Speedup NCBI mapview file import

Instead of querying the existing mappings for overlap and either
updating or inserting depending on the result, we now delete
overlapping mappings first and then only insert.

This is roughly twice as fast. But of course still a horrible
setup compared to some kind of UPSERT functionality which is
unfortunately missing in current PostgreSQL.

mutalyzer/db/models.py

@@ -422,37 +422,30 @@ class TranscriptMapping(db.Base):
                          source, transcript=1, cds=None,
                          select_transcript=False, version=None):
         """
-        Returns an existing :class:`TranscriptMapping` instance with the given
-        values for `chromosome`, `accession`, `version`, `gene`, and
-        `transcript` if it exists, or a new instance otherwise.
+        Returns an :class:`TranscriptMapping` instance with the given values.
+        If a row with a duplicate key already exists, it is deleted first.
 
         .. note:: Unfortunately, SQLAlchemy does not have `ON DUPLICATE KEY
             UPDATE` functionality, which would performance-wise be the best
-            way to update transcript mappings. This class method implements an
-            alternative albeit at the cost of querying the table for an
-            existing entry on each update.
+            way to update transcript mappings. Even if it had, PostgreSQL does
+            not. This class method implements an alternative albeit at the
+            cost of querying the table for an existing entry on each update.
+
+            From PostgreSQL 9.5 we do have ``INSERT ... ON CONFLICT DO UPDATE``
+            which we might want to use in the future.
+
+            http://stackoverflow.com/questions/17267417/how-do-i-do-an-upsert-merge-insert-on-duplicate-update-in-postgresql
         """
-        instance = cls.query.filter_by(
+        # Actually we should do a `lock transcript_mappings in exclusive mode;`
+        # to prevent concurrent reads to miss this entry.
+        cls.query.filter_by(
             chromosome=chromosome, accession=accession, version=version,
-            gene=gene, transcript=transcript).first()
-        if instance is None:
-            instance = cls(chromosome, reference_type, accession, gene,
-                           orientation, start, stop, exon_starts, exon_stops,
-                           source, transcript=transcript, cds=cds,
-                           select_transcript=select_transcript,
-                           version=version)
-        else:
-            instance.reference_type = reference_type
-            instance.orientation = orientation
-            instance.start = start
-            instance.stop = stop
-            instance.bin = binning.assign_bin(start - 1, stop)
-            instance.exon_starts = exon_starts
-            instance.exon_stops = exon_stops
-            instance.source = source
-            instance.cds = cds
-            instance.select_transcript = select_transcript
-        return instance
+            gene=gene, transcript=transcript
+        ).delete()
+        return cls(chromosome, reference_type, accession, gene, orientation,
+                   start, stop, exon_starts, exon_stops, source,
+                   transcript=transcript, cds=cds,
+                   select_transcript=select_transcript, version=version)
 
     @property
     def coding(self):