diff --git a/extras/migrations/010-db-chrname-add-organelle.migration b/extras/migrations/010-db-chrname-add-organelle.migration
new file mode 100755
index 0000000000000000000000000000000000000000..c7e541af02cb8bc03b021697fa4696b474a9abf6
--- /dev/null
+++ b/extras/migrations/010-db-chrname-add-organelle.migration
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+"""
+Add a column 'organelle_type' to the 'ChrName' tables.
+
+Usage:
+ ./010-db-chrname-add-organelle.migration [migrate]
+"""
+
+
+import migration
+
+
+def check():
+ """
+ Check if migration is needed.
+ """
+ connection = migration.db_connect('hg18')
+ cursor = connection.cursor()
+ cursor.execute('SHOW COLUMNS FROM ChrName WHERE field = "organelle_type";')
+ has_column_hg18 = len(cursor.fetchall()) > 0
+ connection.close()
+
+ connection = migration.db_connect('hg19')
+ cursor = connection.cursor()
+ cursor.execute('SHOW COLUMNS FROM ChrName WHERE field = "organelle_type";')
+ has_column_hg19 = len(cursor.fetchall()) > 0
+ connection.close()
+
+ if has_column_hg19 != has_column_hg19:
+ migration.fatal('Installation is not in a recognizable state. Fix manually.')
+ return not has_column_hg19
+
+
+def migrate():
+ """
+ Perform migration.
+ """
+ connection = migration.db_connect('hg18')
+ cursor = connection.cursor()
+ cursor.execute("""
+ ALTER TABLE ChrName
+ ADD COLUMN organelle_type enum('chromosome','mitochondrion') NOT NULL DEFAULT 'chromosome' AFTER name;""")
+ connection.commit()
+ cursor = connection.cursor()
+ cursor.execute("""
+ UPDATE ChrName SET organelle_type = 'mitochondrion' WHERE name = 'chrM';""")
+ connection.commit()
+ connection.close()
+ migration.info('Added column hg18.ChrName.organelle_type')
+
+ connection = migration.db_connect('hg19')
+ cursor = connection.cursor()
+ cursor.execute("""
+ ALTER TABLE ChrName
+ ADD COLUMN organelle_type enum('chromosome','mitochondrion') NOT NULL DEFAULT 'chromosome' AFTER name;""")
+ connection.commit()
+ cursor = connection.cursor()
+ cursor.execute("""
+ UPDATE ChrName SET organelle_type = 'mitochondrion' WHERE name = 'chrM';""")
+ connection.commit()
+ connection.close()
+ migration.info('Added column hg19.ChrName.organelle_type')
+
+
+if __name__ == '__main__':
+ migration.main(check, migrate)
diff --git a/extras/post-install.sh b/extras/post-install.sh
index 0103866511708e77460e27ef9d78ec3a3eba3fad..b32c9c8d2ce0188fc50c391dd6d66ee98310b1e0 100644
--- a/extras/post-install.sh
+++ b/extras/post-install.sh
@@ -98,6 +98,7 @@ cat << EOF | mysql -u mutalyzer -D hg18
CREATE TABLE ChrName (
AccNo char(20) NOT NULL,
name char(20) NOT NULL,
+ organelle_type enum('chromosome','mitochondrion') NOT NULL DEFAULT 'chromosome',
PRIMARY KEY (AccNo)
) ENGINE = MYISAM;
CREATE TABLE Mapping (
@@ -118,33 +119,33 @@ CREATE TABLE Mapping (
source varchar(20) DEFAULT NULL,
INDEX (transcript)
) ENGINE = MYISAM;
-INSERT INTO ChrName (AccNo, name) VALUES
-('NC_000001.9', 'chr1'),
-('NC_000002.10', 'chr2'),
-('NC_000003.10', 'chr3'),
-('NC_000004.10', 'chr4'),
-('NC_000005.8', 'chr5'),
-('NC_000006.10', 'chr6'),
-('NC_000007.12', 'chr7'),
-('NC_000008.9', 'chr8'),
-('NC_000009.10', 'chr9'),
-('NC_000010.9', 'chr10'),
-('NC_000011.8', 'chr11'),
-('NC_000012.10', 'chr12'),
-('NC_000013.9', 'chr13'),
-('NC_000014.7', 'chr14'),
-('NC_000015.8', 'chr15'),
-('NC_000016.8', 'chr16'),
-('NC_000017.9', 'chr17'),
-('NC_000018.8', 'chr18'),
