feat: improve lib type inference for SRA PE samples (#161)

* feat: add asumed mates

* update get lib type tests

* lower lib_type_mate_cutoff

htsinfer/cli.py

@@ -232,7 +232,7 @@ def __call__(
         dest="lib_type_mates_cutoff",
         metavar="FLOAT",
         type=float,
-        default=0.95,
+        default=0.85,
         help=(
             "minimum fraction of mates that can be mapped to compatible loci "
             "and are considered concordant pairs / all mates"

htsinfer/get_library_type.py

@@ -127,6 +127,21 @@ def _evaluate_mate_relationship(
                 self.mapping.library_type.relationship = (
                     StatesTypeRelationship.split_mates
                 )
+            # Infer mate relationship, even when assumed to be single
+            elif (
+                self.results.file_1 == StatesType.single and
+                self.results.file_2 == StatesType.single
+            ) and (
+                self.library_source.file_1.short_name is not None or
+                self.library_source.file_2.short_name is not None
+            ):
+                LOGGER.debug("Determining mate relationship by alignment...")
+                self.mapping.library_type.relationship \
+                    = StatesTypeRelationship.not_available
+                self.mapping.library_source = self.library_source
+                self.mapping.paths = self.path_1, self.path_2
+                self.mapping.evaluate()
+                self._align_mates()
         elif (
             self.library_source.file_1.short_name is not None or
             self.library_source.file_2.short_name is not None
@@ -209,15 +224,15 @@ def _align_mates(self):
         LOGGER.debug(f"Number of aligned reads file 2: {aligned_mate2}")
         LOGGER.debug(f"Number of concordant reads: {concordant}")
 
-        self._update_relationship(
+        self._update_relationship_type(
             concordant, min(aligned_mate1, aligned_mate2)
         )
 
         samfile1.close()
         samfile2.close()
 
-    def _update_relationship(self, concordant, aligned_reads):
-        """Helper function to update relationship based on alignment."""
+    def _update_relationship_type(self, concordant, aligned_reads):
+        """Helper function to update relationship and type."""
         try:
             ratio = concordant / aligned_reads
         except ZeroDivisionError:
@@ -238,6 +253,18 @@ def _update_relationship(self, concordant, aligned_reads):
                 self.results.relationship = (
                     StatesTypeRelationship.not_mates
                 )
+        if self.results.relationship == (
+            StatesTypeRelationship.split_mates
+        ) and (
+            self.results.file_1 == StatesType.single and
+            self.results.file_2 == StatesType.single
+        ) or (
+            self.results.file_1 == StatesType.not_available and
+            self.results.file_2 == StatesType.not_available
+        ):
+            # Update first and second relationship
+            self.results.file_1 = StatesType.first_mate_assumed
+            self.results.file_2 = StatesType.second_mate_assumed
 
     class AlignedSegment:
         """Placeholder class for mypy "Missing attribute"

htsinfer/models.py

@@ -155,9 +155,11 @@ class StatesType(Enum):
             that the library represents a single-end library.
     """
     first_mate = "first_mate"
+    first_mate_assumed = "first_mate_assumed"
     mixed_mates = "mixed_mates"
     not_available = None
     second_mate = "second_mate"
+    second_mate_assumed = "second_mate_assumed"
     single = "single"
 
 
@@ -438,7 +440,7 @@ class Args(BaseModel):
     lib_source_min_match_pct: float = 2
     lib_source_min_freq_ratio: float = 2
     lib_type_max_distance: int = 1000
-    lib_type_mates_cutoff: float = 0.95
+    lib_type_mates_cutoff: float = 0.85
     read_orientation_min_mapped_reads: int = 20
     read_orientation_min_fraction: float = 0.75
     path_1_processed: Path = Path()

tests/test_get_library_type.py

@@ -113,6 +113,34 @@ def test_evaluate_mate_relationship_split_mates(self):
             StatesTypeRelationship.split_mates
         )
 
+    def test_evaluate_mate_relationship_assumed_single(self, tmpdir):
+        """Test mate relationship evaluation logic with input files being
+        mates of a paired-end library but assumed single based on seq_ids.
+        """
+        CONFIG.args.path_1_processed = FILE_MATE_1
+        CONFIG.args.path_2_processed = FILE_MATE_2
+        CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
+        CONFIG.args.tmp_dir = tmpdir
+        CONFIG.results.library_source = ResultsSource(
+            file_1=Source(short_name="hsapiens", taxon_id=9606),
+            file_2=Source(short_name="hsapiens", taxon_id=9606),
+        )
+        MAPPING.paths = (FILE_MATE_1, FILE_MATE_2)
+        MAPPING.transcripts_file = FILE_TRANSCRIPTS
+        MAPPING.tmp_dir = tmpdir
+        test_instance = GetLibType(config=CONFIG,
+                                   mapping=MAPPING)
+        test_instance.results.file_1 = StatesType.single
+        test_instance.results.file_2 = StatesType.single
+        test_instance._evaluate_mate_relationship(
+            ids_1=["A", "B", "C"],
+            ids_2=["A", "B", "C"],
+        )
+        assert (
+            test_instance.results.relationship ==
+            StatesTypeRelationship.not_available
+        )
+
     def test_evaluate_mate_relationship_not_mates(self, tmpdir):
         """Test mate relationship evaluation logic with input files that are
         mates, but the relationship is not enough to trigger split_mates.
@@ -167,7 +195,7 @@ def test_evaluate_mate_relationship_not_available(self, tmpdir):
             StatesTypeRelationship.not_available
         )
 
-    def test_update_relationship_not_mates(self, tmpdir):
+    def test_update_relationship_type_not_mates(self, tmpdir):
         """Test update_relationship logic."""
         CONFIG.args.path_1_processed = FILE_IDS_NOT_MATCH_1
         CONFIG.args.path_2_processed = FILE_MATE_2
@@ -185,8 +213,8 @@ def test_update_relationship_not_mates(self, tmpdir):
         concordant = 0
         read_counter = 20
 
-        # Call the _update_relationship method
-        test_instance._update_relationship(concordant, read_counter)
+        # Call the _update_relationship_type method
+        test_instance._update_relationship_type(concordant, read_counter)
 
         assert (
             test_instance.results.relationship ==