diff --git a/tests/test_crossmap.py b/tests/test_crossmap.py
index ce3d81d428c8bdce9375d128d4f81b22b8ea1a44..230a70835978596ab431a733349cd87ce68323fc 100644
--- a/tests/test_crossmap.py
+++ b/tests/test_crossmap.py
@@ -48,7 +48,9 @@ class TestCrossmap():
103528, 119465, 119537, 144687, 144810, 148418, 149215]
cds = [27925, 74736]
cm = Crossmap(rna, cds, 1)
- assert_equal(cm.tuple2string(cm.g2x(5001)), '-304-u1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(5001)), '-304-u1')
+ assert_equal(cm.tuple2string(cm.g2x(5001)), '-305')
assert_equal(cm.tuple2string(cm.g2x(5124)), '-182')
assert_equal(cm.tuple2string(cm.g2x(5126)), '-181+1')
assert_equal(cm.tuple2string(cm.g2x(27924)), '-1')
@@ -58,7 +60,9 @@ class TestCrossmap():
assert_equal(cm.tuple2string(cm.g2x(74737)), '*1')
assert_equal(cm.tuple2string(cm.g2x(103408)), '*32-1')
assert_equal(cm.tuple2string(cm.g2x(103410)), '*33')
- assert_equal(cm.tuple2string(cm.g2x(149216)), '*1146+d1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(149216)), '*1146+d1')
+ assert_equal(cm.tuple2string(cm.g2x(149216)), '*1147')
def test_g2x_reverse(self):
"""
@@ -69,7 +73,9 @@ class TestCrossmap():
76535, 92453, 92554, 123276, 123470, 146090, 146213]
cds = [76479, 123290]
cm = Crossmap(rna, cds, -1)
- assert_equal(cm.tuple2string(cm.g2x(146214)), '-304-u1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(146214)), '-304-u1')
+ assert_equal(cm.tuple2string(cm.g2x(146214)), '-305')
assert_equal(cm.tuple2string(cm.g2x(146091)), '-182')
assert_equal(cm.tuple2string(cm.g2x(146089)), '-181+1')
assert_equal(cm.tuple2string(cm.g2x(123291)), '-1')
@@ -79,7 +85,9 @@ class TestCrossmap():
assert_equal(cm.tuple2string(cm.g2x(76478)), '*1')
assert_equal(cm.tuple2string(cm.g2x(47807)), '*32-1')
assert_equal(cm.tuple2string(cm.g2x(47805)), '*33')
- assert_equal(cm.tuple2string(cm.g2x(1999)), '*1146+d1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(1999)), '*1146+d1')
+ assert_equal(cm.tuple2string(cm.g2x(1999)), '*1147')
def test_x2g_more(self):
"""
@@ -184,10 +192,14 @@ class TestCrossmap():
rna = [5002, 5125, 27745, 27939, 58661, 58762, 74680, 74767, 103409,
103528, 119465, 119537, 144687, 144810, 148418, 149215]
cm = Crossmap(rna, [], 1)
- assert_equal(cm.tuple2string(cm.g2x(5001)), '1-u1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(5001)), '1-u1')
+ assert_equal(cm.tuple2string(cm.g2x(5001)), '-1')
assert_equal(cm.tuple2string(cm.g2x(5002)), '1')
assert_equal(cm.tuple2string(cm.g2x(5126)), '124+1')
- assert_equal(cm.tuple2string(cm.g2x(149216)), '1624+d1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(149216)), '1624+d1')
+ assert_equal(cm.tuple2string(cm.g2x(149216)), '*1')
def test_g2x_noncoding_reverse(self):
"""
@@ -197,10 +209,14 @@ class TestCrossmap():
rna = [2000, 2797, 6405, 6528, 31678, 31750, 47687, 47806, 76448,
76535, 92453, 92554, 123276, 123470, 146090, 146213]
cm = Crossmap(rna, [], -1)
- assert_equal(cm.tuple2string(cm.g2x(146214)), '1-u1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(146214)), '1-u1')
+ assert_equal(cm.tuple2string(cm.g2x(146214)), '-1')
assert_equal(cm.tuple2string(cm.g2x(146213)), '1')
assert_equal(cm.tuple2string(cm.g2x(146089)), '124+1')
- assert_equal(cm.tuple2string(cm.g2x(1999)), '1624+d1')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(1999)), '1624+d1')
+ assert_equal(cm.tuple2string(cm.g2x(1999)), '*1')
def test_x2g_noncoding(self):
"""
@@ -253,8 +269,11 @@ class TestCrossmap():
[-156, -1, 1, 196, 197, 299, 300, 388, 389, 509, 510,
583, 584, 708, 709, 1507])
assert_equal(cm.x2g(1, 0), 23777833)
- assert_equal(cm.tuple2string(cm.g2x(2123)), '-156-u23752936')
- assert_equal(cm.tuple2string(cm.g2x(2124)), '-156-u23752935')
+ # Fix for r536: disable the -u and +d convention.
