diff --git a/extras/assemblies/GRCh36.json b/extras/assemblies/GRCh36.json
index 7225d3f855e353b1a72e9df507e0f777e223c212..ca0459f631fa01b74b7cf8aa211f04f99bf9824b 100644
--- a/extras/assemblies/GRCh36.json
+++ b/extras/assemblies/GRCh36.json
@@ -5,137 +5,137 @@
"taxonomy_common_name": "Homo sapiens",
"chromosomes": [
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr1",
"accession": "NC_000001.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr2",
"accession": "NC_000002.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr3",
"accession": "NC_000003.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr4",
"accession": "NC_000004.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr5",
"accession": "NC_000005.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6",
"accession": "NC_000006.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr7",
"accession": "NC_000007.12"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr8",
"accession": "NC_000008.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr9",
"accession": "NC_000009.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr10",
"accession": "NC_000010.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr11",
"accession": "NC_000011.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr12",
"accession": "NC_000012.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr13",
"accession": "NC_000013.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr14",
"accession": "NC_000014.7"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr15",
"accession": "NC_000015.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr16",
"accession": "NC_000016.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr17",
"accession": "NC_000017.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr18",
"accession": "NC_000018.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr19",
"accession": "NC_000019.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr20",
"accession": "NC_000020.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr21",
"accession": "NC_000021.7"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr22",
"accession": "NC_000022.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrX",
"accession": "NC_000023.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrY",
"accession": "NC_000024.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_cox_hap1",
"accession": "NT_113891.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr22_h2_hap1",
"accession": "NT_113959.1"
},
{
- "organelle_type": "mitochondrion",
+ "organelle": "mitochondrion",
"name": "chrM",
"accession": "NC_001807.4"
}
diff --git a/extras/assemblies/GRCh37.json b/extras/assemblies/GRCh37.json
index 1095003b6652f4f37a318e2218f64d28d2424762..56a2b46bdd4ca5f24a68cd3af636228543340abe 100644
--- a/extras/assemblies/GRCh37.json
+++ b/extras/assemblies/GRCh37.json
@@ -5,172 +5,172 @@
"taxonomy_common_name": "Homo sapiens",
"chromosomes": [
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr1",
"accession": "NC_000001.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr2",
"accession": "NC_000002.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr3",
"accession": "NC_000003.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr4",
"accession": "NC_000004.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr5",
"accession": "NC_000005.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6",
"accession": "NC_000006.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr7",
"accession": "NC_000007.13"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr8",
"accession": "NC_000008.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr9",
"accession": "NC_000009.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr10",
"accession": "NC_000010.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr11",
"accession": "NC_000011.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr12",
"accession": "NC_000012.11"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr13",
"accession": "NC_000013.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr14",
"accession": "NC_000014.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr15",
"accession": "NC_000015.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr16",
"accession": "NC_000016.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr17",
"accession": "NC_000017.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr18",
"accession": "NC_000018.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr19",
"accession": "NC_000019.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr20",
"accession": "NC_000020.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr21",
"accession": "NC_000021.8"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr22",
"accession": "NC_000022.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrX",
"accession": "NC_000023.10"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrY",
"accession": "NC_000024.9"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_apd_hap1",
"accession": "NT_167244.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_cox_hap2",
"accession": "NT_113891.2"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_dbb_hap3",
"accession": "NT_167245.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_mann_hap4",
"accession": "NT_167246.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_mcf_hap5",
"accession": "NT_167247.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_qbl_hap6",
"accession": "NT_167248.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6_ssto_hap7",
"accession": "NT_167249.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr4_ctg9_hap1",
"accession": "NT_167250.1"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr17_ctg5_hap1",
"accession": "NT_167251.1"
},
{
- "organelle_type": "mitochondrion",
+ "organelle": "mitochondrion",
"name": "chrM",
"accession": "NC_012920.1"
}
diff --git a/extras/assemblies/GRCm38.json b/extras/assemblies/GRCm38.json
index 4550b0d0bf9d1de15530cf19bbc9579458893961..73806e8125b78cb9f6b2de3efab7f9b22e5aa9aa 100644
--- a/extras/assemblies/GRCm38.json
+++ b/extras/assemblies/GRCm38.json
@@ -5,112 +5,112 @@
"taxonomy_common_name": "Mus musculus",
"chromosomes": [
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr1",
"accession": "NC_000067.65"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr2",
"accession": "NC_000068.70"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr3",
"accession": "NC_000069.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr4",
"accession": "NC_000070.66"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr5",
"accession": "NC_000071.65"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr6",
"accession": "NC_000072.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr7",
"accession": "NC_000073.61"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr8",
"accession": "NC_000074.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr9",
"accession": "NC_000075.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr10",
"accession": "NC_000076.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr11",
"accession": "NC_000077.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr12",
"accession": "NC_000078.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr13",
"accession": "NC_000079.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr14",
"accession": "NC_000080.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr15",
"accession": "NC_000081.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr16",
"accession": "NC_000082.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr17",
"accession": "NC_000083.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr18",
"accession": "NC_000084.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chr19",
"accession": "NC_000085.60"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrX",
"accession": "NC_000086.71"
},
{
- "organelle_type": "chromosome",
+ "organelle": "nucleus",
"name": "chrY",
"accession": "NC_000087.74"
},
{
- "organelle_type": "mitochondrion",
+ "organelle": "mitochondrion",
"name": "chrM",
"accession": "NC_005089.1"
}
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 4c54beb8ae01594c8d5edbe72efca3dd966da64e..920ce36c2a8546433bd1d56702547e391039e184 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -304,9 +304,11 @@ class Chromosome(db.Base):
#: Chromosome accession number (e.g., ``NC_000001.10``, ``NC_012920.1``).
