From 851e71fef32e4f4861a7609077ff02c97b069622 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 22 Sep 2015 09:16:24 +0200
Subject: [PATCH] Visualise protein change, also with alternative start
In the case of an alternative start codon (in the reference CDS),
protein changes were not visualised. This is fixed and a WALTSTART
warning is also issued.
Also, if a new non-reference start codon is created by the variant,
visualise this as such.
---
mutalyzer/util.py | 4 --
mutalyzer/variantchecker.py | 124 +++++++++++++++++++++++------------
tests/test_variantchecker.py | 93 ++++++++++++++++++++++++--
3 files changed, 172 insertions(+), 49 deletions(-)
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 4f95f643..16667d58 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -600,10 +600,6 @@ def protein_description(cds_stop, s1, s2):
else:
description = in_frame_description(s1, s2)
- if not s2 or s1[0] != s2[0]:
- # Mutation in start codon.
- return 'p.?', description[1], description[2], description[3]
-
return description
#protein_description
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index ca35dd49..a3bc7a8d 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1329,6 +1329,30 @@ def _add_transcript_info(mutator, transcript, output):
# Add protein prediction to output.
if transcript.translate:
+ # Data added to the output object:
+ # - origCDS: Original CDS.
+ # - newCDS: Variant CDS.
+ # - oldprotein: Original protein sequence, ending with '*'.
+ # - newprotein:
+ # - If variant CDS could not be translated, this is '?'.
+ # - If start codon was affected, this is '?'.
+ # - If variant protein equals original protein, this is unset.
+ # - Otherwise, this is the variant protein sequence, ending with
+ # '*' if a stop codon was found.
+ # - altStart:
+ # - If variant CDS could be translated and variant created a new
+ # start codon, this is the new start codon.
+ # - Unset otherwise.
+ # - altProtein:
+ # - If variant CDS could be translated and variant created a new
+ # start codon, and variant protein does not equal original
+ # protein, this is the variant protein sequence, ending with '*'
+ # if a stop codon was found.
+ # - oldProteinFancy, newProteinFancy, altProteinFancy: Versions of the
+ # protein sequences formatted for HTML.
+ # - oldProteinFancyText, newProteinFancyText, altProteinFancyText:
+ # Versions of the protein sequences formatted for plaintext.
+
cds_original = util.splice(mutator.orig, transcript.CDS.positionList)
cds_original.alphabet = IUPAC.unambiguous_dna
@@ -1343,8 +1367,6 @@ def _add_transcript_info(mutator, transcript, output):
transcript.CM.orientation)
cds_variant.alphabet = IUPAC.unambiguous_dna
- #output.addOutput('origCDS', cds_original)
-
if transcript.CM.orientation == -1:
cds_original = cds_original.reverse_complement()
cds_variant = cds_variant.reverse_complement()
@@ -1361,8 +1383,17 @@ def _add_transcript_info(mutator, transcript, output):
'In frame stop codon found.')
return
+ if not protein_original.startswith('M'):
+ protein_original = 'M' + protein_original[1:]
+ output.addMessage(__file__, 2, 'WALTSTART',
+ 'Reference protein translated from alternative '
+ 'start codon %s.' % (unicode(cds_original[:3])))
+
protein_variant = cds_variant.translate(table=transcript.txTable)
+ if protein_variant:
+ protein_variant = 'M' + protein_variant[1:]
+
# Up to and including the first '*', or the entire string.
try:
stop = unicode(protein_variant).index('*')
@@ -1370,8 +1401,6 @@ def _add_transcript_info(mutator, transcript, output):
except ValueError:
pass
- # Note: addOutput('origCDS', ...) was first before the possible
- # reverse complement operation above.
output.addOutput('origCDS', unicode(cds_original))
output.addOutput("newCDS", unicode(cds_variant[:len(protein_variant) * 3]))
@@ -1381,34 +1410,43 @@ def _add_transcript_info(mutator, transcript, output):
# website.py.
# I think it would also be nice to include the mutated list of splice
# sites.
- if not protein_variant or unicode(protein_variant[0]) != 'M':
- # Todo: Protein differences are not color-coded,
- # use something like below in protein_description().
+
+ if not protein_variant or unicode(cds_variant[:3]) != unicode(cds_original[:3]):
+ # Could not translate variant CDS or variant hits start codon. In
+ # that case we predict p.? and see if a non-reference start codon
+ # was created.
util.print_protein_html(unicode(protein_original), 0, 0,
output, 'oldProteinFancy')
util.print_protein_html(unicode(protein_original), 0, 0,
output, 'oldProteinFancyText', text=True)
- if unicode(cds_variant[0:3]) in \
- CodonTable.unambiguous_dna_by_id[transcript.txTable].start_codons:
- output.addOutput('newprotein', '?')