+ #assert_equal(cm.tuple2string(cm.g2x(2123)), '-156-u23752936')
+ #assert_equal(cm.tuple2string(cm.g2x(2124)), '-156-u23752935')
+ assert_equal(cm.tuple2string(cm.g2x(2123)), '-23753092')
+ assert_equal(cm.tuple2string(cm.g2x(2124)), '-23753091')
def test_cds_start_on_splice_site_reverse(self):
"""
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index ec834f85ad3e0db02a2f329addd9b0354ca5e847..3dbdfbf36da016f766353d509d6042dcf9aaeec8 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -58,8 +58,11 @@ class TestConverter():
"""
converter = self._converter('hg19')
coding = converter.chrom2c('NC_000022.10:g.51016285_51017117del123456789', 'list')
- assert 'NM_001145134.1:c.-138-u21_60del123456789' in coding
- assert 'NR_021492.1:c.1-u5170_1-u4338del123456789' in coding
+ # Fix for r536: disable the -u and +d convention.
+ #assert 'NM_001145134.1:c.-138-u21_60del123456789' in coding
+ #assert 'NR_021492.1:c.1-u5170_1-u4338del123456789' in coding
+ assert 'NM_001145134.1:c.-159_60del123456789' in coding
+ assert 'NR_021492.1:c.-5170_-4338del123456789' in coding
def test_S_Venkata_Suresh_Kumar(self):
"""
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index 3b502b7d5e1f42a367c42a1251f95ac032f7ed6a..0a9096c551958496a90b89d6aece597aab5cc20f 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -123,9 +123,13 @@ class TestServicesSoap():
variant='NC_000011.9:g.111959693G>T',
gene='C11orf57')
assert_equal(type(r.string), list)
- assert 'NM_001082969.1:c.*2178+d3819G>T' in r.string
- assert 'NM_001082970.1:c.*2178+d3819G>T' in r.string
- assert 'NM_018195.3:c.*2178+d3819G>T' in r.string
+ # Fix for r536: disable the -u and +d convention.
+ #assert 'NM_001082969.1:c.*2178+d3819G>T' in r.string
+ #assert 'NM_001082970.1:c.*2178+d3819G>T' in r.string
+ #assert 'NM_018195.3:c.*2178+d3819G>T' in r.string
+ assert 'NM_001082969.1:c.*5997G>T' in r.string
+ assert 'NM_001082970.1:c.*5997G>T' in r.string
+ assert 'NM_018195.3:c.*5997G>T' in r.string
def test_numberconversion_gtoc_no_transcripts(self):
"""
@@ -146,7 +150,9 @@ class TestServicesSoap():
variant='chr7:g.345T>C',
gene='LOC100132858')
assert_equal(type(r.string), list)
- assert 'XM_001715131.2:c.1155+d19483A>G' in r.string
+ # Fix for r536: disable the -u and +d convention.
+ #assert 'XM_001715131.2:c.1155+d19483A>G' in r.string
+ assert 'XM_001715131.2:c.*19483A>G' in r.string
def test_gettranscriptsbygenename_valid(self):
"""
diff --git a/tests/test_website.py b/tests/test_website.py
index 7451baa14a82f8c3b3098d9de5f27cd9e653673c..97aed79e72d529d5aa2213ff8dc71cac8cd84a56 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -252,7 +252,9 @@ class TestWSGI():
r = self.app.get('/check?name=%s' % urllib.quote('NG_012337.1:g.7055C>T'))
r.mustcontain('0 Errors')
r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1:g.7055C>T')))
- r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-30-u2103G>A')))
+ # Fix for r536: disable the -u and +d convention.
+ #r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-30-u2103G>A')))
+ r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(TIMM8B_v001):c.-2133G>A')))
r.mustcontain('"check?name=%s"' % cgi.escape(urllib.quote('NG_012337.1(SDHD_v001):c.204C>T')))
@skip