accession = Column(String(30), nullable=False)
- #: Type of organelle.
- organelle_type = Column(Enum('chromosome', 'mitochondrion',
- name='organelle_type'))
+ # Todo: Use constant definitions for this type.
+ #: Enclosing organelle. Used to differentiate between references requiring
+ #: ``m.`` and ``g.`` descriptions.
+ organelle = Column(Enum('nucleus', 'mitochondrion',
+ name='organelle'))
#: The :class:`Assembly` this chromosome is in.
assembly = relationship(
@@ -317,11 +319,11 @@ class Chromosome(db.Base):
cascade='all, delete-orphan',
passive_deletes=True))
- def __init__(self, assembly, name, accession, organelle_type):
+ def __init__(self, assembly, name, accession, organelle):
self.assembly = assembly
self.name = name
self.accession = accession
- self.organelle_type = organelle_type
+ self.organelle = organelle
def __repr__(self):
return '<Chromosome %r accession=%r>' % (self.name, self.accession)
diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index 1d8fea65f090239d930cd92798b341e2ba84dd58..613ba1974468a3fa6384167d09f8dd4315d0e4f9 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/mutalyzer/entrypoints/admin.py
@@ -60,7 +60,7 @@ def add_assembly(assembly_file):
for chromosome_definition in definition['chromosomes']:
chromosome = Chromosome(assembly, chromosome_definition['name'],
chromosome_definition['accession'],
- chromosome_definition['organelle_type'])
+ chromosome_definition['organelle'])
session.add(chromosome)
session.commit()
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 2a4e534e059fc2ef030cb0d1072b243ec7bd9c23..ed751d0829728a814a900ea96112a56712ff5cdb 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -532,7 +532,7 @@ class Converter(object) :
else:
description = '[' + ';'.join(descriptions) + ']'
- if self.mapping.chromosome.organelle_type == 'mitochondrion':
+ if self.mapping.chromosome.organelle == 'mitochondrion':
return "%s:m.%s" % (self.mapping.chromosome.accession, description)
else:
return "%s:g.%s" % (self.mapping.chromosome.accession, description)
diff --git a/tests/fixtures.py b/tests/fixtures.py
index 6d6d4ffeba2905f05d68ca04866379b4c7eeab11..d699912beb051ce53fc4c925c81c1e4019960a49 100644
--- a/tests/fixtures.py
+++ b/tests/fixtures.py
@@ -172,41 +172,41 @@ def hg19():
assembly = Assembly('GRCh37', 9606, 'Homo sapiens', alias='hg19')
session.add(assembly)
- session.add_all(Chromosome(assembly, name, accession, organelle_type)
- for accession, name, organelle_type in [
- ('NC_000001.10', 'chr1', 'chromosome'),
- ('NC_000002.11', 'chr2', 'chromosome'),
- ('NC_000003.11', 'chr3', 'chromosome'),
- ('NC_000004.11', 'chr4', 'chromosome'),
- ('NC_000005.9', 'chr5', 'chromosome'),
- ('NC_000006.11', 'chr6', 'chromosome'),