- util.print_protein_html('?', 0, 0, output, 'newProteinFancy')
- util.print_protein_html('?', 0, 0, output,
- 'newProteinFancyText', text=True)
- output.addOutput('altStart', unicode(cds_variant[0:3]))
- if unicode(protein_original[1:]) != unicode(protein_variant[1:]):
- output.addOutput('altProtein',
- 'M' + unicode(protein_variant[1:]))
- util.print_protein_html('M' + unicode(protein_variant[1:]), 0,
- 0, output, 'altProteinFancy')
- util.print_protein_html('M' + unicode(protein_variant[1:]), 0,
- 0, output, 'altProteinFancyText', text=True)
- else :
- output.addOutput('newprotein', '?')
- util.print_protein_html('?', 0, 0, output, 'newProteinFancy')
- util.print_protein_html('?', 0, 0, output,
- 'newProteinFancyText', text=True)
+ output.addOutput('newprotein', '?')
+ util.print_protein_html('?', 0, 0, output, 'newProteinFancy')
+ util.print_protein_html('?', 0, 0, output,
+ 'newProteinFancyText', text=True)
+
+ if protein_variant:
+ # Variant CDS could be translated, but start codon was
+ # affected.
+ start_codons = CodonTable.unambiguous_dna_by_id[
+ transcript.txTable].start_codons
+
+ if unicode(cds_variant[0:3]) in start_codons:
+ # A non-reference start codon was created.
+ output.addOutput('altStart', unicode(cds_variant[0:3]))
+
+ if unicode(protein_original) != unicode(protein_variant):
+ # The resulting protein is actually different, so
+ # visualise the difference.
+ # Todo: Protein differences are not color-coded,
+ # use something like below in protein_description().
+ output.addOutput('altProtein', unicode(protein_variant))
+ util.print_protein_html(unicode(protein_variant), 0,
+ 0, output, 'altProteinFancy')
+ util.print_protein_html(unicode(protein_variant), 0,
+ 0, output, 'altProteinFancyText', text=True)
else:
+ # Variant CDS was translated and start codon is unchanged.
cds_length = util.cds_length(
mutator.shift_sites(transcript.CDS.positionList))
descr, first, last_original, last_variant = \
@@ -1840,23 +1878,27 @@ def check_variant(description, output):
# So we manually translate the first codon to M. But only
# if it was not affected by the variant.
protein_variant = cds_variant.translate(table=transcript.txTable)
- if unicode(cds_variant[:3]) == unicode(cds_original[:3]):
+ if protein_variant and unicode(cds_variant[:3]) == unicode(cds_original[:3]):
protein_variant = protein_original[0] + protein_variant[1:]
- # Up to and including the first '*', or the entire string.
- try:
- stop = unicode(protein_variant).index('*')
- protein_variant = protein_variant[:stop + 1]
- except ValueError:
- pass
-
- try:
- cds_length = util.cds_length(
- mutator.shift_sites(transcript.CDS.positionList))
- transcript.proteinDescription = util.protein_description(
- cds_length, unicode(protein_original), unicode(protein_variant))[0]
- except IndexError:
- # Todo: Probably CDS start was hit by removal of exon..
+ # Up to and including the first '*', or the entire string.
+ try:
+ stop = unicode(protein_variant).index('*')
+ protein_variant = protein_variant[:stop + 1]
+ except ValueError:
+ pass
+
+ try:
+ cds_length = util.cds_length(
+ mutator.shift_sites(transcript.CDS.positionList))
+ transcript.proteinDescription = util.protein_description(
+ cds_length, unicode(protein_original), unicode(protein_variant))[0]
+ except IndexError:
+ # Todo: Probably CDS start was hit by removal of exon..
+ transcript.proteinDescription = 'p.?'
+
+ else:
+ # Mutation in start codon.
transcript.proteinDescription = 'p.?'
else:
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 4c5509ef..f45fbb01 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -1357,6 +1357,7 @@ class TestVariantchecker(MutalyzerTest):
"""
check_variant('AB026906.1:c.276C>T', self.output)
assert 'AB026906.1(SDHD_i001):p.(=)' in self.output.getOutput('protDescriptions')
+ assert not self.output.getOutput('newProteinFancy')
@fix(cache('NM_024426.4'))
def test_synonymous_p_is_alt_start(self):
@@ -1366,17 +1367,27 @@ class TestVariantchecker(MutalyzerTest):
"""
check_variant('NM_024426.4:c.1107A>G', self.output)
assert 'NM_024426.4(WT1_i001):p.(=)' in self.output.getOutput('protDescriptions')
- assert 'CTG' in self.output.getOutput('altStart')
+ assert not self.output.getOutput('newProteinFancy')
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 1
+ assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert not self.output.getOutput('newProtein')
+ assert not self.output.getOutput('altStart')
+ assert not self.output.getOutput('altProteinFancy')
@fix(cache('AB026906.1'))
def test_start_codon(self):
"""
Mutation of start codon should yield a p.? description.
"""
- check_variant('AB026906.1:c.1A>T', self.output)
+ check_variant('AB026906.1:c.1A>G', self.output)
assert 'AB026906.1(SDHD_i001):p.?' in self.output.getOutput('protDescriptions')
- west = self.output.getMessagesWithErrorCode('WSTART')
- assert len(west) == 1
+ wstart = self.output.getMessagesWithErrorCode('WSTART')
+ assert len(wstart) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 0
+ assert not self.output.getOutput('altStart')
@fix(cache('NM_024426.4'))
def test_start_codon_alt_start(self):
@@ -1388,3 +1399,77 @@ class TestVariantchecker(MutalyzerTest):
assert 'NM_024426.4(WT1_i001):p.?' in self.output.getOutput('protDescriptions')
west = self.output.getMessagesWithErrorCode('WSTART')
assert len(west) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 1
+ assert not self.output.getOutput('altStart')
+
+ @fix(cache('AB026906.1'))
+ def test_start_codon_yield_start_p_is(self):
+ """
+ Silent mutation creating new start codon should yield a p.?
+ description. The visualisation should also render the case for the new
+ start codon.
+ """
+ check_variant('AB026906.1:c.1A>T', self.output) # yields TTG start codon
+ assert 'AB026906.1(SDHD_i001):p.?' in self.output.getOutput('protDescriptions')
+ wstart = self.output.getMessagesWithErrorCode('WSTART')
+ assert len(wstart) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 0
+ assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert 'TTG' in self.output.getOutput('altStart')
+ assert not self.output.getOutput('altProteinFancy')
+
+ @fix(cache('NM_024426.4'))
+ def test_start_codon_alt_start_yield_start_p_is(self):
+ """
+ Silent mutation creating new start codon should yield a p.?
+ description, also with an alternative start codon. The visualisation
+ should also render the case for the new start codon.
+ """
+ check_variant('NM_024426.4:c.1C>A', self.output) # yields ATG start codon
+ assert 'NM_024426.4(WT1_i001):p.?' in self.output.getOutput('protDescriptions')
+ west = self.output.getMessagesWithErrorCode('WSTART')
+ assert len(west) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 1
+ assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert 'ATG' in self.output.getOutput('altStart')
+ assert not self.output.getOutput('altProteinFancy')
+
+ @fix(cache('AB026906.1'))
+ def test_start_codon_yield_start(self):
+ """
+ Mutation creating new start codon should yield a p.? description. The
+ visualisation should also render the case for the new start codon.
+ """
+ check_variant('AB026906.1:c.1_4delinsTTGA', self.output) # yields TTG start codon
+ assert 'AB026906.1(SDHD_i001):p.?' in self.output.getOutput('protDescriptions')
+ wstart = self.output.getMessagesWithErrorCode('WSTART')
+ assert len(wstart) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 0
+ assert 'TTG' in self.output.getOutput('altStart')
+ assert self.output.getOutput('altProtein')[0].startswith('M')
+
+ @fix(cache('NM_024426.4'))
+ def test_start_codon_alt_start_yield_start(self):
+ """
+ Mutation creating new start codon should yield a p.? description, also
+ with an alternative start codon. The visualisation should also render
+ the new start codon.
+ """
+ check_variant('NM_024426.4:c.1_4delinsATGA', self.output) # yields ATG start codon
+ assert 'NM_024426.4(WT1_i001):p.?' in self.output.getOutput('protDescriptions')
+ west = self.output.getMessagesWithErrorCode('WSTART')
+ assert len(west) == 1
+ assert self.output.getOutput('newprotein')[0] == '?'
+ waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
+ assert len(waltstart) == 1
+ assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert 'ATG' in self.output.getOutput('altStart')
+ assert self.output.getOutput('altProtein')[0].startswith('M')
--
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