diff --git a/src/Modules/Mutator.py b/src/Modules/Mutator.py
index a913397ae094269556202566304553c9121018a7..f9af2303c2659bca45c07f3862565de9eb7955e6 100644
--- a/src/Modules/Mutator.py
+++ b/src/Modules/Mutator.py
@@ -22,7 +22,7 @@ The original as well as the mutated string are stored here.
# - Mutator ; Mutate a string and register all shift points.
-from itertools import izip_longest
+from itertools import ifilter, izip_longest
from Bio import Restriction
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
@@ -43,6 +43,8 @@ class Mutator() :
where the modifications in length are stored.
Each first element of the tuples in this list
is unique, each second element is non-zero.
+ - __removed_sites ; Set of splice sites to ignore in mutated
+ string.
- __restrictionBatch ;
Public variables:
@@ -106,6 +108,7 @@ class Mutator() :
self.__config = config
self.__output = output
self.__shift = []
+ self.__removed_sites = set()
self.__restrictionBatch = Restriction.RestrictionBatch([], ['N'])
self.orig = orig
@@ -363,6 +366,19 @@ class Mutator() :
return ret
#shiftpos
+ def add_removed_sites(self, sites):
+ """
+ Add sites to the set of splice sites to ignore in the mutated string.
+
+ @arg sites: A list of splice sites to ignore.
+ @type sites: list of int
+
+ @todo: Resulting list of ignored sites should always be even.
+ """
+ for site in sites:
+ self.__removed_sites.add(site)
+ #add_ignore_sites
+
def newSplice(self, sites) :
"""
Generate a list of new splice sites.
@@ -374,7 +390,7 @@ class Mutator() :
@rtype: list of int
- Example 1 (DNA): NG_012772.1
+ Example 1 (DNA): NG_012772.1(BRCA2_v001)
...---------[=========]----------...
^ ^
@@ -430,8 +446,9 @@ class Mutator() :
new_sites = []
- prev_donor = sites[0] - 1
- sites_iter = iter(sites)
+ prev_donor = None
+ sites_iter = ifilter(lambda s: s not in self.__removed_sites, sites)
+
for acceptor, donor in izip_longest(sites_iter, sites_iter):
# We don't want to do the -1+1 dance if
@@ -446,7 +463,8 @@ class Mutator() :
# 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):
+ if not prev_donor or prev_donor == acceptor - 1 or \
+ self.shift_minus_at(acceptor):
new_sites.append(self.shiftpos(acceptor))
else:
new_sites.append(self.shiftpos(acceptor - 1) + 1)
diff --git a/src/Mutalyzer.py b/src/Mutalyzer.py
index 3a3edeaa22db37995152afd7c1797fb1fef888f0..6a7a24d5485828e01285e00e7f0880cf7100315c 100644
--- a/src/Mutalyzer.py
+++ b/src/Mutalyzer.py
@@ -536,7 +536,7 @@ def __overSplice(pos1, pos2, sites) :
@arg pos1: The first coordinate of the range in g. notation.
@type pos1: integer
- @arg pos2: The first coordinate of the range in g. notation.
+ @arg pos2: The second coordinate of the range in g. notation.
@type pos2: integer
@arg sites: A list of splice sites in g. notation.
@type sites: list(integer)
@@ -1043,6 +1043,7 @@ def checkInsertion(start_g, end_g, Arg1, MUU, GenRecordInstance, O) :
Arg1, start_g, start_g + 1,
MUU.mutated[newStart + shift:newStop + shift],
newStart + shift, newStart + shift + 1))
+ #if
if shift != roll[1]:
O.addMessage(__file__, 1, "IROLLBACK",
"Insertion of %s at position %i_%i was not corrected to an " \
@@ -1055,6 +1056,7 @@ def checkInsertion(start_g, end_g, Arg1, MUU, GenRecordInstance, O) :
GenRecordInstance.name(start_g, start_g + 1, "ins",
MUU.mutated[newStart + shift:newStop + shift] , "",
(roll[0], shift))
+ #else
#checkInsertion
def __ivs2g(location, transcript) :
@@ -1149,7 +1151,10 @@ def __normal2g(RawVar, transcript) :
def __rv(MUU, RawVar, GenRecordInstance, parts, O, transcript) :
"""
+ Process one raw variant.
+
@todo: documentation
+ @todo: parts argument is not used
"""
# FIXME check this
@@ -1229,10 +1234,54 @@ def __rv(MUU, RawVar, GenRecordInstance, parts, O, transcript) :
Arg1 = Bio.Seq.reverse_complement(RawVar.Arg1)
Arg2 = Bio.Seq.reverse_complement(RawVar.Arg2)
+ splice_abort = False
+
+ # If we hit a splice site, issue a warning. Later on we decide if we
+ # can still process this variant in any way (e.g. if it deletes an
+ # entire exon).
if transcript and __overSplice(start_g, end_g, transcript.CM.RNA) :
+ splice_abort = True
O.addMessage(__file__, 2, "WOVERSPLICE",
"Variant hits one or more splice sites.")
+ # If we have a deletion, and it covers exactly an even number of splice
+ # sites, remove these splice sites.
+ # Todo: Special cases for first/last exon? Upstream/downstream exons?
+ # Note, this is not the same as __overSplice(). Here we collect
+ # sites where the delection borders the exon/intron boundary.
+ if transcript and RawVar.MutationType == 'del':
+ removed_sites = []
+ sites = iter(transcript.CM.RNA)
+ for acceptor, donor in izip_longest(sites, sites):
+ if start_g <= acceptor <= end_g + 1:
+ removed_sites.append(acceptor)
+ if start_g - 1 <= donor <= end_g:
+ removed_sites.append(donor)
+
+ if len(removed_sites) and not len(removed_sites) % 2:
+ # An even number of splice sites was removed. We can deal with
+ # this, but issue a warning.
