feat: add basic support for ranges

genotype.enbf

@@ -50,10 +50,10 @@ VARIANT_DEFINITION = @:IDENTIFIER {("," | ";") [sep] @:IDENTIFIER}*;
 
 BINARY_VARIANT = "+" | "-";
 
-RANGE = "[" [type:RANGE_SEQUENCE_TYPE] start:INTEGER "_" end:INTEGER "]"
-      | "[" [type:RANGE_SEQUENCE_TYPE] pos:INTEGER "]";
+RANGE = "[" [level:RANGE_SEQUENCE_LEVEL] start:INTEGER "_" end:INTEGER "]"
+      | "[" [level:RANGE_SEQUENCE_LEVEL] pos:INTEGER "]";
 
-RANGE_SEQUENCE_TYPE = ("c" | "p") ".";
+RANGE_SEQUENCE_LEVEL = @:("c" | "p") ".";
 
 (* NOTE ACCESSION with its optional ":" can be ambiguous when it is used within a fusion and the IDENTIFIER is not numeric.
    In these cases, a DATABASE should be specified. *)

gnomic/grammar.py

@@ -17,7 +17,7 @@
 from grako.util import re, RE_FLAGS
 
 
-__version__ = (2016, 1, 19, 8, 48, 30, 1)
+__version__ = (2016, 3, 31, 14, 28, 44, 3)
 
 __all__ = [
     'GnomicParser',
@@ -373,8 +373,8 @@ def _RANGE_(self):
             with self._option():
                 self._token('[')
                 with self._optional():
-                    self._RANGE_SEQUENCE_TYPE_()
-                    self.ast['type'] = self.last_node
+                    self._RANGE_SEQUENCE_LEVEL_()
+                    self.ast['level'] = self.last_node
                 self._INTEGER_()
                 self.ast['start'] = self.last_node
                 self._token('_')
@@ -384,27 +384,28 @@ def _RANGE_(self):
             with self._option():
                 self._token('[')
                 with self._optional():
-                    self._RANGE_SEQUENCE_TYPE_()
-                    self.ast['type'] = self.last_node
+                    self._RANGE_SEQUENCE_LEVEL_()
+                    self.ast['level'] = self.last_node
                 self._INTEGER_()
                 self.ast['pos'] = self.last_node
                 self._token(']')
             self._error('no available options')
 
         self.ast._define(
-            ['type', 'start', 'end', 'pos'],
+            ['level', 'start', 'end', 'pos'],
             []
         )
 
     @graken()
-    def _RANGE_SEQUENCE_TYPE_(self):
+    def _RANGE_SEQUENCE_LEVEL_(self):
         with self._group():
             with self._choice():
                 with self._option():
                     self._token('c')
                 with self._option():
                     self._token('p')
                 self._error('expecting one of: c p')
+        self.ast['@'] = self.last_node
         self._token('.')
 
     @graken()
@@ -518,7 +519,7 @@ def BINARY_VARIANT(self, ast):
     def RANGE(self, ast):
         return ast
 
-    def RANGE_SEQUENCE_TYPE(self, ast):
+    def RANGE_SEQUENCE_LEVEL(self, ast):
         return ast
 
     def ACCESSION(self, ast):

gnomic/models.py

@@ -249,6 +249,29 @@ def __repr__(self):
                                          for key, value in self.__dict__.items() if value))
 
 
+class Range(object):
+    """
+    An inclusive range at a coding (DNA), RNA or protein level.
+    """
+    def __init__(self, level, start, end):
+        self.level = level
+        self.start = start
+        self.end = end
+
+    def __hash__(self):
+        return hash(self.level) + \
+               hash(self.start) + \
+               hash(self.end)
+
+    def __len__(self):
+        return self.end - self.start + 1
+
+    def __repr__(self):
+        if self.start == self.end:
+            return '{}({}, {})'.format(self.__class__.__name__, repr(self.level), self.start)
+        return '{}({}, {}, {})'.format(self.__class__.__name__, repr(self.level), self.start, self.end)
+
+
 class Organism(object):
     def __init__(self, name, aliases=None):
         self.name = name

gnomic/semantics.py

@@ -1,4 +1,4 @@
-from gnomic.models import Mutation, Fusion, Plasmid, Feature, Organism, Accession, Type, FeatureTree
+from gnomic.models import Mutation, Fusion, Plasmid, Feature, Organism, Accession, Type, FeatureTree, Range
 from gnomic.grammar import GnomicSemantics
 
