diff --git a/src/Modules/Mutator.py b/src/Modules/Mutator.py
index b4eb1baf18aca0bce75529c03692d071dc08933e..a913397ae094269556202566304553c9121018a7 100644
--- a/src/Modules/Mutator.py
+++ b/src/Modules/Mutator.py
@@ -430,17 +430,22 @@ class Mutator() :
new_sites = []
- prev_donor = -1
+ prev_donor = sites[0] - 1
sites_iter = iter(sites)
for acceptor, donor in izip_longest(sites_iter, sites_iter):
# We don't want to do the -1+1 dance if
# 1) there is a deletion directly before the exon, or
- # 2) there is another exon directly before this exon.
+ # 2) there is another exon directly before this exon, or
+ # 3) this is the first site in the list.
#
# A consequence of check 2) is that insertions between two
# directly adjacent exons are seen as insertions in the first
# exon.
+ #
+ # Condition 3) makes sure we don't include insertions directly
+ # in front of CDS start in the CDS. It also affects translation
+ # start, but this should be no problem.
if prev_donor == acceptor - 1 or self.shift_minus_at(acceptor):
new_sites.append(self.shiftpos(acceptor))
else:
@@ -449,7 +454,15 @@ class Mutator() :
# Should never happen since splice sites come in pairs.
if not donor: continue
- new_sites.append(self.shiftpos(donor + 1) - 1)
+ # We don't want to do the +1-1 dance if this is the last site
+ # in the list. This makes sure we don't include insertions
+ # directly at CDS end in the CDS. It also affects translation
+ # end, but this should be no problem.
+ if donor == sites[-1]:
+ new_sites.append(self.shiftpos(donor))
+ else:
+ new_sites.append(self.shiftpos(donor + 1) - 1)
+
prev_donor = donor
return new_sites
diff --git a/src/tests/test_mutalyzer.py b/src/tests/test_mutalyzer.py
new file mode 100755
index 0000000000000000000000000000000000000000..b6169e52a650625c6ae09b953d5d176054e7e5d7
--- /dev/null
+++ b/src/tests/test_mutalyzer.py
@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+
+"""
+Tests for the Mutalyzer module.
+"""
+
+#import logging; logging.basicConfig()
+import re
+import os
+import random
+import unittest
+import site
+from Bio.Seq import Seq
+
+# Todo: Can this be done in a more elegant way?
+os.chdir('../..')
+site.addsitedir('src')
+
+from Modules import Config
+from Modules import Output
+import Mutalyzer
+
+
+class TestMutalyzer(unittest.TestCase):
+ """
+ Test the Mutalyzer module.
+ """
+
+ def setUp(self):
+ """
+ Initialize test Mutalyzer module.
+ """
+ self.config = Config.Config()
+ self.output = Output.Output(__file__, self.config.Output)
+
+ def test_roll(self):
+ """
+ Just a variant where we should roll.
+ """
+ Mutalyzer.process('NM_003002.2:c.273del', self.config, self.output)
+ wroll = self.output.getMessagesWithErrorCode('WROLL')
+ self.assertTrue(len(wroll) > 0)
+
+ def test_no_roll(self):
+ """
+ Just a variant where we should not roll.
+ """
+ Mutalyzer.process('NM_003002.2:c.274del', self.config, self.output)
+ wroll = self.output.getMessagesWithErrorCode('WROLL')
+ self.assertTrue(len(wroll) == 0)
+
+ def test_ins_cds_start(self):
+ """
+ Insertion on CDS start boundary should not be included in CDS.
+ """
+ Mutalyzer.process('NM_000143.3:c.-1_1insCAT', self.config, self.output)
+ self.assertEqual(self.output.getIndexedOutput("newprotein", 0), None)
+
+ def test_ins_cds_start_after(self):
+ """
+ Insertion after CDS start boundary should be included in CDS.
+ """
+ Mutalyzer.process('NM_000143.3:c.1_2insCAT', self.config, self.output)
+ self.assertEqual(self.output.getIndexedOutput("newprotein", 0), '?')
+
+
+if __name__ == '__main__':
+ # Usage:
+ # ./test_mutalyzer.py -v
+ # Or, selecting a specific test:
+ # ./test_mutalyzer.py -v TestMutalyzer.test_ins_cds_start
+ unittest.main()
diff --git a/src/tests/test_mutator.py b/src/tests/test_mutator.py
index e4cd02533f65bd50d077b14dc13b4b9e9fe77310..fd6af9fa2430998e98b310142d36f8d7aed2634e 100755
--- a/src/tests/test_mutator.py
+++ b/src/tests/test_mutator.py
@@ -285,6 +285,16 @@ class TestMutator(unittest.TestCase):
m.insM(13, 'A') # g.13_14insA
self.assertEqual(m.newSplice(sites), [4, 9, 14, 18, 26, 28])
+ def test_newSplice_first_acc_ins_on(self):
+ """
+ Insertion in first intron/exon boundary not be included.
