diff --git a/migrations/versions/56ddeb75114e_add_ebi_to_mappings_source_enum.py b/migrations/versions/56ddeb75114e_add_ebi_to_mappings_source_enum.py
new file mode 100644
index 0000000000000000000000000000000000000000..7556cedd329cb0517ebfad71ce6a09501b978477
--- /dev/null
+++ b/migrations/versions/56ddeb75114e_add_ebi_to_mappings_source_enum.py
@@ -0,0 +1,64 @@
+"""Add EBI to mappings source enum
+
+Revision ID: 56ddeb75114e
+Revises: 1ed411f9fdfa
+Create Date: 2016-02-11 04:21:40.658981
+
+"""
+
+from __future__ import unicode_literals
+
+# revision identifiers, used by Alembic.
+revision = '56ddeb75114e'
+down_revision = u'1ed411f9fdfa'
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+ context = op.get_context()
+
+ if context.bind.dialect.name == 'postgresql':
+ # In PostgreSQL < 9.1 there was no ALTER TYPE for enums, so it would
+ # have been something like:
+ #
+ # ALTER TABLE foo ALTER COLUMN bar TYPE new_type USING bar::text::new_type;
+ #
+ # However, all my installations are PostgreSQL >= 9.1 and I think the
+ # USING syntax is PostgreSQL-specific, so let's ignore that. It would
+ # also come with all the hassle of moving old column values into the
+ # new column.
+ if context.bind.dialect.server_version_info >= (9, 3):
+ op.execute('COMMIT')
+ op.execute("ALTER TYPE source ADD VALUE IF NOT EXISTS 'ebi'")
+ return
+ if context.bind.dialect.server_version_info >= (9, 1):
+ op.execute('COMMIT')
+ op.execute("ALTER TYPE source ADD VALUE 'ebi'")
+ return
+
+ elif context.bind.dialect.name == 'sqlite':
+ # SQLite doesn't support altering columns, so we have to wrap this in
+ # a batch operation.
+ with op.batch_alter_table('transcript_mappings') as batch_op:
+ batch_op.alter_column(
+ 'source', nullable=False,
+ type_=sa.Enum('ucsc', 'ncbi', 'ebi', 'reference', name='source')
+ )
+ return
+
+ elif context.bind.dialect.name == 'mysql':
+ # In MySQL we can simply alter the column.
+ op.alter_column(
+ 'transcript_mappings', 'source', nullable=False,
+ type_=sa.Enum('ucsc', 'ncbi', 'ebi', 'reference', name='source'),
+ existing_type=sa.Enum('ucsc', 'ncbi', 'reference', name='source')
+ )
+ return
+
+ raise Exception('Sorry, only PostgreSQL >= 9.1, SQLite, and MySQL are supported by this migration')
+
+
+def downgrade():
+ raise Exception('Downgrade not supported by this migration')
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index b6e397e34bd543e02f729243edfa17a493a79b07..73a99c48994c3240b13875057bef2f113b823236 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -375,11 +375,11 @@ class TranscriptMapping(db.Base):
#: If `False`, variant descriptions can use just the accession number
#: without gene and transcript selector (e.g., ``NM_000020:c.1del``,
#: ``LRG_1:c.1del``). If `True`, gene and transcript selection is
- #: necessary (e.g., ``NC_012920(TRNI_v001):c.1del``, ``LRG_1_t1:c.1del``).
+ #: necessary (e.g., ``NC_012920(TRNI_v001):c.1del``, ``LRG_1t1:c.1del``).
select_transcript = Column(Boolean, nullable=False)
#: Source of the mapping.
- source = Column(Enum('ucsc', 'ncbi', 'reference', name='source'),
+ source = Column(Enum('ucsc', 'ncbi', 'ebi', 'reference', name='source'),
nullable=False)
#: The :class:`Assembly` this chromosome is in.
