diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 73a99c48994c3240b13875057bef2f113b823236..8d47461bb4457bdbee805a1a6975e138428b5586 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -468,6 +468,38 @@ class TranscriptMapping(db.Base):
def cds(self, cds):
self.cds_start, self.cds_stop = cds or (None, None)
+ def get_reference(self, include_version=True):
+ """
+ Get fully qualified reference for this transcript.
+
+ You would usually want to use the simpler :attr:`reference` property
+ instead, except if the accession number may not include version number
+ (which we consider bad practice).
+ """
+ if include_version and self.version:
+ accession = '%s.%i' % (self.accession, self.version)
+ else:
+ accession = self.accession
+
+ if self.select_transcript:
+ if self.reference_type == 'lrg':
+ selector = 't%d' % self.transcript
+ elif self.transcript:
+ selector = '(%s_v%.3i)' % (self.gene, self.transcript)
+ else:
+ selector = '(%s)' % self.gene
+ else:
+ selector = ''
+
+ return '%s%s' % (accession, selector)
+
+ @property
+ def reference(self):
+ """
+ Fully qualified reference for this transcript.
+ """
+ return self.get_reference()
+
Index('transcript_mapping_transcript',
TranscriptMapping.accession, TranscriptMapping.version,
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index d71f3aeaec8e31e989413872fb3f2e83f335bd62..e0ae81adfa79088b804bf1add7d66520ce74ed93 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -735,20 +735,7 @@ class Converter(object) :
if not core_mapping:
#balen
continue
- # construct the variant description
- if self.mapping.reference_type == 'lrg':
- accNo = self.mapping.accession
- else:
- accNo = "%s.%s" % (self.mapping.accession, self.mapping.version)
- if self.mapping.select_transcript:
- if self.mapping.reference_type == 'lrg':
- selector = 't%d' % self.mapping.transcript
- elif self.mapping.transcript:
- selector = '(%s_v%.3i)' % (self.mapping.gene, self.mapping.transcript)
- else:
- selector = '(%s)' % self.mapping.gene
- else:
- selector = ''
+ reference = self.mapping.reference
geneName = self.mapping.gene
strand = self.mapping.orientation == 'forward'
@@ -798,7 +785,7 @@ class Converter(object) :
else:
mutation = '[' + ';'.join(mutations) + ']'
- description = "%s%s:%c.%s" % (accNo, selector, mtype, mutation)
+ description = "%s:%c.%s" % (reference, mtype, mutation)
HGVS_notatations[geneName].append(description)
NM_list.append(description)
#for
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 93ca06898087fb1273e2cfc6aeb506fe84190187..767c6a5f811ec637fc09f77b7f26f8c055c1a5f5 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -264,24 +264,8 @@ class MutalyzerService(ServiceBase):
"Finished processing getTranscripts(%s %s %s %s)"
% (build, chrom, pos, versions))
- 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
+ return [mapping.get_reference(include_version=versions)
+ for mapping in mappings]
#getTranscripts
@srpc(Mandatory.Unicode, Mandatory.Unicode, _returns=Array(Mandatory.Unicode))
@@ -309,24 +293,7 @@ class MutalyzerService(ServiceBase):
L.addMessage(__file__, -1, "INFO",
"Finished processing getTranscriptsByGene(%s %s)" % (build, name))
- 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
+ return [mapping.reference for mapping in mappings]
#getTranscriptsByGeneName
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
@@ -414,24 +381,8 @@ class MutalyzerService(ServiceBase):
"Finished processing getTranscriptsRange(%s %s %s %s %s)" % (
build, chrom, pos1, pos2, method))
- 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
+ return [mapping.get_reference(include_version=versions)
+ for mapping in mappings]
#getTranscriptsRange
@srpc(Mandatory.Unicode, Mandatory.Unicode, Mandatory.Integer,
@@ -527,22 +478,7 @@ class MutalyzerService(ServiceBase):
for mapping in mappings:
t = TranscriptMappingInfo()
-
- 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.transcript = mapping.reference
t.name = mapping.accession
t.version = mapping.version
t.gene = mapping.gene