+ """
+ l = 30
+ sites = [4, 9, 14, 17, 25, 27]
+ m = self._mutator(_seq(l))
+ m.insM(3, 'A') # g.3_4insA
+ self.assertEqual(m.newSplice(sites), [5, 10, 15, 18, 26, 28])
+
def test_newSplice_acc_ins_after(self):
"""
Insertion 1 position after intron/exon boundary.
@@ -315,6 +325,16 @@ class TestMutator(unittest.TestCase):
m.insM(17, 'A') # g.17_18insA
self.assertEqual(m.newSplice(sites), [4, 9, 14, 18, 26, 28])
+ def test_newSplice_last_don_ins_on(self):
+ """
+ Insertion in last exon/intron boundary should not be included.
+ """
+ l = 30
+ sites = [4, 9, 14, 17, 25, 27]
+ m = self._mutator(_seq(l))
+ m.insM(27, 'A') # g.27_28insA
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 17, 25, 27])
+
def test_newSplice_don_ins_after(self):
"""
Insertion 1 position after exon/intron boundary.
@@ -339,15 +359,15 @@ class TestMutator(unittest.TestCase):
m.insM(12, 'AT') # g.12_13insAT
self.assertEqual(m.newSplice(sites), [4, 9, 16, 19, 27, 29])
- def test_newSplice_acc_ins2_on(self):
+ def test_newSplice_first_acc_ins2_on(self):
"""
- Insertion of 2 in intron/exon boundary.
+ Insertion of 2 in last exon/intron boundary should not be included.
"""
l = 30
sites = [4, 9, 14, 17, 25, 27]
m = self._mutator(_seq(l))
- m.insM(13, 'AT') # g.13_14insAT
- self.assertEqual(m.newSplice(sites), [4, 9, 14, 19, 27, 29])
+ m.insM(3, 'AT') # g.3_4insAT
+ self.assertEqual(m.newSplice(sites), [6, 11, 16, 19, 27, 29])
def test_newSplice_acc_ins2_after(self):
"""
@@ -369,15 +389,15 @@ class TestMutator(unittest.TestCase):
m.insM(16, 'AT') # g.16_17insAT
self.assertEqual(m.newSplice(sites), [4, 9, 14, 19, 27, 29])
- def test_newSplice_don_ins2_on(self):
+ def test_newSplice_last_don_ins2_on(self):
"""
- Insertion of 2 in exon/intron boundary.
+ Insertion of 2 in last exon/intron boundary should not be included.
"""
l = 30
sites = [4, 9, 14, 17, 25, 27]
m = self._mutator(_seq(l))
- m.insM(17, 'AT') # g.17_18insAT
- self.assertEqual(m.newSplice(sites), [4, 9, 14, 19, 27, 29])
+ m.insM(27, 'AT') # g.27_28insAT
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 17, 25, 27])
def test_newSplice_don_ins2_after(self):
"""
@@ -413,6 +433,16 @@ class TestMutator(unittest.TestCase):
m.insM(13, 'ATT') # g.13_14insATT
self.assertEqual(m.newSplice(sites), [4, 9, 14, 20, 28, 30])
+ def test_newSplice_first_acc_ins3_on(self):
+ """
+ Insertion of 3 in first intron/exon boundary should not be included.
+ """
+ l = 30
+ sites = [4, 9, 14, 17, 25, 27]
+ m = self._mutator(_seq(l))
+ m.insM(3, 'ATT') # g.3_4insATT
+ self.assertEqual(m.newSplice(sites), [7, 12, 17, 20, 28, 30])
+
def test_newSplice_acc_ins3_after(self):
"""
Insertion of 3 1 position after intron/exon boundary.
@@ -443,6 +473,16 @@ class TestMutator(unittest.TestCase):
m.insM(17, 'ATT') # g.17_18insATT
self.assertEqual(m.newSplice(sites), [4, 9, 14, 20, 28, 30])
+ def test_newSplice_last_don_ins3_on(self):
+ """
+ Insertion of 3 in last exon/intron boundary should not be included.
+ """
+ l = 30
+ sites = [4, 9, 14, 17, 25, 27]
+ m = self._mutator(_seq(l))
+ m.insM(27, 'ATT') # g.27_28insATT
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 17, 25, 27])
+
def test_newSplice_don_ins3_after(self):
"""
Insertion of 3 1 position after exon/intron boundary.