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index b9a55afefdec70ecddbb1dd98eede58420ec95f1..31e67e4d210c543b76831ec67344a70c2db49184 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -151,9 +151,9 @@ class Converter(object) :
"Could not parse the given variant")
return None
#if
- if not parseTree.RefSeqAcc: #In case of LRG for example
+ if not (parseTree.RefSeqAcc or parseTree.LrgAcc):
self.__output.addMessage(__file__, 4, "EONLYGB",
- "Currently we only support GenBank Records")
+ "Currently we only support GenBank and LRG records")
return None
#if
self.parseTree = parseTree
@@ -175,7 +175,6 @@ class Converter(object) :
"""
versions = [m.version for m in TranscriptMapping.query.filter(
TranscriptMapping.accession == acc,
- TranscriptMapping.version != None,
TranscriptMapping.chromosome.has(assembly=self.assembly))]
if not versions:
@@ -207,10 +206,10 @@ class Converter(object) :
if not self.mapping:
self.__output.addMessage(__file__, 4, "EACCNOTINDB",
- "The accession number %s version %s "
+ "The accession number %s %s"
"with transcript %s version %s could not be found "
"in our database." %
- (acc, version, selector, selector_version))
+ (acc, 'version %s ' % version if version else '', selector, selector_version))
return
if not version:
@@ -417,7 +416,7 @@ class Converter(object) :
"""
variant = "%s:%s" % (accNo, mutation)
if self._parseInput(variant) :
- acc = self.parseTree.RefSeqAcc
+ acc = self.parseTree.LrgAcc or self.parseTree.RefSeqAcc
try:
version = int(self.parseTree.Version)
except ValueError:
@@ -503,7 +502,7 @@ class Converter(object) :
@rtype: unicode
"""
if self._parseInput(variant):
- acc = self.parseTree.RefSeqAcc
+ acc = self.parseTree.LrgAcc or self.parseTree.RefSeqAcc
try:
version = int(self.parseTree.Version)
except ValueError:
@@ -511,6 +510,10 @@ class Converter(object) :
if self.parseTree.Gene:
selector = self.parseTree.Gene.GeneSymbol
selector_version = int(self.parseTree.Gene.TransVar or 1)
+ elif self.parseTree.LRGTranscriptID:
+ selector = None
+ selector_version = int(self.parseTree.LRGTranscriptID)
+ pass
else:
selector = selector_version = None
self._get_mapping(acc, version, selector, selector_version)
@@ -669,7 +672,7 @@ class Converter(object) :
if not self._parseInput(variant) :
return None
- acc = self.parseTree.RefSeqAcc
+ acc = self.parseTree.LrgAcc or self.parseTree.RefSeqAcc
version = self.parseTree.Version
chromosome = Chromosome.query \
@@ -733,9 +736,14 @@ class Converter(object) :
#balen
continue
# construct the variant description
- accNo = "%s.%s" % (self.mapping.accession, self.mapping.version)
+ 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.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
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 9cf89b9c979e558241f0f90640a7e8f9cbe5e3a4..e0137d9330aef341b422aa154309af15c5e8cb3b 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -558,7 +558,7 @@ class MutalyzerService(ServiceBase):
@type LOVD_ver: string
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
- @arg accNo: The NM accession number and version.
+ @arg accNo: The NM accession number and version or LRG.
@type accNo: string
@arg variant: The variant.
@type variant: string
@@ -614,7 +614,7 @@ class MutalyzerService(ServiceBase):
@type LOVD_ver: string
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
- @arg accNo: The NM accession number and version.
+ @arg accNo: The NM accession number and version or LRG.
@type accNo: string
@return: Complex object:
@@ -729,7 +729,7 @@ class MutalyzerService(ServiceBase):
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
- @arg acc: The NM accession number (version NOT included).
+ @arg acc: The NM accession number (version NOT included) or LRG.
@type acc: string
@return: The name of a chromosome.
@@ -768,7 +768,7 @@ class MutalyzerService(ServiceBase):
@arg build: The genome build (hg19, hg18, mm10).
@type build: string
@arg variant: The variant in either I{c.} or I{g.} notation, full HGVS
- notation, including NM_ or NC_ accession number.
+ notation, including NM_, NC_, or LRG_ accession number.
