diff --git a/extras/soap-tools/getTranscriptsAndInfo.py b/extras/soap-tools/getTranscriptsAndInfo.py
index ce3b1a223c562a50595c9e0aca03a3c08eed6650..ee5a9e72ddee475713f003527cee930d625688cd 100755
--- a/extras/soap-tools/getTranscriptsAndInfo.py
+++ b/extras/soap-tools/getTranscriptsAndInfo.py
@@ -40,15 +40,18 @@ def main(genomic_reference, gene=None):
Locus tag: %s
Link method: %s
Translation:
- Start: %s (c), %s (g)
- End: %s (c), %s (g)
+ Start: %s (c), %s (g), %s (chrom)
+ End: %s (c), %s (g), %s (chrom)
Sortable end: %s
CDS:
- Start: %s (c), %s (g)
- End: %s (c), %s (g)""" % \
+ Start: %s (c), %s (g), %s (chrom)
+ End: %s (c), %s (g), %s (chrom)""" % \
(t.name, t.id, t.product, t.locusTag, t.linkMethod, t.cTransStart,
- t.gTransStart, t.cTransEnd, t.gTransEnd, t.sortableTransEnd,
- t.cCDSStart, t.gCDSStart, t.cCDSStop, t.gCDSStop)
+ t.gTransStart, t.chromTransStart if 'chromTransStart' in t else '-',
+ t.cTransEnd, t.gTransEnd, t.chromTransEnd if 'chromTransEnd' in t else '-',
+ t.sortableTransEnd, t.cCDSStart, t.gCDSStart,
+ t.chromCDSStart if 'chromCDSStart' in t else '-', t.cCDSStop, t.gCDSStop,
+ t.chromCDSStop if 'chromCDSStop' in t else '-')
if 'proteinTranscript' in t:
print """ Protein:
@@ -61,8 +64,10 @@ def main(genomic_reference, gene=None):
if 'exons' in t:
print ' Exons:'
for e in t.exons.ExonInfo:
- print ' %s - %s (c), %s - %s (g)' % \
- (e.cStart, e.cStop, e.gStart, e.gStop)
+ print ' %s - %s (c), %s - %s (g), %s - %s (chrom)' % \
+ (e.cStart, e.cStop, e.gStart, e.gStop,
+ e.chromStart if 'chromStart' in e else '-',
+ e.chromStop if 'chromStop' in e else '-')
if __name__ == '__main__':
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index 90d50c0f16a67764cc83e49944b9fc8bf04e976d..91ddb1994c9cacd1506391ee476c65dbff00e34b 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -351,6 +351,8 @@ class Record(object) :
@return: chromosomal g. position
@rtype: integer
"""
+ if not self.chromOffset:
+ return None
if self.orientation == 1 :
return self.chromOffset + i - 1
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index d539e91356e6ff2a20046716b58ebad4dbea8fb1..41c3afd82ad45a256e1d6c49b6660d5cef7cf37e 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -147,8 +147,10 @@ class ExonInfo(ClassModel):
cStart = Mandatory.String
gStart = Mandatory.Integer
+ chromStart = Integer
cStop = Mandatory.String
gStop = Mandatory.Integer
+ chromStop = Integer
#ExonInfo
@@ -168,9 +170,11 @@ class TranscriptInfo(ClassModel):
"""
Used in return type of SOAP method getTranscriptsAndInfo.
- @todo: Decide on 'stop' versus 'end'. Web interface uses 'stop' for
- both trans and CDS. Ivar asked for 'end'. Internally, we have
- trans 'end' and CDS 'stop'.
+ @todo: Decide on 'stop' versus 'end'. Web interface uses 'stop' for both
+ trans and CDS. Ivar asked for 'end'. Internally, we have trans 'end'
+ and CDS 'stop'.
+ @todo: We should really also provide the chromosome (or its accession
+ number) next to the chromosomal positions, if available.
"""
__namespace__ = SOAP_NAMESPACE
@@ -180,14 +184,18 @@ class TranscriptInfo(ClassModel):
cTransStart = Mandatory.String
gTransStart = Mandatory.Integer
+ chromTransStart = Integer
cTransEnd = Mandatory.String
gTransEnd = Mandatory.Integer
+ chromTransEnd = Integer
sortableTransEnd = Mandatory.Integer
cCDSStart = Mandatory.String
gCDSStart = Mandatory.Integer
+ chromCDSStart = Integer
cCDSStop = Mandatory.String
gCDSStop = Mandatory.Integer
+ chromCDSStop = Integer
locusTag = Mandatory.String
linkMethod = Mandatory.String
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index 34568dc2bc1f3ddc94dd55e75665578d4a6c451c..b6d384ff80c33a7b6a979d6cedb51a39cd36b597 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -501,7 +501,11 @@ class GBparser():
geneDict = {}
accInfo = biorecord.annotations['accessions']
- if len(accInfo) >= 3 and accInfo[1] == "REGION:" :
+ if len(accInfo) >= 3 and accInfo[1] == "REGION:":
+ # Todo: This information is present in the genbank file if it is a
+ # UD sliced from a chromosome. We can get the same information
+ # for NM references from our mapping database and that way
+ # also provide chromosomal variant descriptions for those.