-('NC_000019.8', 'chr19'),
-('NC_000020.9', 'chr20'),
-('NC_000021.7', 'chr21'),
-('NC_000022.9', 'chr22'),
-('NC_000023.9', 'chrX'),
-('NC_000024.8', 'chrY'),
-('NC_001807.4', 'chrM'),
-('NT_113891.1', 'chr6_cox_hap1'),
+INSERT INTO ChrName (AccNo, name, organelle_type) VALUES
+('NC_000001.9', 'chr1', 'chromosome'),
+('NC_000002.10', 'chr2', 'chromosome'),
+('NC_000003.10', 'chr3', 'chromosome'),
+('NC_000004.10', 'chr4', 'chromosome'),
+('NC_000005.8', 'chr5', 'chromosome'),
+('NC_000006.10', 'chr6', 'chromosome'),
+('NC_000007.12', 'chr7', 'chromosome'),
+('NC_000008.9', 'chr8', 'chromosome'),
+('NC_000009.10', 'chr9', 'chromosome'),
+('NC_000010.9', 'chr10', 'chromosome'),
+('NC_000011.8', 'chr11', 'chromosome'),
+('NC_000012.10', 'chr12', 'chromosome'),
+('NC_000013.9', 'chr13', 'chromosome'),
+('NC_000014.7', 'chr14', 'chromosome'),
+('NC_000015.8', 'chr15', 'chromosome'),
+('NC_000016.8', 'chr16', 'chromosome'),
+('NC_000017.9', 'chr17', 'chromosome'),
+('NC_000018.8', 'chr18', 'chromosome'),
+('NC_000019.8', 'chr19', 'chromosome'),
+('NC_000020.9', 'chr20', 'chromosome'),
+('NC_000021.7', 'chr21', 'chromosome'),
+('NC_000022.9', 'chr22', 'chromosome'),
+('NC_000023.9', 'chrX', 'chromosome'),
+('NC_000024.8', 'chrY', 'chromosome'),
+('NC_001807.4', 'chrM', 'mitochondrion'),
+('NT_113891.1', 'chr6_cox_hap1', 'chromosome'),
('NT_113959.1', 'chr22_h2_hap1');
EOF
@@ -164,6 +165,7 @@ cat << EOF | mysql -u mutalyzer -D hg19
CREATE TABLE ChrName (
AccNo char(20) NOT NULL,
name char(20) NOT NULL,
+ organelle_type enum('chromosome','mitochondrion') NOT NULL DEFAULT 'chromosome',
PRIMARY KEY (AccNo)
) ENGINE = MYISAM;
CREATE TABLE Mapping (
@@ -184,41 +186,41 @@ CREATE TABLE Mapping (
source varchar(20) DEFAULT NULL,
INDEX (transcript)
) ENGINE = MYISAM;
-INSERT INTO ChrName (AccNo, name) VALUES
-('NC_000001.10', 'chr1'),
-('NC_000002.11', 'chr2'),
-('NC_000003.11', 'chr3'),
-('NC_000004.11', 'chr4'),
-('NC_000005.9', 'chr5'),
-('NC_000006.11', 'chr6'),
-('NC_000007.13', 'chr7'),
-('NC_000008.10', 'chr8'),
-('NC_000009.11', 'chr9'),
-('NC_000010.10', 'chr10'),
-('NC_000011.9', 'chr11'),
-('NC_000012.11', 'chr12'),
-('NC_000013.10', 'chr13'),
-('NC_000014.8', 'chr14'),
-('NC_000015.9', 'chr15'),
-('NC_000016.9', 'chr16'),
-('NC_000017.10', 'chr17'),
-('NC_000018.9', 'chr18'),
-('NC_000019.9', 'chr19'),
-('NC_000020.10', 'chr20'),
-('NC_000021.8', 'chr21'),
-('NC_000022.10', 'chr22'),
-('NC_000023.10', 'chrX'),
-('NC_000024.9', 'chrY'),
-('NC_012920.1', 'chrM'),
-('NT_167244.1', 'chr6_apd_hap1'),
-('NT_113891.2', 'chr6_cox_hap2'),
-('NT_167245.1', 'chr6_dbb_hap3'),
-('NT_167246.1', 'chr6_mann_hap4'),
-('NT_167247.1', 'chr6_mcf_hap5'),
-('NT_167248.1', 'chr6_qbl_hap6'),
-('NT_167249.1', 'chr6_ssto_hap7'),
-('NT_167250.1', 'chr4_ctg9_hap1'),
-('NT_167251.1', 'chr17_ctg5_hap1');
+INSERT INTO ChrName (AccNo, name, organelle_type) VALUES
+('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'),
+('NC_012920.1', 'chrM', 'mitochondrion'),
+('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');
EOF
echo -e "${COLOR_INFO}Populating Mapping table with NCBI data (hg19)${COLOR_END}"
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index ae295b3cf0601854323bafc6ed7bd609019c797a..42386156f539cf0f583124c9d6a5d870da4d8f83 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -480,14 +480,14 @@ class Mapping(Db) :
"""
statement = """
- SELECT AccNo
+ SELECT AccNo, organelle_type
