From 302ba055e79103b1bc4b740d8d79330c1f88f704 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 10 Oct 2011 10:27:42 +0000
Subject: [PATCH] Accept IVS locations in Variant_info LOVD interface
The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.
Fixes #63
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@387 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/Crossmap.py | 3 +--
mutalyzer/mapping.py | 32 ++++++++++++++++++++++----------
tests/test_website.py | 9 +++++++++
3 files changed, 32 insertions(+), 12 deletions(-)
diff --git a/mutalyzer/Crossmap.py b/mutalyzer/Crossmap.py
index cd289e3e..20fb8edc 100644
--- a/mutalyzer/Crossmap.py
+++ b/mutalyzer/Crossmap.py
@@ -428,8 +428,7 @@ class Crossmap() :
@return: The converted notation (may be unaltered)
@rtype: integer
"""
-
- if s[0] == '*' :
+ if s[0] == '*':
return self.__STOP + int(s[1:])
return int(s)
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 0cb27e7e..afc5b837 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -254,15 +254,27 @@ class Converter(object) :
@rtype: triple (integer, integer, integer)
"""
if Type == 'c' :
- main = C.main2int(Loc.MainSgn + Loc.Main)
- offset = C.offset2int(Loc.OffSgn + Loc.Offset)
- g = C.x2g(main, offset)
- main, offset = C.g2x(g)
- #if
- else :
- g = int(Loc.Main)
+ if Loc.IVSLoc:
+ ivs_number = int(Loc.IVSLoc.IVSNumber)
+ if ivs_number < 1 or ivs_number > C.numberOfIntrons():
+ # Todo: Error handling in this entire module is 'suboptimal'
+ raise Exception('Invalid intron')
+ if Loc.IVSLoc.OffSgn == '+':
+ g = C.getSpliceSite(ivs_number * 2 - 1) + \
+ C.orientation * int(Loc.IVSLoc.Offset)
+ else:
+ g = C.getSpliceSite(ivs_number * 2) - \
+ C.orientation * int(Loc.IVSLoc.Offset)
+ main, offset = C.g2x(g)
+ else:
+ main = C.main2int(Loc.PtLoc.MainSgn + Loc.PtLoc.Main)
+ offset = C.offset2int(Loc.PtLoc.OffSgn + Loc.PtLoc.Offset)
+ g = C.x2g(main, offset)
+ main, offset = C.g2x(g)
+ else:
+ g = int(Loc.PtLoc.Main)
main, offset = C.g2x(g)
- #else
+
return (main, offset, g)
#_getcoords
@@ -285,13 +297,13 @@ class Converter(object) :
# Get the coordinates of the start position
startmain, startoffset, start_g = \
- self._getcoords(Cross, mutation.StartLoc.PtLoc,
+ self._getcoords(Cross, mutation.StartLoc,
self.parseTree.RefType)
# If there is an end position, calculate the coordinates.
if mutation.EndLoc :
endmain, endoffset, end_g = \
- self._getcoords(Cross, mutation.EndLoc.PtLoc,
+ self._getcoords(Cross, mutation.EndLoc,
self.parseTree.RefType)
else :
end_g, endmain, endoffset = start_g, startmain, startoffset
diff --git a/tests/test_website.py b/tests/test_website.py
index 61a7206b..29ba034f 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -589,6 +589,15 @@ facilisi."""
expected = '\n'.join(['-612', '7720', '2016'])
assert_equal(r.body, expected)
+ def test_variantinfo_ivs(self):
+ """
+ Test the /Variant_info interface used by LOVD2 (with IVS positioning).
+ """
+ r = self.app.get('/Variant_info?LOVD_ver=2.0-33&build=hg19&acc=NM_000249.3&var=c.IVS10%2B3A%3EG')
+ assert_equal(r.content_type, 'text/plain')
+ expected = '\n'.join(['884', '3', '884', '3', '37059093', '37059093', 'subst'])
+ assert_equal(r.body, expected)
+
def test_upload_local_file(self):
"""
Test the genbank uploader.
--
GitLab