Merge pull request #81 from epifluidlab/coverage-fix

Update utils.py

CHANGELOG.md

@@ -5,7 +5,17 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [0.6.2] - 2024-05-30
+
+### Fixed
+- adjusted handling of contig, start, stop for `frag_generator` so that
+`coverage` does not throw exceptions for genomewide intervals.
+
+### Added
+- test for `single_coverage`
+
 ## [0.6.1] - 2024-05-26
+
 ### Changed
 - add `__version` attribute
 - `finaletoolkit --version` displays package version

src/finaletoolkit/__init__.py

@@ -3,4 +3,4 @@
 cell-free DNA from paired-end sequencing data.
 """
 
-__version__ = "0.6.1"
+__version__ = "0.6.2"

src/finaletoolkit/utils/utils.py

@@ -291,8 +291,10 @@ def frag_generator(
 
         # Raise exception if start and stop specified but not contig
         if contig is None and not (start is None and stop is None):
-            raise ValueError("contig should be specified if start or "
-                             "stop given.")
+            if contig is None and start==0 and stop is None:
+                pass
+            else:
+                raise ValueError("contig should be specified if start or stop given.")
 
         if is_sam:
             for read in sam_file.fetch(contig, start, stop):

tests/test_cli_entry.py

@@ -10,63 +10,63 @@ class TestCLIEntryPoint:
     Test all CLI subcommands related to end_motifs and MDS, genomewide
     and intervals.
     """
-    def test_coverage(self, request):
+    def test_coverage(self):
         exit_status = os.system('finaletoolkit coverage --help')
         assert exit_status == 0
 
-    def test_frag_length_bins(self, request):
+    def test_frag_length_bins(self):
         exit_status = os.system('finaletoolkit frag-length-bins --help')
         assert exit_status == 0
 
-    def test_frag_length_intervals(self, request):
+    def test_frag_length_intervals(self):
         exit_status = os.system('finaletoolkit frag-length-intervals --help')
         assert exit_status == 0
 
-    def test_cleavage_profile(self, request):
+    def test_cleavage_profile(self):
         exit_status = os.system('finaletoolkit cleavage-profile --help')
         assert exit_status == 0
 
-    def test_wps(self, request):
+    def test_wps(self):
         exit_status = os.system('finaletoolkit wps --help')
         assert exit_status == 0
 
-    def test_agg_wps(self, request):
+    def test_agg_wps(self):
         exit_status = os.system('finaletoolkit adjust-wps --help')
         assert exit_status == 0
 
-    def test_delfi(self, request):
+    def test_delfi(self):
         exit_status = os.system('finaletoolkit delfi --help')
         assert exit_status == 0
 
-    def test_delfi_gc_correct(self, request):
+    def test_delfi_gc_correct(self):
         exit_status = os.system('finaletoolkit delfi-gc-correct --help')
         assert exit_status == 0
 
-    def test_end_motif(self, request):
+    def test_end_motif(self):
         exit_status = os.system('finaletoolkit end-motifs --help')
         assert exit_status == 0
 
-    def test_mds(self, request):
+    def test_mds(self):
         exit_status = os.system('finaletoolkit mds --help')
         assert exit_status == 0
 
-    def test_interval_end_motif(self, request):
+    def test_interval_end_motif(self):
         exit_status = os.system('finaletoolkit interval-end-motifs --help')
         assert exit_status == 0
 
-    def test_interval_mds(self, request):
+    def test_interval_mds(self):
         exit_status = os.system('finaletoolkit interval-mds --help')
         assert exit_status == 0
 
-    def test_filter_bam(self, request):
+    def test_filter_bam(self):
         exit_status = os.system('finaletoolkit filter-bam --help')
         assert exit_status == 0
 
-    def test_agg_bw(self, request):
+    def test_agg_bw(self):
         exit_status = os.system('finaletoolkit agg-bw --help')
         assert exit_status == 0
 
-    def test_gap_bed(self, request):
+    def test_gap_bed(self):
         exit_status = os.system('finaletoolkit gap-bed --help')
         assert exit_status == 0
 

tests/test_coverage.py

@@ -0,0 +1,45 @@
+"""
+Tests for finaletoolkit.frag.coverage module and associated
+subcommands, which calculate fragment coverage.
+"""
+
+import os
+import filecmp
+import difflib
+
+import pytest
+
+from finaletoolkit.frag.coverage import *
+
+class TestSingleCoverage:
+    def test_coverage(self, request):
+        bam = request.path.parent / 'data' / '12.3444.b37.bam'
+        chrom, start, stop, name, cov = single_coverage(bam, '12', 0, None, quality_threshold=0)
+
+        assert chrom == '12'
+        assert start == 0
+        assert cov == pytest.approx(17)
+
+    def test_coverage_interval(self, request):
+        bam = request.path.parent / 'data' / '12.3444.b37.bam'
+        chrom, start, stop, name, cov = single_coverage(
+            bam, '12', 34443000, 34447000, quality_threshold=0)
+
+        assert chrom == '12'
+        assert start == 34443000
+        assert stop == 34447000
+        assert cov == pytest.approx(17)
+
+    def test_coverage_interval_midpoints(self, request):
+        bam = request.path.parent / 'data' / '12.3444.b37.bam'
+        chrom, start, stop, name, cov = single_coverage(
+            bam, '12', 34443400, 34443600, quality_threshold=0)
+
+        assert chrom == '12'
+        assert start == 34443400
+        assert stop == 34443600
+        assert cov == pytest.approx(2)
+
+class TestCoverage:
+    def coverage(self, request):
+        pass