 
@@ -37,6 +37,20 @@ def replacement(self, ast):
     def deletion(self, ast):
         return Mutation(ast.old, None, marker=ast.marker)
 
+    def RANGE(self, ast):
+        level = {
+            'c': 'coding',
+            'r': 'RNA',
+            'p': 'protein'
+        }[ast.level]
+
+        if ast.pos:
+            return Range(level, ast.pos, ast.pos)
+        return Range(level, ast.start, ast.end)
+
+    def INTEGER(self, ast):
+        return int(ast)
+
     def ACCESSION(self, ast):
         return Accession(ast['id'], ast['db'])
 

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='gnomic',
-    version='0.1.1',
+    version='0.2.0',
     packages=find_packages(exclude=['*tests*']),
     license='Apache',
     author='Lars Schöning',

tests/test_genotype.py

@@ -1,6 +1,6 @@
 from unittest import TestCase, SkipTest
 
-from gnomic import Genotype, Feature, Ins, Del, Fusion, Sub, Type
+from gnomic import Genotype, Feature, Ins, Del, Fusion, Sub, Type, Range
 
 
 class BaseTestCase(TestCase):
@@ -118,6 +118,40 @@ def test_no_delete_if_present(self):
             Del(Feature(name='geneA')),
         }, self.chain('+geneA(x)', '-geneA').changes())
 
+
+class GenotypeRangeTestCase(BaseTestCase):
+
+    def test_delete_range_basic(self):
+        self.assertEqual({
+            Del(Feature(name='geneA', range=Range('coding', 5, 10))),
+        }, self.chain('-geneA[c.5_10]').changes())
+
+        self.assertEqual({
+            Del(Feature(name='geneA', range=Range('protein', 5, 5))),
+        }, self.chain('-geneA[p.5]').changes())
+
+    def test_delete_insert(self):
+        self.assertEqual({
+            Ins(Feature(name='geneA')),
+        }, self.chain('-geneA[c.5_10]', '+geneA').changes())
+
+    @SkipTest
+    def test_delete_multiple_ranges(self):
+        # TODO in the current implementation, only the most recently deleted range is accounted for.
+        # TODO this implementation may change
+
+        self.assertEqual({
+        #    Del(Feature(name='geneA', range=Range('coding', 5, 10))),
+            Del(Feature(name='geneA', range=Range('coding', 11, 12))),
+        }, self.chain('-geneA[c.5_10]', '-geneA[c.11_12]').changes())
+
+        self.assertEqual({
+            Del(Feature(name='geneA'))
+        }, self.chain('-geneA[c.5_10]', '-geneA').changes())
+
+
+    # TODO detailed tracking of different bits & pieces of features.
+
 class GenotypeFusionsTestCase(BaseTestCase):
 
     @SkipTest

tests/test_grammar.py

@@ -25,17 +25,22 @@ def test_parse_simple_insertions(self):
         ], parse('+fooF'))
 
         self.assertEqual([
-            Ins(Feature(name='fooF', accession=Accession(identifier='123', database='FOO')))
+            Ins(Feature(name='fooF', accession=Accession(identifier=123, database='FOO')))
         ], parse('+fooF#FOO:123'))
 
         self.assertEqual([
-            Ins(Feature(accession=Accession(identifier='123', database='FOO')))
+            Ins(Feature(accession=Accession(identifier=123, database='FOO')))
         ], parse('+#FOO:123'))
 
         self.assertEqual([
-            Ins(Feature(accession=Accession(identifier='123')))
+            Ins(Feature(accession=Accession(identifier='BAR', database='FOO')))
+        ], parse('+#FOO:BAR'))
+
+        self.assertEqual([
+            Ins(Feature(accession=Accession(identifier=123)))
         ], parse('+#123'))
 
+
     def test_parse_variants(self):
         self.assertEqual([
             Feature(type=Type('phene'), name='A', variant='wild-type')
@@ -69,7 +74,7 @@ def test_parse_variants(self):
 
         self.assertEqual([
             Feature(type=Type('phene'),
-                    accession=Accession(identifier='123', database='FOO'),
+                    accession=Accession(identifier=123, database='FOO'),
                     variant='wild-type')
         ], parse('#FOO:123+'))