diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index 73c400467b58d51d68c4c159b6504f69c9919675..5bd25f3396680cd42ad2eeeb19f42ed23706bffe 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -275,7 +275,7 @@ class Mapping(Db) :
return self.query(statement)
#get_Transcripts
- def get_TranscriptsByGeneName(self, geneName) :
+ def get_TranscriptsByGeneName(self, gene):
"""
Get a list of transcripts, given a gene name.
@@ -288,21 +288,19 @@ class Mapping(Db) :
Returns:
list ; A list of transcripts.
"""
-
statement = """
- SELECT transcript, version
+ SELECT transcript,
+ start, stop,
+ cds_start, cds_stop,
+ exon_starts, exon_stops,
+ gene, chromosome,
+ orientation, protein,
+ version
FROM Mapping
WHERE gene = %s;
- """, geneName
+ """, gene
- ret = self.query(statement)
- if ret :
- l = []
- for i in ret :
- l.append(i[0] + '.' + str(i[1]))
- return l
- #if
- return []
+ return self.query(statement)
#get_TranscriptsByGeneName
def get_GeneName(self, mrnaAcc) :
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index f3c55a250217df507465ff77af5478eeff83012c..3117f2b36906994282a71c1b4fd2e3df781bf8ed 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -511,12 +511,15 @@ class Converter(object) :
return variant
#correctChrVariant
- def chrom2c(self, variant, rt) :
+ def chrom2c(self, variant, rt, gene=None):
"""
@arg variant: a variant description
@type variant: string
@arg rt: the return type
@type rt: string
+ @kwarg gene: Optional gene name. If given, return variant descriptions
+ on all transcripts for this gene.
+ @type gene: string
@return: HGVS_notatations ;
@rtype: dictionary or list
@@ -543,14 +546,20 @@ class Converter(object) :
loc2 = int(self.parseTree.RawVar.EndLoc.PtLoc.Main)
else :
loc2 = loc
- transcripts = self.__database.get_Transcripts(\
- chrom, loc-5000, loc2+5000, 1)
+
+ if gene:
+ transcripts = self.__database.get_TranscriptsByGeneName(gene)
+ else:
+ transcripts = self.__database.get_Transcripts(chrom, loc-5000, loc2+5000, 1)
HGVS_notatations = defaultdict(list)
NM_list = []
for transcript in transcripts :
self._reset()
self._FieldsFromValues(transcript)
+ if self.dbFields['chromosome'] != chrom:
+ # Could be the case if we got transcripts by gene name
+ continue
M = self._coreMapping()
if M is None :
#balen
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index 2feecd256ef36e4f5ba652eae8cc0192aa5b57a9..e969c04249cd6a823e57662a28edc77808a3ebe8 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -213,7 +213,13 @@ class MutalyzerService(DefinitionBase):
"Finished processing getTranscriptsByGene(%s %s)" % (
build, name))
- return ret
+ if ret :
+ l = []
+ for i in ret :
+ l.append(i[0] + '.' + str(i[11]))
+ return l
+
+ return []
#getTranscriptsByGene
@soap(Mandatory.String, Mandatory.String, Mandatory.Integer,
@@ -481,17 +487,19 @@ class MutalyzerService(DefinitionBase):
return result
#chromosomeName
- @soap(Mandatory.String, Mandatory.String, _returns = Array(Mandatory.String))
- def numberConversion(self, build, variant) :
+ @soap(Mandatory.String, Mandatory.String, String, _returns = Array(Mandatory.String))
+ def numberConversion(self, build, variant, gene=None):
"""
Converts I{c.} to I{g.} notation or vice versa
-
@arg build: The human genome build (hg19 or hg18).
@type build: string
@arg variant: The variant in either I{c.} or I{g.} notation, full HGVS
- notation, including NM_ or NC_ accession number.
+ notation, including NM_ or NC_ accession number.
@type variant: string
+ @kwarg gene: Optional gene name. If given, return variant descriptions
+ on all transcripts for this gene.
+ @type gene: string
@return: The variant(s) in either I{g.} or I{c.} notation.
@rtype: list
@@ -507,7 +515,7 @@ class MutalyzerService(DefinitionBase):
if "c." in variant :
result = [converter.c2chrom(variant)]
elif "g." in variant :
- result = converter.chrom2c(variant, "list")
+ result = converter.chrom2c(variant, "list", gene=gene)
else:
result = [""]
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index d470168056906ad52ddb6e0a72165a988d3c354f..5c7437843943c9473338402ce4db0825391a091c 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -116,6 +116,40 @@ class TestWebservice():
assert_equal(type(r.string), list)
assert 'NC_000001.10:g.159272155del' in r.string
+ def test_numberconversion_gtoc_gene(self):
+ """
+ Running numberConversion with valid g variant and a gene name should
+ give a list of c variant names on transcripts for the given gene.
+ """
+ r = self.client.service.numberConversion(build='hg19',
+ 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
+
+ def test_numberconversion_gtoc_no_transcripts(self):
+ """
+ Running numberConversion with valid g variant but no transcripts
+ close to it should give an empty list.
+ """
+ r = self.client.service.numberConversion(build='hg19',
+ variant='chr7:g.345T>C')
+ assert_false(r)
+
+ def test_numberconversion_gtoc_required_gene(self):
+ """
+ Running numberConversion with valid g variant but no transcripts
+ close to it, but with a gene name, should give a list of c variant
+ names on transcripts for the given gene.
+ """
+ r = self.client.service.numberConversion(build='hg19',
+ variant='chr7:g.345T>C',
+ gene='LOC100132858')
+ assert_equal(type(r.string), list)
+ assert 'XM_001715131.2:c.1155+d19483A>G' in r.string
+
def test_gettranscriptsbygenename_valid(self):
"""
Running getTranscriptsByGeneName with valid gene name should give a
@@ -133,6 +167,15 @@ class TestWebservice():
'NM_004022.2']:
assert t in r.string
+ def test_gettranscriptsbygenename_invalid(self):
+ """
+ Running getTranscriptsByGeneName with invalid gene name should not
+ give a result.
+ """
+ r = self.client.service.getTranscriptsByGeneName(build='hg19',
+ name='BOGUSGENE')
+ assert_false(r)
+
def test_gettranscriptsandinfo_valid(self):
"""
Running getTranscriptsAndInfo with a valid genomic reference should
@@ -206,7 +249,7 @@ class TestWebservice():
def test_gettranscripts(self):
"""
- Running getTranscriptsByGeneName should give a list of transcripts.
+ Running getTranscripts should give a list of transcripts.
"""
r = self.client.service.getTranscripts(build='hg19', chrom='chrX',
pos=32237295)
@@ -222,7 +265,7 @@ class TestWebservice():
def test_gettranscripts_with_versions(self):
"""
- Running getTranscriptsByGeneName with versions=True should give a list
+ Running getTranscripts with versions=True should give a list
of transcripts with version numbers.
"""
r = self.client.service.getTranscripts(build='hg19', chrom='chrX',