Parser().parse_any_variant does not parse any variant

[reece]

Originally reported by: andrew_mcmurry (Bitbucket: andrew_mcmurry, GitHub: hyperfl0w)

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Expected: parse_any_variant returns any variant type defined in the Grammar.
Actual: parse_any_variant is inherited method of the Parser construction and doesn't actually traverse the grammar.

Suspected Cause: parse_any_variant was accidentally included by inheritance.

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• Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/167

[reece]

Original comment by andrew_mcmurry (Bitbucket: andrew_mcmurry, GitHub: hyperfl0w):

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updated grammar to support parse_any_edit and parse_any_position

can I please have commit access?
diff is below

[reece]

Original comment by andrew_mcmurry (Bitbucket: andrew_mcmurry, GitHub: hyperfl0w):

---

#!bash

diff -r a988c99ef912 hgvs/data/hgvs.pymeta
--- a/hgvs/data/hgvs.pymeta	Thu Apr 17 14:50:00 2014 -0700
+++ b/hgvs/data/hgvs.pymeta	Wed Apr 23 22:52:22 2014 -0700
@@ -79,11 +79,13 @@
 g_edit   = gmn_edit
 m_edit   = gmn_edit
 n_edit   = gmn_edit
-gmn_edit = gmn_type:type '.' gmn_posedit:posedit -> hgvs.variant.SequenceVariant(None,type,posedit)
+gmn_edit = gmn_type:type '.' gmn_posedit:posedit -> hgvs.variant.PosEdit(None,type,posedit)
 c_edit   = 'c':type '.'   c_posedit:posedit -> hgvs.variant.SequenceVariant(None,type,posedit)
 p_edit   = 'p':type '.'   p_posedit:posedit -> hgvs.variant.SequenceVariant(None,type,posedit)
 r_edit   = 'r':type '.'   r_posedit:posedit -> hgvs.variant.SequenceVariant(None,type,posedit)
 
+any_edit = gmn_edit | c_edit | r_edit | p_edit
+
 
 ############################################################################
 ## HGVS Position -- e.g., NM_01234.5:c.22+6 (without an edit)
@@ -97,11 +99,12 @@
 p_hgvs_position   = accn:ac ':' 'p':type      '.'   p_interval:pos -> hgvs.hgvsposition.HGVSPosition(ac, type, pos)
 r_hgvs_position   = accn:ac ':' 'r':type      '.'   r_interval:pos -> hgvs.hgvsposition.HGVSPosition(ac, type, pos)
 
+any_position = gmn_hgvs_position | c_hgvs_position | p_hgvs_position | r_hgvs_position
 
 ############################################################################
 ## PosEdits -- position + edit objects
 
-# any_posedit = g_posedit | m_posedit | n_posedit | c_posedit | r_posedit | p_posedit 
+any_posedit = g_posedit | m_posedit | n_posedit | c_posedit | r_posedit | p_posedit 
 
 g_posedit   = gmn_posedit
 m_posedit   = gmn_posedit
diff -r a988c99ef912 tests/test_hgvs_parser.py
--- a/tests/test_hgvs_parser.py	Thu Apr 17 14:50:00 2014 -0700
+++ b/tests/test_hgvs_parser.py	Wed Apr 23 22:52:22 2014 -0700
@@ -50,6 +50,56 @@
         #self.assertEqual( str(self.parser.parse_p_posedit('=?')), '(=)' )
         self.assertEqual( str(self.parser.parse_p_posedit('(=)')), '(=)' )
 
+
+    def test_Parse_any_edit(self):
+        """
+        any_edit = gmn_edit | c_edit | r_edit | p_edit
+        Test conditions include edit annotations from PubTator and
+         (c|r|p) edits of a BRCA2 variant stripped of its accession (NM_000059.3)
+        """
+        c_edit = 'c.424G>C'
+        r_edit = 'r.518G>C'
+        p_edit = 'p.L152P'
+        pubtator_edits = [c_edit, r_edit, p_edit]
+
+        c_edit = 'c.9218A>G'
+        r_edit = 'r.9445A>G'
+        p_edit = 'p.(Asp3073Gly)'
+        p_edit2= 'p.Asp3073Gly'
+        brca2_edits = [c_edit, r_edit, p_edit, p_edit]
+
+        unknown_edit = 'C152G'
+
+        for any_edit in pubtator_edits+brca2_edits:
+            variant = self.parser.parse_any_edit(any_edit)
+            self.assertIsNotNone(variant)
+
+        # Special case, we dont want this unknown text to be parsed!
+        can_parse = True
+        try:
+             self.parser.parse_any_edit(unknown_edit)
+        except:
+            can_parse = False
+        finally:
+            self.assertFalse(can_parse)
+
+    def test_Parse_any_position(self):
+        """
+        any_position = gmn_hgvs_position | c_hgvs_position | p_hgvs_position | r_hgvs_position
+        BRCA2 variant was first mapped into (c|p|r) space and then manually truncated of the edit,
+        containing only the position.
+        """
+        c_hgvs_position = 'NM_000059.3:c.9218'
+        p_hgvs_position = 'NM_000059.3:r.9445'
+        r_hgvs_position = 'NP_000050.2:p.(Asp3073)'
+
+        for any_position in [c_hgvs_position, p_hgvs_position, r_hgvs_position]:
+            variant = self.parser.parse_any_position(any_position)
+            self.assertIsNotNone(variant)
+
+
+
+
 if __name__ == '__main__':
     unittest.main()
 

[reece]

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):

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As discussed in person, the intent of the any_variant rule was solely to parse strings of the form :.<arbitrary_text> . However, the SV returned from this is not very useful, or is at least confusing.

I have commented out that rule from hgvs.pymeta until there is a well-defined need.

commit edbf482e0774