diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index e0137d9330aef341b422aa154309af15c5e8cb3b..ce2287a8d929100509e36ae0d624aca1ba3e8e7a 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -264,11 +264,24 @@ class MutalyzerService(ServiceBase):
"Finished processing getTranscripts(%s %s %s %s)"
% (build, chrom, pos, versions))
- #filter out the accNo
- if versions:
- return ['%s.%s' % (m.accession, m.version) for m in mappings]
- else:
- return [m.accession for m in mappings]
+ transcripts = []
+ for mapping in mappings:
+ if versions and mapping.version:
+ accession = '%s.%i' % (mapping.accession, mapping.version)
+ else:
+ accession = mapping.accession
+ if mapping.select_transcript:
+ if mapping.reference_type == 'lrg':
+ selector = 't%d' % mapping.transcript
+ elif mapping.transcript:
+ selector = '(%s_v%.3i)' % (mapping.gene, mapping.transcript)
+ else:
+ selector = '(%s)' % mapping.gene
+ else:
+ selector = ''
+ transcripts.append('%s%s' % (accession, selector))
+
+ return transcripts
#getTranscripts
@srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Array(Mandatory.Unicode))
@@ -296,12 +309,30 @@ class MutalyzerService(ServiceBase):
L.addMessage(__file__, -1, "INFO",
"Finished processing getTranscriptsByGene(%s %s)" % (build, name))
- return ['%s.%s' % (m.accession, m.version) for m in mappings]
- #getTranscriptsByGene
+ transcripts = []
+ for mapping in mappings:
+ if mapping.version:
+ accession = '%s.%i' % (mapping.accession, mapping.version)
+ else:
+ accession = mapping.accession
+ if mapping.select_transcript:
+ if mapping.reference_type == 'lrg':
+ selector = 't%d' % mapping.transcript
+ elif mapping.transcript:
+ selector = '(%s_v%.3i)' % (mapping.gene, mapping.transcript)
+ else:
+ selector = '(%s)' % mapping.gene
+ else:
+ selector = ''
+ transcripts.append('%s%s' % (accession, selector))
+
+ return transcripts
+ #getTranscriptsByGeneName
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
- Mandatory.Integer, Mandatory.Integer, _returns=Array(Mandatory.Unicode))
- def getTranscriptsRange(build, chrom, pos1, pos2, method) :
+ Mandatory.Integer, Mandatory.Integer, Boolean,
+ _returns=Array(Mandatory.Unicode))
+ def getTranscriptsRange(build, chrom, pos1, pos2, method, versions=False):
"""
Get all the transcripts that overlap with a range on a chromosome.
@@ -319,6 +350,8 @@ class MutalyzerService(ServiceBase):
- 0 ; Return only the transcripts that completely fall in the range
[pos1, pos2].
- 1 ; Return all hit transcripts.
+ @kwarg versions: If set to True, also include transcript versions.
+ @type versions: bool
@return: A list of transcripts.
@rtype: list
@@ -381,7 +414,24 @@ class MutalyzerService(ServiceBase):
"Finished processing getTranscriptsRange(%s %s %s %s %s)" % (
build, chrom, pos1, pos2, method))
- return [m.accession for m in mappings]
+ transcripts = []
+ for mapping in mappings:
+ if versions and mapping.version:
+ accession = '%s.%i' % (mapping.accession, mapping.version)
+ else:
+ accession = mapping.accession
+ if mapping.select_transcript:
+ if mapping.reference_type == 'lrg':
+ selector = 't%d' % mapping.transcript
+ elif mapping.transcript:
+ selector = '(%s_v%.3i)' % (mapping.gene, mapping.transcript)
+ else:
+ selector = '(%s)' % mapping.gene
+ else:
+ selector = ''
+ transcripts.append('%s%s' % (accession, selector))
+
+ return transcripts
#getTranscriptsRange
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
@@ -476,6 +526,9 @@ class MutalyzerService(ServiceBase):
for mapping in mappings:
t = TranscriptMappingInfo()
+ # TODO: This doesn't work so well for mappings with select_transcript
+ # set, for example LRG and mtDNA mappings, but it's not so easy to
+ # fix in a backwards compatible way.
t.name = mapping.accession
t.version = mapping.version
t.gene = mapping.gene
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index 37a5799fba0a02f0a26aeeabbe906e4936250b3c..a02146da3b1b353d97caad85b3a4d53b4c37bb45 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -166,6 +166,52 @@ def test_numberconversion_gtoc_required_gene(api):
assert 'XM_001715131.2:c.*19483A>G' in r.string
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscripts_lrg(api):
+ """
+ Running getTranscripts should give us overlapping transcripts.
+ list of transcripts including LRG transcripts.
+ """
+ r = api('getTranscripts', build='hg19', chrom='chr1',
+ pos=207646118)
+ assert type(r.string) == list
+ assert 'LRG_348t1' in r.string
+
+
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscripts_mtdna(api):
+ """
+ Running getTranscripts should give us overlapping transcripts.
+ list of transcripts, also on chrM.
+ """
+ r = api('getTranscripts', build='hg19', chrom='chrM',
+ pos=10765)
+ assert type(r.string) == list
+ assert 'NC_012920(ND4_v001)' in r.string
+
+
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscriptsrange_lrg(api):
+ """
+ Running getTranscriptsRange should give us overlapping transcripts.
+ list of transcripts including LRG transcripts.
+ """
+ r = api('getTranscriptsRange', 'hg19', 'chr1', 207646118, 207646118, 1)
+ assert type(r.string) == list
+ assert 'LRG_348t1' in r.string
+
+
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscriptsrange_mtdna(api):
+ """
+ Running getTranscripts should give us overlapping transcripts.
+ list of transcripts, also on chrM.
+ """
+ r = api('getTranscriptsRange', 'hg19', 'chrM', 10765, 10765, 1)
+ assert type(r.string) == list
+ assert 'NC_012920(ND4_v001)' in r.string
+
+
@pytest.mark.usefixtures('hg19_transcript_mappings')
def test_gettranscriptsbygenename_valid(api):
"""
@@ -180,6 +226,28 @@ def test_gettranscriptsbygenename_valid(api):
assert t in r.string
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscriptsbygenename_valid_lrg(api):
+ """
+ Running getTranscriptsByGeneName with valid gene name should give a
+ list of transcripts including LRG transcripts.
+ """
+ r = api('getTranscriptsByGeneName', build='hg19', name='CR2')
+ assert type(r.string) == list
+ assert 'LRG_348t1' in r.string
+
+
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscriptsbygenename_valid_mtdna(api):
+ """
+ Running getTranscriptsByGeneName with valid gene name should give a
+ list of transcripts also on chrM.
+ """
+ r = api('getTranscriptsByGeneName', build='hg19', name='ND4')
+ assert type(r.string) == list
+ assert 'NC_012920.1(ND4_v001)' in r.string
+
+
@pytest.mark.usefixtures('hg19_transcript_mappings')
def test_gettranscriptsbygenename_invalid(api):
"""