- ('NC_000007.13', 'chr7', 'chromosome'),
- ('NC_000008.10', 'chr8', 'chromosome'),
- ('NC_000009.11', 'chr9', 'chromosome'),
- ('NC_000010.10', 'chr10', 'chromosome'),
- ('NC_000011.9', 'chr11', 'chromosome'),
- ('NC_000012.11', 'chr12', 'chromosome'),
- ('NC_000013.10', 'chr13', 'chromosome'),
- ('NC_000014.8', 'chr14', 'chromosome'),
- ('NC_000015.9', 'chr15', 'chromosome'),
- ('NC_000016.9', 'chr16', 'chromosome'),
- ('NC_000017.10', 'chr17', 'chromosome'),
- ('NC_000018.9', 'chr18', 'chromosome'),
- ('NC_000019.9', 'chr19', 'chromosome'),
- ('NC_000020.10', 'chr20', 'chromosome'),
- ('NC_000021.8', 'chr21', 'chromosome'),
- ('NC_000022.10', 'chr22', 'chromosome'),
- ('NC_000023.10', 'chrX', 'chromosome'),
- ('NC_000024.9', 'chrY', 'chromosome'),
- ('NT_167244.1', 'chr6_apd_hap1', 'chromosome'),
- ('NT_113891.2', 'chr6_cox_hap2', 'chromosome'),
- ('NT_167245.1', 'chr6_dbb_hap3', 'chromosome'),
- ('NT_167246.1', 'chr6_mann_hap4', 'chromosome'),
- ('NT_167247.1', 'chr6_mcf_hap5', 'chromosome'),
- ('NT_167248.1', 'chr6_qbl_hap6', 'chromosome'),
- ('NT_167249.1', 'chr6_ssto_hap7', 'chromosome'),
- ('NT_167250.1', 'chr4_ctg9_hap1', 'chromosome'),
- ('NT_167251.1', 'chr17_ctg5_hap1', 'chromosome'),
+ session.add_all(Chromosome(assembly, name, accession, organelle)
+ for accession, name, organelle in [
+ ('NC_000001.10', 'chr1', 'nucleus'),
+ ('NC_000002.11', 'chr2', 'nucleus'),
+ ('NC_000003.11', 'chr3', 'nucleus'),
+ ('NC_000004.11', 'chr4', 'nucleus'),
+ ('NC_000005.9', 'chr5', 'nucleus'),
+ ('NC_000006.11', 'chr6', 'nucleus'),
+ ('NC_000007.13', 'chr7', 'nucleus'),
+ ('NC_000008.10', 'chr8', 'nucleus'),
+ ('NC_000009.11', 'chr9', 'nucleus'),
+ ('NC_000010.10', 'chr10', 'nucleus'),
+ ('NC_000011.9', 'chr11', 'nucleus'),
+ ('NC_000012.11', 'chr12', 'nucleus'),
+ ('NC_000013.10', 'chr13', 'nucleus'),
+ ('NC_000014.8', 'chr14', 'nucleus'),
+ ('NC_000015.9', 'chr15', 'nucleus'),
+ ('NC_000016.9', 'chr16', 'nucleus'),
+ ('NC_000017.10', 'chr17', 'nucleus'),
+ ('NC_000018.9', 'chr18', 'nucleus'),
+ ('NC_000019.9', 'chr19', 'nucleus'),
+ ('NC_000020.10', 'chr20', 'nucleus'),
+ ('NC_000021.8', 'chr21', 'nucleus'),
+ ('NC_000022.10', 'chr22', 'nucleus'),
+ ('NC_000023.10', 'chrX', 'nucleus'),
+ ('NC_000024.9', 'chrY', 'nucleus'),
+ ('NT_167244.1', 'chr6_apd_hap1', 'nucleus'),
+ ('NT_113891.2', 'chr6_cox_hap2', 'nucleus'),
+ ('NT_167245.1', 'chr6_dbb_hap3', 'nucleus'),
+ ('NT_167246.1', 'chr6_mann_hap4', 'nucleus'),
+ ('NT_167247.1', 'chr6_mcf_hap5', 'nucleus'),
+ ('NT_167248.1', 'chr6_qbl_hap6', 'nucleus'),
+ ('NT_167249.1', 'chr6_ssto_hap7', 'nucleus'),
+ ('NT_167250.1', 'chr4_ctg9_hap1', 'nucleus'),
+ ('NT_167251.1', 'chr17_ctg5_hap1', 'nucleus'),
('NC_012920.1', 'chrM', 'mitochondrion')])
session.commit()