@type variant: string
@kwarg gene: Optional gene name. If given, return variant descriptions
on all transcripts for this gene.
diff --git a/mutalyzer/website/templates/position-converter.html b/mutalyzer/website/templates/position-converter.html
index 0db57523fd018b27136e7e3cf98ec9217e1cbcc5..db9c6c1ae4beae009b26796ace56e21e6211b6dc 100644
--- a/mutalyzer/website/templates/position-converter.html
+++ b/mutalyzer/website/templates/position-converter.html
@@ -29,8 +29,16 @@ normalize it to HGVS. Use the <a href="{{ url_for('.name_checker') }}">Name Chec
<label for="description">Variant description</label>
<input type="text" name="description" id="description" value="{{ description }}"
class="form-control form-pre" placeholder="Variant description using HGVS format">
- <p>Examples: <code class="example-input"
- data-for="description">NM_003002.3:c.274G>T</code>, <code class="example-input" data-for="description">chr11:g.111959693G>T</code> and <code class="example-input" data-for="description">NC_000011.9:g.111959693G>T</code></p>
+ <p>Examples:
+ <code class="example-input"
+ data-for="description">NM_003002.3:c.274G>T</code>,
+ <code class="example-input"
+ data-for="description">LRG_9t1:c.274G>T</code>,
+ <code class="example-input"
+ data-for="description">chr11:g.111959693G>T</code> and
+ <code class="example-input"
+ data-for="description">NC_000011.9:g.111959693G>T</code>
+ </p>
</div>
<div class="form-group button-group">
<input type="submit" class="btn btn-primary" value="Convert variant description">
diff --git a/tests/fixtures.py b/tests/fixtures.py
index f96a9c3a82c62d83e166d77265107ad79681f604..28e168f12e12d62473b5984597b9d2eab76fbdea 100644
--- a/tests/fixtures.py
+++ b/tests/fixtures.py
@@ -593,6 +593,54 @@ def hg19_transcript_mappings(db, hg19):
cds=(37035039, 37092144),
select_transcript=False,
version=3))
+ db.session.add(TranscriptMapping(
+ hg19.chromosomes.filter_by(name='chr17').one(),
+ 'lrg',
+ 'LRG_1',
+ 'COL1A1',
+ 'reverse',
+ 48261457,
+ 48279000,
+ [48261457, 48263139, 48263678, 48264001, 48264376, 48264845, 48265237,
+ 48265457, 48265891, 48266103, 48266264, 48266529, 48266738, 48267040,
+ 48267220, 48267362, 48267688, 48267904, 48268178, 48268744, 48269149,
+ 48269341, 48269836, 48270001, 48270158, 48270355, 48271304, 48271491,
+ 48271710, 48271934, 48272082, 48272408, 48272593, 48272795, 48272928,
+ 48273284, 48273516, 48273675, 48273845, 48273978, 48274371, 48274541,
+ 48275093, 48275310, 48275522, 48275794, 48276587, 48276779, 48276917,
+ 48277114, 48278772],
+ [48263009, 48263381, 48263868, 48264283, 48264483, 48264898, 48265344,
+ 48265510, 48265998, 48266156, 48266371, 48266636, 48266899, 48267093,
+ 48267273, 48267469, 48267741, 48267957, 48268285, 48268851, 48269247,
+ 48269385, 48269889, 48270054, 48270211, 48270408, 48271402, 48271544,
+ 48271808, 48271987, 48272189, 48272461, 48272691, 48272839, 48273026,
+ 48273337, 48273560, 48273728, 48273889, 48274031, 48274424, 48274594,
+ 48275146, 48275363, 48275566, 48275865, 48276688, 48276814, 48276951,
+ 48277308, 48279000],
+ 'ebi',
+ transcript=1,
+ cds=(48262863, 48278874),
+ select_transcript=True))
+ db.session.add(TranscriptMapping(
+ hg19.chromosomes.filter_by(name='chr1').one(),
+ 'lrg',
+ 'LRG_348',
+ 'CR2',
+ 'forward',
+ 207627645,
+ 207663240,
+ [207627645, 207639871, 207641872, 207642145, 207642495, 207643040,
+ 207644085, 207644342, 207644768, 207646117, 207646890, 207647146,
+ 207647586, 207648169, 207649579, 207651230, 207652602, 207653323,
+ 207658809, 207662487],
+ [207627821, 207640257, 207642060, 207642244, 207642577, 207643447,
+ 207644261, 207644432, 207644844, 207646524, 207647066, 207647230,
+ 207647668, 207648561, 207649764, 207651415, 207652625, 207653398,
+ 207658917, 207663240],
+ 'ebi',
+ transcript=1,
+ cds=(207627764, 207658899),
+ select_transcript=True))
db.session.commit()
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 30b4c7efd8bebd9f0fa650a73b6ac88c763efed6..8ce9d64418db2a5566fbcacc87f9c32d792d989c 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -14,6 +14,39 @@ from mutalyzer.db.models import TranscriptMapping
from mutalyzer import mapping
+# Some example positional coding/chromosomal mappings we use in the tests.
