                assert name == '.'
+                assert cov == pytest.approx(437500.0)