Actually include block in includeInStrand

askomics · Aug 11, 2023 · 855f286 · 855f286
1 parent 4937323
commit 855f286
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Showing 4 changed files with 15 additions and 6 deletions.
diff --git a/askomics/libaskomics/BedFile.py b/askomics/libaskomics/BedFile.py
@@ -329,9 +329,11 @@ def generate_rdf_content(self):
                 block_reference = self.rdfize(self.format_uri("{}_{}".format(feature.chrom, slice_block)))
                 self.graph_chunk.add((entity, self.namespace_internal["includeInReference"], block_reference))
                 if faldo_strand:
-                    self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], faldo_strand))
                     strand_ref = self.get_reference_strand_uri(feature.chrom, faldo_strand, slice_block)
                     for sref in strand_ref:
                         self.graph_chunk.add((entity, self.namespace_internal["includeInReferenceStrand"], sref))
+                    strand_ref = self.get_reference_strand_uri(None, faldo_strand, slice_block)
+                    for sref in strand_ref:
+                        self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], sref))
 
             yield
diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
@@ -737,9 +737,8 @@ def generate_rdf_content(self):
                                 for sref in strand_ref:
                                     self.graph_chunk.add((entity, self.namespace_internal["includeInReferenceStrand"], sref))
                         if faldo_strand:
-                            self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], faldo_strand))
-                            if faldo_strand == self.faldo.BothStrandPosition:
-                                self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], self.faldo.ForwardStrandPosition))
-                                self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], self.faldo.ReverseStrandPosition))
+                            strand_ref = self.get_reference_strand_uri(None, faldo_strand, slice_block)
+                            for sref in strand_ref:
+                                self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], sref))
 
                 yield
diff --git a/askomics/libaskomics/File.py b/askomics/libaskomics/File.py
@@ -464,6 +464,12 @@ def get_reference_strand_uri(self, reference, strand, block=None):
             self.faldo.ReverseStrandPosition: "ReverseStrand",
             self.faldo.BothStrandPosition: "BothStrand"
         }
+        if reference is None:
+            if strand == self.faldo.BothStrandPosition:
+                return [self.rdfize(self.format_uri("s{}_{}".format(dstrand, block))) for dstrand in faldo_dict.values()]
+
+            return [self.rdfize(self.format_uri("s{}_{}".format(faldo_dict[strand], block)))]
+
         if block is None:
             if strand == self.faldo.BothStrandPosition:
                 return [self.rdfize(self.format_uri("{}_s{}s".format(reference, dstrand))) for dstrand in faldo_dict.values()]

diff --git a/askomics/libaskomics/GffFile.py b/askomics/libaskomics/GffFile.py
@@ -434,10 +434,12 @@ def generate_rdf_content(self):
                     block_reference = self.rdfize(self.format_uri("{}_{}".format(rec.id, slice_block)))
                     self.graph_chunk.add((entity, self.namespace_internal["includeInReference"], block_reference))
                     if faldo_strand:
-                        self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], faldo_strand))
                         strand_ref = self.get_reference_strand_uri(rec.id, faldo_strand, slice_block)
                         for sref in strand_ref:
                             self.graph_chunk.add((entity, self.namespace_internal["includeInReferenceStrand"], sref))
+                        strand_ref = self.get_reference_strand_uri(None, faldo_strand, slice_block)
+                        for sref in strand_ref:
+                            self.graph_chunk.add((entity, self.namespace_internal["includeInStrand"], sref))
 
                 yield