+LRG_1_T1_POSITIONS = [
+ ('-150', 48279024),
+ ('-126', 48279000),
+ ('-1', 48278875),
+ ('1', 48278874),
+ ('103', 48278772),
+ ('103+5', 48278767),
+ ('104-5', 48277313),
+ ('104', 48277308),
+ ('870', 48273878),
+ ('4248', 48263139),
+ ('4249', 48263009),
+ ('4395', 48262863),
+ ('*1', 48262862),
+ ('*1406', 48261457),
+ ('*1407', 48261456),
+ ('*1417', 48261446)]
+LRG_348_T1_POSITIONS = [
+ ('-150', 207627614),
+ ('-119', 207627645),
+ ('-1', 207627763),
+ ('1', 207627764),
+ ('58', 207627821),
+ ('58+5', 207627826),
+ ('59-5', 207639866),
+ ('59', 207639871),
+ ('3279', 207658899),
+ ('*1', 207658900),
+ ('*772', 207663240),
+ ('*780', 207663248)]
+
+
pytestmark = pytest.mark.usefixtures('hg19_transcript_mappings')
@@ -328,6 +361,44 @@ def test_ins_seq_seq_c2chrom_reverse(converter):
assert genomic == 'NC_000011.9:g.111957482_111957483ins[GAT;AAA]'
+@pytest.mark.parametrize('coding,chromosomal', LRG_1_T1_POSITIONS)
+def test_lrg_1t1_c2chrom(converter, coding, chromosomal):
+ """
+ Conversion from LRG reference on reverse strand.
+ """
+ chromosomal_descr = converter.c2chrom('LRG_1t1:c.%sdel' % coding)
+ assert chromosomal_descr == 'NC_000017.10:g.%ddel' % chromosomal
+
+
+@pytest.mark.parametrize('coding,chromosomal', LRG_1_T1_POSITIONS)
+def test_lrg_1t1_chrom2c(converter, coding, chromosomal):
+ """
+ Conversion to LRG reference on reverse strand.
+ """
+ coding_descr = converter.chrom2c(
+ 'NC_000017.10:g.%ddel' % chromosomal, 'list')
+ assert 'LRG_1t1:c.%sdel' % coding in coding_descr
+
+
+@pytest.mark.parametrize('coding,chromosomal', LRG_348_T1_POSITIONS)
+def test_lrg_348t1_c2chrom(converter, coding, chromosomal):
+ """
+ Conversion from LRG reference on forward strand.
+ """
+ chromosomal_descr = converter.c2chrom('LRG_348t1:c.%sdel' % coding)
+ assert chromosomal_descr == 'NC_000001.10:g.%ddel' % chromosomal
+
+
+@pytest.mark.parametrize('coding,chromosomal', LRG_348_T1_POSITIONS)
+def test_lrg_348t1_chrom2c(converter, coding, chromosomal):
+ """
+ Conversion to LRG reference on forward strand.
+ """
+ coding_descr = converter.chrom2c(
+ 'NC_000001.10:g.%ddel' % chromosomal, 'list')
+ assert 'LRG_348t1:c.%sdel' % coding in coding_descr
+
+
def test_import_mapview(hg19):
original_count = TranscriptMapping.query.count()