From af3a57886bc5e0d820ea45276953454cd76ebe9e Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 22 Feb 2016 01:01:07 +0100
Subject: [PATCH] Add transcript in getTranscriptsMapping output
Previously the getTranscriptsMapping webservice method didn't return
enough information to construct a complete transcript name. This is now
reported in a new `transcript` field.
---
mutalyzer/models.py | 1 +
mutalyzer/services/rpc.py | 20 +++++++++++++++++---
tests/test_services_json.py | 3 +++
tests/test_services_soap.py | 19 +++++++++++++++++++
4 files changed, 40 insertions(+), 3 deletions(-)
diff --git a/mutalyzer/models.py b/mutalyzer/models.py
index 7ebade7f..133fc6d8 100644
--- a/mutalyzer/models.py
+++ b/mutalyzer/models.py
@@ -310,6 +310,7 @@ class TranscriptMappingInfo(ComplexModel):
"""
__namespace__ = SOAP_NAMESPACE
+ transcript = Mandatory.Unicode
name = Mandatory.Unicode
version = Mandatory.Integer
gene = Mandatory.Unicode
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index ce2287a8..93ca0689 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -458,6 +458,7 @@ class MutalyzerService(ServiceBase):
- 1 ; Return all hit transcripts.
@return: Array of TranscriptMappingInfo objects with fields:
+ - transcript
- name
- version
- gene
@@ -526,9 +527,22 @@ 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.
+
+ 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 = ''
+ t.transcript = '%s%s' % (accession, selector)
+
t.name = mapping.accession
t.version = mapping.version
t.gene = mapping.gene
diff --git a/tests/test_services_json.py b/tests/test_services_json.py
index e47e306e..76bcb8c4 100644
--- a/tests/test_services_json.py
+++ b/tests/test_services_json.py
@@ -220,6 +220,7 @@ def test_get_transcripts_mapping(api):
r = api('getTranscriptsMapping', 'hg19', 'chr11', 111955524, 111966518)
assert r == [{'cds_start': 111957492,
'cds_stop': 111956019,
+ 'transcript': 'NM_012459.2',
'name': 'NM_012459',
'stop': 111955524,
'start': 111957522,
@@ -228,6 +229,7 @@ def test_get_transcripts_mapping(api):
'orientation': '-'},
{'cds_start': None,
'cds_stop': None,
+ 'transcript': 'NR_028383.1',
'name': 'NR_028383',
'stop': 111955524,
'start': 111957522,
@@ -236,6 +238,7 @@ def test_get_transcripts_mapping(api):
'orientation': '-'},
{'cds_start': 111957632,
'cds_stop': 111965694,
+ 'transcript': 'NM_003002.2',
'name': 'NM_003002',
'stop': 111966518,
'start': 111957571,
diff --git a/tests/test_services_soap.py b/tests/test_services_soap.py
index a02146da..83792b7f 100644
--- a/tests/test_services_soap.py
+++ b/tests/test_services_soap.py
@@ -258,6 +258,22 @@ def test_gettranscriptsbygenename_invalid(api):
assert not r
+@pytest.mark.usefixtures('hg19_transcript_mappings')
+def test_gettranscriptsmapping_mtdna(api):
+ """
+ Running getTranscriptsMapping on mtDNA should give a list of transcripts
+ including their complete identification in the transcript attribute.
+ """
+ r = api('getTranscriptsMapping', 'hg19', 'chrM', 10765, 10765, 1)
+ assert type(r.TranscriptMappingInfo) == list
+ assert len(r.TranscriptMappingInfo) == 1
+ info = r.TranscriptMappingInfo[0]
+ assert 'NC_012920' == info.name
+ assert 1 == info.version
+ assert 'ND4' == info.gene
+ assert 'NC_012920.1(ND4_v001)' == info.transcript
+
+
@with_references('AF230870.1')
def test_gettranscriptsandinfo_valid(api):
"""
@@ -804,6 +820,7 @@ def test_get_transcripts_mapping(api):
for t_real, t_expected in
zip(r.TranscriptMappingInfo, [{'cds_start': 111957492,
'cds_stop': 111956019,
+ 'transcript': 'NM_012459.2',
'name': 'NM_012459',
'stop': 111955524,
'start': 111957522,
@@ -812,6 +829,7 @@ def test_get_transcripts_mapping(api):
'orientation': '-'},
{'cds_start': None,
'cds_stop': None,
+ 'transcript': 'NR_028383.1',
'name': 'NR_028383',
'stop': 111955524,
'start': 111957522,
@@ -820,6 +838,7 @@ def test_get_transcripts_mapping(api):
'orientation': '-'},
{'cds_start': 111957632,
'cds_stop': 111965694,
+ 'transcript': 'NM_003002.2',
'name': 'NM_003002',
'stop': 111966518,
'start': 111957571,
--
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