From 8590f9b9e002fa9f75dc605252575088194d0eba Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 12 Feb 2013 12:20:33 +0000
Subject: [PATCH] Include exon table for selected transcript in webservice
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@668 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/runMutalyzer.py | 6 ++++++
mutalyzer/models.py | 32 ++++++++++++++++---------------
mutalyzer/services/rpc.py | 13 +++++++++++++
tests/test_services_soap.py | 25 +++++++++++++++++++++---
4 files changed, 58 insertions(+), 18 deletions(-)
diff --git a/extras/soap-tools/runMutalyzer.py b/extras/soap-tools/runMutalyzer.py
index 852e467b..0a2d1e75 100755
--- a/extras/soap-tools/runMutalyzer.py
+++ b/extras/soap-tools/runMutalyzer.py
@@ -76,6 +76,12 @@ def main(description, verbosity=None):
print 'Affected proteins:'
print '\n'.join(result.proteinDescriptions.string)
+ if 'exons' in result:
+ print '\nExon table for selected transcript:'
+ print '\t'.join(['Number', 'Start (g.)', 'Stop (g.)', 'Start (c.)', 'Stop (c.)'])
+ for i, exon in enumerate(result.exons.ExonInfo, start=1):
+ print '\t'.join([str(i), str(exon.gStart), str(exon.gStop), exon.cStart, exon.cStop])
+
if __name__ == '__main__':
if len(sys.argv) < 2:
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index cd1a4637..1665d68d 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -123,6 +123,21 @@ class Allele(ComplexModel):
#Allele
+class ExonInfo(ComplexModel):
+ """
+ Used in TranscriptInfo and MutalyzerOutput data types.
+ """
+ __namespace__ = SOAP_NAMESPACE
+
+ cStart = Mandatory.String
+ gStart = Mandatory.Integer
+ chromStart = Integer
+ cStop = Mandatory.String
+ gStop = Mandatory.Integer
+ chromStop = Integer
+#ExonInfo
+
+
class MutalyzerOutput(ComplexModel):
"""
Return type of SOAP method runMutalyzer.
@@ -158,6 +173,8 @@ class MutalyzerOutput(ComplexModel):
transcriptDescriptions = Array(String)
proteinDescriptions = Array(String)
+ exons = Array(ExonInfo)
+
rawVariants = Array(RawVariant)
messages = Array(SoapMessage)
@@ -175,21 +192,6 @@ class TranscriptNameInfo(ComplexModel):
#TranscriptNameInfo
-class ExonInfo(ComplexModel):
- """
- Used in TranscriptInfo data type.
- """
- __namespace__ = SOAP_NAMESPACE
-
- cStart = Mandatory.String
- gStart = Mandatory.Integer
- chromStart = Integer
- cStop = Mandatory.String
- gStop = Mandatory.Integer
- chromStop = Integer
-#ExonInfo
-
-
class ProteinTranscript(ComplexModel):
"""
Used in TranscriptInfo data type.
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 1866df35..9b676542 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -763,6 +763,12 @@ class MutalyzerService(ServiceBase):
represented by an object with fields:
- description: Description of the raw variant.
- visualisation: ASCII visualisation of the raw variant.
+ - exons: If a transcript is selected, array of ExonInfo objects
+ for each exon in the selected transcript with fields:
+ - cStart
+ - gStart
+ - cStop
+ - gStop
- messages: List of (error) messages.
"""
O = Output(__file__)
@@ -804,6 +810,13 @@ class MutalyzerService(ServiceBase):
result.transcriptDescriptions = O.getOutput("descriptions")
result.proteinDescriptions = O.getOutput("protDescriptions")
+ if O.getIndexedOutput('hasTranscriptInfo', 0, False):
+ result.exons = []
+ for e in O.getOutput('exonInfo'):
+ exon = ExonInfo()
+ exon.gStart, exon.gStop, exon.cStart, exon.cStop = e
+ result.exons.append(exon)
+
raw_variants = []
for v in O.getOutput("visualisation"):
r = RawVariant()
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index c610645a..135983f0 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -28,7 +28,8 @@ logging.basicConfig(level=logging.INFO)
for logger in ('suds.metrics', 'suds.wsdl', 'suds.xsd.schema',
'suds.xsd.sxbasic', 'suds.xsd.sxbase', 'suds.xsd.query',
'suds.transport.http', 'suds.xsd.deplist', 'suds.mx.core',
- 'suds.mx.literal', 'suds.resolver', 'suds.client'):
+ 'suds.mx.literal', 'suds.resolver', 'suds.client',
+ 'suds.umx.typed'):
logging.getLogger(logger).setLevel(logging.ERROR)
@@ -59,8 +60,8 @@ class TestServicesSoap():
@todo: Start the standalone server and stop it in self.tearDown
instead of depending on some running instance at a fixed address.
"""
- self.client = Client(WSDL_URL) #, cache=None)
- self.client.options.cache.setduration(seconds=120)
+ self.client = Client(WSDL_URL, cache=None)
+ #self.client.options.cache.setduration(seconds=120)
def test_checksyntax_valid(self):
"""
@@ -472,6 +473,24 @@ class TestServicesSoap():
assert_equal(r.sourceGi, '256574794')
assert_equal(r.molecule, 'g')
+ def test_runmutalyzer_exons(self):
+ """
+ Exon table in runMutalyzer output.
+ """
+ r = self.client.service.runMutalyzer('NM_004959.4:c.630_636del')
+ assert_equal(r.errors, 0)
+ expected_exons = [(1, 172, '-187', '-16'),
+ (173, 289, '-15', '102'),
+ (290, 431, '103', '244'),
+ (432, 1057, '245', '870'),
+ (1058, 1177, '871', '990'),
+ (1178, 1325, '991', '1138'),
+ (1326, 3095, '1139', '*1522')]
+ assert_equal(len(r.exons.ExonInfo), len(expected_exons))
+ for exon, expected_exon in zip(r.exons.ExonInfo, expected_exons):
+ assert_equal((exon.gStart, exon.gStop, exon.cStart, exon.cStop),
+ expected_exon)
+
def test_gettranscriptsandinfo_slice(self):
"""
Running getTranscriptsAndInfo on a chromosomal slice should include
--
GitLab