Added mapping class, get read orientation does not work for merged SA…

…M files
zavolanlab · Jun 16, 2023 · d975f8a · d975f8a
1 parent 2a4b122
commit d975f8a
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Showing 4 changed files with 431 additions and 339 deletions.
diff --git a/htsinfer/get_library_type.py b/htsinfer/get_library_type.py
@@ -21,9 +21,7 @@
     SeqIdFormats,
     Config,
 )
-from htsinfer.get_read_orientation import (
-    GetOrientation,
-)
+from htsinfer.mapping import Mapping
 
 LOGGER = logging.getLogger(__name__)
 
@@ -62,15 +60,15 @@ class GetLibType:
     def __init__(
         self,
         config: Config,
+        mapping: Mapping,
     ):
         """Class constructor."""
         self.path_1: Path = config.args.path_1_processed
         self.path_2: Optional[Path] = config.args.path_2_processed
         self.library_source = config.results.library_source
         self.results: ResultsType = ResultsType()
         self.tmp_dir = config.args.tmp_dir
-        self.get_read_orientation: \
-            GetOrientation = GetOrientation(config=config)
+        self.mapping = mapping
         self.max_distance = config.args.lib_type_max_distance
         self.cutoff = config.args.lib_type_mates_cutoff
 
@@ -127,19 +125,17 @@ def _evaluate_mate_relationship(
                     StatesTypeRelationship.split_mates
                 )
         else:
-            self.get_read_orientation.library_type.relationship \
+            self.mapping.library_type.relationship \
                 = StatesTypeRelationship.not_available
-            self.get_read_orientation.library_source = self.library_source
-            _ = self.get_read_orientation.evaluate()
+            self.mapping.library_source = self.library_source
+            _ = self.mapping.evaluate()
             self._align_mates()
 
     def _align_mates(self):
         """Decide mate relationship by alignment."""
 
-        alignment_1 = Path(self.tmp_dir) \
-            / "alignments" / "file_1" / "Aligned.out.sam"
-        alignment_2 = Path(self.tmp_dir) \
-            / "alignments" / "file_2" / "Aligned.out.sam"
+        alignment_1 = self.mapping.star_dirs[0] / 'Aligned.out.sam'
+        alignment_2 = self.mapping.star_dirs[1] / 'Aligned.out.sam'
 
         samfile1 = pysam.AlignmentFile(alignment_1, 'r')
         samfile2 = pysam.AlignmentFile(alignment_2, 'r')