+ splice_abort = False
+ MUU.add_removed_sites(removed_sites)
+ O.addMessage(__file__, 1, "IDELSPLICE", "Removed %i splice " \
+ "sites from transcript." % len(removed_sites))
+
+ # If splice_abort is set, this basically means WOVERSPLICE was called and
+ # IDELSPLICE was not called.
+ # I guess in that case we do want to generate the visualisation, the
+ # genomic description, and affected transcripts. But NOT the predicted
+ # protein.
+ # The following solution is a bit of a hack. By setting the .translate
+ # field of the transcript to False, we force that no protein is predicted.
+ if splice_abort:
+ #return
+ transcript.translate = False
+ # The affected protein description for this transcript will now be
+ # a question mark, e.g. "NG_012772.1(BRCA2_i001):?". But protein
+ # descriptions for other transcripts (where splice sites are also
+ # crippled) are still shown. I think we ideally would not want this.
+ # However, some transcripts might be unaffected and should be shown.
+
if RawVar.MutationType in ["del", "dup", "subst", "delins"] :
__checkOptArg(MUU.orig, start_g, end_g, Arg1, O)
diff --git a/src/tests/test_mutalyzer.py b/src/tests/test_mutalyzer.py
index d6420ec8fbf05f1ca31d820d0855df401055a330..a1996b39e519e9da89fdf67a673351faa374163e 100755
--- a/src/tests/test_mutalyzer.py
+++ b/src/tests/test_mutalyzer.py
@@ -84,6 +84,7 @@ class TestMutalyzer(unittest.TestCase):
"""
Mutalyzer.process('NM_000143.3:c.-1_1insCAT', self.config, self.output)
self.assertEqual(self.output.getIndexedOutput("newprotein", 0), None)
+ # Todo: is this a good test?
def test_ins_cds_start_after(self):
"""
@@ -91,6 +92,100 @@ class TestMutalyzer(unittest.TestCase):
"""
Mutalyzer.process('NM_000143.3:c.1_2insCAT', self.config, self.output)
self.assertEqual(self.output.getIndexedOutput("newprotein", 0), '?')
+ # Todo: is this a good test?
+
+ def test_del_splice_site(self):
+ """
+ Deletion hitting one splice site should not be possible.
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.632-5_670del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) == 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertFalse(self.output.getOutput('newprotein'))
+
+ def test_del_exon(self):
+ """
+ Deletion of an entire exon should be possible.
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.632-5_681+7del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) > 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertTrue(self.output.getOutput('newprotein'))
+
+ def test_del_exon_in_frame(self):
+ """
+ Deletion of an entire exon with length a triplicate should give a
+ proteine product with just this deletion (and possibly substitutions
+ directly before and after).
+
+ NG_012772.1(BRCA2_v001):c.68-7_316+7del is such a variant, since
+ positions 68 through 316 are exactly one exon and (316-68+1)/3 = 83.
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.68-7_316+7del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) > 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertTrue(self.output.getOutput('newprotein'))
+ # Todo: assert that protein products indeed have only this difference.
+
+ def test_del_exons(self):
+ """
+ Deletion of two entire exons should be possible.
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.632-5_793+7del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) > 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertTrue(self.output.getOutput('newprotein'))
+
+ def test_del_intron(self):
+ """
+ Deletion of an entire intron should be possible (fusion of remaining
+ exonic parts).
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.622_674del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) > 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertTrue(self.output.getOutput('newprotein'))
+
+ def test_del_intron_in_frame(self):
+ """
+ Deletion of an entire intron should be possible (fusion of remaining
+ exonic parts).
+ """
+ Mutalyzer.process('NG_012772.1(BRCA2_v001):c.622_672del',
+ self.config, self.output)
+ woversplice = self.output.getMessagesWithErrorCode('WOVERSPLICE')
+ self.assertTrue(len(woversplice) > 0)
+ idelsplice = self.output.getMessagesWithErrorCode('IDELSPLICE')
+ self.assertTrue(len(idelsplice) > 0)
+ # Todo: For now, the following is how to check if no proteins
+ # prediction is done.
+ self.assertTrue(self.output.getOutput('newprotein'))
+ # Todo: assert that protein products indeed have only this difference.
if __name__ == '__main__':
diff --git a/src/tests/test_mutator.py b/src/tests/test_mutator.py
index fd6af9fa2430998e98b310142d36f8d7aed2634e..7f942ccf93ff93f9e8c61f29d2a9c1744a6a4805 100755
--- a/src/tests/test_mutator.py
+++ b/src/tests/test_mutator.py
@@ -668,6 +668,30 @@ class TestMutator(unittest.TestCase):
m.insM(18, 'AT') # g.18_19insAT
self.assertEqual(m.newSplice(sites), [4, 9, 10, 17, 18, 29])
+ def test_newSplice_removed_sites(self):
+ """
+ After removing splice sites, newSplice() should filter them.
+ """
+ l = 40
+ sites = [4, 9, 14, 19, 25, 27, 32, 38]
+ m = self._mutator(_seq(l))
+ m.add_removed_sites([19, 25])
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 27, 32, 38])
+ m.add_removed_sites([27, 32])
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 38])
+ m.insM(13, 'A') # g.13_14insA
+ self.assertEqual(m.newSplice(sites), [4, 9, 14, 39])
+
+ def test_sites_even_invariant(self):
+ """
+ The number of splice sites should always be even. Modifying the list
+ of splice sites must always prevent the result of an odd number of
+ splice sites.
+
+ Todo: this test.
+ """
+ pass
+
if __name__ == '__main__':
# Usage: