diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py
index c04a112a2ce1c8c2df0988f4ecd1a0e406d77d0e..73d01804173a088c492768852be55b420f11d033 100644
--- a/mutalyzer/entrypoints/mutalyzer.py
+++ b/mutalyzer/entrypoints/mutalyzer.py
@@ -115,8 +115,8 @@ def check_name(description):
described_allele = extractor.describe_dna(reference_sequence,
sample_sequence)
#described_protein_allele = describe.describe(
- # O.getIndexedOutput("oldprotein", 0),
- # O.getIndexedOutput("newprotein", 0, default=""),
+ # O.getIndexedOutput("oldProtein", 0),
+ # O.getIndexedOutput("newProtein", 0, default=""),
# DNA=False)
described_protein_allele = ""
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index d0315fd138ab47ae6de018e663675ef3ec41b66f..fde784055806dbce4c3f26016e25f0306c46a4ef 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -840,8 +840,8 @@ class MutalyzerService(ServiceBase):
result.origCDS = O.getIndexedOutput("origCDS", 0)
result.newCDS = O.getIndexedOutput("newCDS", 0)
- result.origProtein = O.getIndexedOutput("oldprotein", 0)
- result.newProtein = O.getIndexedOutput("newprotein", 0)
+ result.origProtein = O.getIndexedOutput("oldProtein", 0)
+ result.newProtein = O.getIndexedOutput("newProtein", 0)
result.altProtein = O.getIndexedOutput("altProtein", 0)
result.chromDescription = \
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index a3bc7a8d36e6fe59515653cf5dfb8dce6d592ffa..9da54db856fc344472f1a2cfff9eb6ac7229555f 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1332,8 +1332,8 @@ def _add_transcript_info(mutator, transcript, output):
# Data added to the output object:
# - origCDS: Original CDS.
# - newCDS: Variant CDS.
- # - oldprotein: Original protein sequence, ending with '*'.
- # - newprotein:
+ # - 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.
@@ -1404,26 +1404,17 @@ def _add_transcript_info(mutator, transcript, output):
output.addOutput('origCDS', unicode(cds_original))
output.addOutput("newCDS", unicode(cds_variant[:len(protein_variant) * 3]))
- output.addOutput('oldprotein', unicode(protein_original))
+ # Under which name to store the variant protein sequence. Can be:
+ # - 'new': Normal case.
+ # - 'alt': New start codon was created.
+ # - None: Don't show variant protein sequence.
+ protein_variant_output = None
- # Todo: Don't generate the fancy HTML protein views here, do this in
- # website.py.
- # I think it would also be nice to include the mutated list of splice
- # sites.
-
- if not protein_variant or unicode(cds_variant[:3]) != unicode(cds_original[:3]):
+ 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)
- 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.
@@ -1433,37 +1424,63 @@ def _add_transcript_info(mutator, transcript, output):
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)
+ protein_variant_output = 'alt'
else:
# Variant CDS was translated and start codon is unchanged.
+ protein_variant_output = 'new'
+
+ # Todo: Don't generate the fancy HTML protein views here, do this in
+ # website.py.
+ # I think it would also be nice to include the mutated list of splice
+ # sites.
+
+ if protein_variant_output:
+ # Show protein sequence. We start by calculating offsets for diff
+ # coloring.
cds_length = util.cds_length(
mutator.shift_sites(transcript.CDS.positionList))
- descr, first, last_original, last_variant = \
- util.protein_description(cds_length,
- unicode(protein_original),
- unicode(protein_variant))
-
- util.print_protein_html(unicode(protein_original), first,
- last_original, output, 'oldProteinFancy')
- util.print_protein_html(unicode(protein_original), first,
- last_original, output, 'oldProteinFancyText', text=True)
+ descr, first, last_original, last_variant = util.protein_description(
+ cds_length, unicode(protein_original), unicode(protein_variant))
+
+ # Show original protein sequence.
+ output.addOutput('oldProtein', unicode(protein_original))
+ util.print_protein_html(
+ unicode(protein_original), first, last_original, output,
+ 'oldProteinFancy')
+ util.print_protein_html(
+ unicode(protein_original), first, last_original, output,
+ 'oldProteinFancyText', text=True)
+
if unicode(protein_original) != unicode(protein_variant):
- output.addOutput('newprotein', unicode(protein_variant))
- util.print_protein_html(unicode(protein_variant), first,
- last_variant, output, 'newProteinFancy')
- util.print_protein_html(unicode(protein_variant), first,
- last_variant, output, 'newProteinFancyText', text=True)
+ # The resulting protein is actually different, so
+ # visualise the difference.
+ output.addOutput(
+ protein_variant_output + 'Protein',
+ unicode(protein_variant))
+ util.print_protein_html(
+ unicode(protein_variant), first, last_variant, output,
+ protein_variant_output + 'ProteinFancy')
+ util.print_protein_html(
+ unicode(protein_variant), first, last_variant, output,
+ protein_variant_output + 'ProteinFancyText', text=True)
+
+ else:
+ # Show original protein sequence, no diff.
+ output.addOutput('oldProtein', unicode(protein_original))
+ 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 not protein_variant_output or protein_variant_output == 'alt':
+ # If we don't show a diff, or it is stored in
+ # altProtein/altProteinFancy, we should still populate the normal
+ # newProtein/newProteinFancy fields with a ?.
+ output.addOutput('newProtein', '?')
+ util.print_protein_html('?', 0, 0, output, 'newProteinFancy')
+ util.print_protein_html('?', 0, 0, output, 'newProteinFancyText',
+ text=True)
#_add_transcript_info
diff --git a/mutalyzer/website/templates/name-checker.html b/mutalyzer/website/templates/name-checker.html
index 470c53093b50c3cd358ba8c9cb314887616a132e..f1db90967a778dd07f5f784eb0a680f2b6a5e0fa 100644
--- a/mutalyzer/website/templates/name-checker.html
+++ b/mutalyzer/website/templates/name-checker.html
@@ -171,7 +171,7 @@
{% endif %}
{% if altStart %}
- <h4>Alternative protein using start codon {{ altStart }}</h4>
+ <h4>Protein predicted from variant coding sequence using start codon {{ altStart }}</h4>
{% if altProtein %}
<pre>
{%- for i in altProtein -%}
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index f45fbb01d851f10e7b79438c7ea450280c1ae8f8..3fac19f9ecc45fe155065338ae5741c3a3708a0a 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -47,7 +47,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54_Gly55delinsSer)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_insertion_in_frame(self):
@@ -62,7 +62,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsIleSer)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_insertion_list_in_frame(self):
@@ -77,7 +77,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsIleSer)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame(self):
@@ -92,7 +92,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_deletion_insertion_list_in_frame(self):
@@ -107,7 +107,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_deletion_insertion_in_frame_complete(self):
@@ -122,7 +122,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('AL449423.14'))
def test_deletion_insertion_list_in_frame_complete(self):
@@ -138,7 +138,7 @@ class TestVariantchecker(MutalyzerTest):
in self.output.getOutput('descriptions')
assert 'AL449423.14(CDKN2A_i001):p.(Met54delinsAsnPro)' \
in self.output.getOutput('protDescriptions')
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NM_003002.2'))
def test_est_warning_nm_est(self):
@@ -315,7 +315,7 @@ class TestVariantchecker(MutalyzerTest):
Insertion on CDS start boundary should not be included in CDS.
"""
check_variant('NM_000143.3:c.-1_1insCAT', self.output)
- assert self.output.getIndexedOutput("newprotein", 0) == None
+ assert self.output.getIndexedOutput("newProtein", 0) == None
# Todo: Is this a good test?
@fix(cache('NM_000143.3'))
@@ -324,7 +324,7 @@ class TestVariantchecker(MutalyzerTest):
Insertion after CDS start boundary should be included in CDS.
"""
check_variant('NM_000143.3:c.1_2insCAT', self.output)
- assert self.output.getIndexedOutput("newprotein", 0) == '?'
+ assert self.output.getIndexedOutput("newProtein", 0) == '?'
# Todo: Is this a good test?
@fix(cache('NG_012772.1'))
@@ -337,7 +337,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == []
# Todo: For now, the following is how to check if no protein
# prediction is done.
- assert not self.output.getOutput('newprotein')
+ assert not self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_exon(self):
@@ -349,7 +349,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_exon_exact(self):
@@ -361,7 +361,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_exon_in_frame(self):
@@ -378,7 +378,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Todo: assert that protein products indeed have only this difference.
@fix(cache('NG_012772.1'))
@@ -391,7 +391,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [4]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_intron(self):
@@ -404,7 +404,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_intron_exact(self):
@@ -415,12 +415,12 @@ class TestVariantchecker(MutalyzerTest):
check_variant('NG_012772.1(BRCA2_v001):c.681+1_682-1del', self.output)
assert self.output.getMessagesWithErrorCode('WOVERSPLICE') == []
assert self.output.getOutput('removedSpliceSites') == [2]
- # Note: The protein prediction is done, but 'newprotein' is not set
+ # Note: The protein prediction is done, but 'newProtein' is not set
# because we have no change. So to check if the prediction is done, we
- # check if 'oldprotein' is set and to check if the prediction is
- # correct, we check if 'newprotein' is not set.
- assert self.output.getOutput('oldprotein')
- assert not self.output.getOutput('newprotein')
+ # check if 'oldProtein' is set and to check if the prediction is
+ # correct, we check if 'newProtein' is not set.
+ assert self.output.getOutput('oldProtein')
+ assert not self.output.getOutput('newProtein')
@fix(cache('NG_012772.1'))
def test_del_intron_in_frame(self):
@@ -433,7 +433,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Todo: assert that protein products indeed have only this difference.
@fix(cache('NG_012772.1'))
@@ -446,7 +446,7 @@ class TestVariantchecker(MutalyzerTest):
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Genomic positions should be centered in flanking introns and unsure.
assert self.output.getIndexedOutput('genomicDescription', 0) == 'NG_012772.1:g.(17550_19725)del'
assert 'NG_012772.1(BRCA2_v001):c.632-?_681+?del' \
@@ -471,7 +471,7 @@ class TestVariantchecker(MutalyzerTest):
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Genomic positions should be centered in flanking introns and unsure.
assert self.output.getIndexedOutput('genomicDescription', 0) == 'NG_012772.1:g.(7324_11720)del'
assert 'NG_012772.1(BRCA2_v001):c.68-?_316+?del' \
@@ -491,7 +491,7 @@ class TestVariantchecker(MutalyzerTest):
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Genomic positions should be centered in flanking introns and unsure.
assert self.output.getIndexedOutput('genomicDescription', 0) == 'NG_012772.1:g.[(17550_19725)del;19017del]'
assert 'NG_012772.1(BRCA2_v001):c.[632-?_681+?del;681+4del]' \
@@ -511,7 +511,7 @@ class TestVariantchecker(MutalyzerTest):
assert len(self.output.getMessagesWithErrorCode('IDELSPLICE')) > 0
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
# Genomic positions should be centered in flanking introns and unsure.
assert self.output.getIndexedOutput('genomicDescription', 0) == 'AL449423.14:g.(60314_63683)del'
assert 'AL449423.14(CDKN2A_v001):c.151-?_457+?del' \
@@ -533,7 +533,7 @@ class TestVariantchecker(MutalyzerTest):
assert self.output.getOutput('removedSpliceSites') == [2]
# Todo: For now, the following is how to check if protein
# prediction is done.
- assert self.output.getOutput('newprotein')
+ assert self.output.getOutput('newProtein')
@fix(cache('NG_008939.1'))
def test_ins_seq(self):
@@ -1370,7 +1370,7 @@ class TestVariantchecker(MutalyzerTest):
assert not self.output.getOutput('newProteinFancy')
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 1
- assert self.output.getOutput('oldprotein')[0].startswith('M')
+ 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')
@@ -1384,7 +1384,7 @@ class TestVariantchecker(MutalyzerTest):
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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 0
assert not self.output.getOutput('altStart')
@@ -1399,7 +1399,7 @@ 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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 1
assert not self.output.getOutput('altStart')
@@ -1415,10 +1415,10 @@ class TestVariantchecker(MutalyzerTest):
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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 0
- assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert self.output.getOutput('oldProtein')[0].startswith('M')
assert 'TTG' in self.output.getOutput('altStart')
assert not self.output.getOutput('altProteinFancy')
@@ -1433,10 +1433,10 @@ 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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 1
- assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert self.output.getOutput('oldProtein')[0].startswith('M')
assert 'ATG' in self.output.getOutput('altStart')
assert not self.output.getOutput('altProteinFancy')
@@ -1450,7 +1450,7 @@ class TestVariantchecker(MutalyzerTest):
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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 0
assert 'TTG' in self.output.getOutput('altStart')
@@ -1467,9 +1467,9 @@ 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] == '?'
+ assert self.output.getOutput('newProtein')[0] == '?'
waltstart = self.output.getMessagesWithErrorCode('WALTSTART')
assert len(waltstart) == 1
- assert self.output.getOutput('oldprotein')[0].startswith('M')
+ assert self.output.getOutput('oldProtein')[0].startswith('M')
assert 'ATG' in self.output.getOutput('altStart')
assert self.output.getOutput('altProtein')[0].startswith('M')