FROM ChrName
WHERE name = %s;
""", name
ret = self.query(statement)
if ret :
- return ret[0][0]
+ return ret[0]
return None
#chromAcc
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 38c0d48e0fdc4baa45b2af78b1a88a4094c74ab7..e005a895bd243f192beee1db4710a2d59b117bc3 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -524,7 +524,10 @@ class Converter(object) :
else:
variants = [self.parseTree.RawVar]
- chromAcc = self.__database.chromAcc(self.dbFields["chromosome"])
+ try:
+ chromAcc, organelle_type = self.__database.chromAcc(self.dbFields["chromosome"])
+ except TypeError:
+ return None
# Construct the variant descriptions
descriptions = []
@@ -555,7 +558,10 @@ class Converter(object) :
else:
description = '[' + ';'.join(descriptions) + ']'
- return "%s:g.%s" % (chromAcc, description)
+ if organelle_type == 'mitochondrion':
+ return "%s:m.%s" % (chromAcc, description)
+ else:
+ return "%s:g.%s" % (chromAcc, description)
#c2chrom
def chromosomal_positions(self, positions, reference, version=None):
@@ -622,8 +628,9 @@ class Converter(object) :
if variant.startswith('chr') and ':' in variant:
preco, postco = variant.split(':', 1)
- chrom = self.__database.chromAcc(preco)
- if chrom is None :
+ try:
+ chrom, _ = self.__database.chromAcc(preco)
+ except TypeError:
self.__output.addMessage(__file__, 4, "ENOTINDB",
"The accession number %s could not be found in our database (or is not a chromosome)." %
preco)
@@ -650,7 +657,7 @@ class Converter(object) :
"""
if not self._parseInput(variant) :
- return None
+ return None
acc = self.parseTree.RefSeqAcc
version = self.parseTree.Version
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index 48b3ee1896214608519c037e7a3c3780c241e5d7..1866df350f0ca39d9c04aa2227993fd18d8765ec 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -582,7 +582,7 @@ class MutalyzerService(ServiceBase):
"Finished processing chromAccession(%s %s)" % (build, name))
del D,L
- return result
+ return result[0]
#chromAccession
@srpc(Mandatory.String, Mandatory.String, _returns=Mandatory.String)
@@ -674,7 +674,7 @@ class MutalyzerService(ServiceBase):
if "c." in variant or "n." in variant:
result = [converter.c2chrom(variant)]
- elif "g." in variant :
+ elif "g." in variant or "m." in variant:
result = converter.chrom2c(variant, "list", gene=gene)
else:
result = [""]
diff --git a/mutalyzer/website.py b/mutalyzer/website.py
index 29c1480f74f8fee58149c0eb77953d99b342e6ab..82151f1bd5b04f38e115039f17ff05204f15e7ea 100644
--- a/mutalyzer/website.py
+++ b/mutalyzer/website.py
@@ -594,7 +594,7 @@ class PositionConverter:
variant = converter.correctChrVariant(variant)
if variant:
- if not(":c." in variant or ":n." in variant or ":g." in variant):
+ if not(":c." in variant or ":n." in variant or ":g." in variant or ":m." in variant):
#Bad name
grammar = Grammar(output)
grammar.parse(variant)
@@ -605,7 +605,7 @@ class PositionConverter:
attr["gName"] = variant
- if variant and ":g." in variant:
+ if variant and (":g." in variant or ":m." in variant):
# Do the g2c dance
variants = converter.chrom2c(variant, "dict")
if variants is None:
@@ -1412,9 +1412,9 @@ class Uploader:
name = 'chr%s' % name
database = Db.Mapping(build)
- accession = database.chromAcc(name)
-
- if not accession:
+ try:
+ accession, _ = database.chromAcc(name)
+ except TypeError:
raise InputException('Chromosome not available for build %s: %s' %
(build, name))