region = accInfo[2]
if "complement" in region :
record.orientation = -1
diff --git a/mutalyzer/webservice.py b/mutalyzer/webservice.py
index 8230647bce26c85ee9c1f377c7a81e75083be706..71c3447b6991e488ca54ed4f866383b231674aea 100644
--- a/mutalyzer/webservice.py
+++ b/mutalyzer/webservice.py
@@ -787,20 +787,26 @@ class MutalyzerService(DefinitionBase):
- product
- cTransStart
- gTransStart
+ - chromTransStart
- cTransEnd
- gTransEnd
+ - chromTransEnd
- sortableTransEnd
- cCDSStart
- gCDSStart
+ - chromCDSStart
- cCDSStop
- gCDSStop
+ - chromCDSStop
- locusTag
- linkMethod
- exons: Array of ExonInfo objects with fields:
- cStart
- gStart
+ - chromStart
- cStop
- gStop
+ - chromStop
- proteinTranscript: ProteinTranscript object with fields:
- name
- id
@@ -847,8 +853,10 @@ class MutalyzerService(DefinitionBase):
exon = ExonInfo()
exon.gStart = transcript.CM.getSpliceSite(i)
exon.cStart = transcript.CM.g2c(exon.gStart)
+ exon.chromStart = GenRecordInstance.record.toChromPos(exon.gStart)
exon.gStop = transcript.CM.getSpliceSite(i + 1)
exon.cStop = transcript.CM.g2c(exon.gStop)
+ exon.chromStop = GenRecordInstance.record.toChromPos(exon.gStop)
t.exons.append(exon)
# Beware that CM.info() gives a made-up value for trans_end,
@@ -861,6 +869,7 @@ class MutalyzerService(DefinitionBase):
t.cTransEnd = str(t.exons[-1].cStop)
t.gTransEnd = t.exons[-1].gStop
+ t.chromTransEnd = GenRecordInstance.record.toChromPos(t.gTransEnd)
t.sortableTransEnd = sortable_trans_end
# Todo: If we have no CDS info, CM.info() gives trans_end as
@@ -873,10 +882,13 @@ class MutalyzerService(DefinitionBase):
t.product = transcript.transcriptProduct
t.cTransStart = str(trans_start)
t.gTransStart = transcript.CM.x2g(trans_start, 0)
+ t.chromTransStart = GenRecordInstance.record.toChromPos(t.gTransStart)
t.cCDSStart = str(cds_start)
t.gCDSStart = transcript.CM.x2g(cds_start, 0)
+ t.chromCDSStart = GenRecordInstance.record.toChromPos(t.gCDSStart)
t.cCDSStop = str(cds_stop)
t.gCDSStop = transcript.CM.x2g(cds_stop, 0)
+ t.chromCDSStop = GenRecordInstance.record.toChromPos(t.gCDSStop)
t.locusTag = transcript.locusTag
t.linkMethod = transcript.linkMethod
@@ -948,6 +960,10 @@ class MutalyzerService(DefinitionBase):
def sliceChromosome(self, chromAccNo, start, end, orientation) :
"""
Todo: documentation, error handling, argument checking, tests.
+
+ @arg orientation: Orientation of the slice. 1 for forward, 2 for
+ reverse complement.
+ @type orientation: integer
"""
O = Output(__file__)
D = Db.Cache()
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index f50ecc3e3597969755d9d69fd77982fdd8006e0a..775e5521569b59305a434a64ee08567ac99cd339 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -59,8 +59,8 @@ class TestWebservice():
@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):
"""
@@ -400,3 +400,37 @@ class TestWebservice():
assert_equal(r.sourceVersion, '1')
assert_equal(r.sourceGi, '256574794')
assert_equal(r.molecule, 'g')
+
+ @skip
+ def test_gettranscriptsandinfo_slice(self):
+ """
+ Running getTranscriptsAndInfo on a chromosomal slice should include
+ chromosomal positions.
+
+ slice: 48284000 - 48259456 (COL1A1 with 5001 and 2001 borders)
+ translation start: 48284000 - 5001 + 1 = 48279000
+ translation end: 48259456 + 2001 = 48261457
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ r = self.client.service.getTranscriptsAndInfo('UD_129646580028')
+ assert_equal(type(r.TranscriptInfo), list)
+ names = [t.name for t in r.TranscriptInfo]
+ assert 'COL1A1_v001' in names
+ for t in r.TranscriptInfo:
+ if t.name != 'COL1A1_v001':
+ continue
+ assert_equal(t.cTransStart, '-126')
+ assert_equal(t.gTransStart, 5001)
+ assert_equal(t.chromTransStart, 48279000)
+ assert_equal(t.cTransEnd, '*1406')
+ assert_equal(t.gTransEnd, 22544)
+ assert_equal(t.chromTransEnd, 48261457)
+ assert_equal(t.sortableTransEnd, 5801)
+ assert_equal(t.cCDSStart, '1')
+ assert_equal(t.gCDSStart, 5127)
+ assert_equal(t.chromCDSStart, 48278874)
+ assert_equal(t.cCDSStop, '4395')
+ assert_equal(t.gCDSStop, 21138)
+ assert_equal(t.chromCDSStop, 48262863)