def scan_dirs(self, dirs):
for dir in dirs:
CGData.log("SCANNING DIR: %s" % (dir))
if os.path.isdir(dir):
filePath= os.path.join(dir, "*")
else:
filePath = dir
for path in glob(filePath):
if os.path.isfile(path):
if path.endswith(".json"):
handle = open(path)
try:
data = json.loads(handle.read())
except ValueError, e:
CGData.error("BAD JSON in " + path + " " + str(e) )
data = None
handle.close()
if (data is not None and 'name' in data
and data['name'] is not None
and 'type' in data):
self.addFile(data['type'], data['name'], path)
if path.endswith("*.cgz"):
cgzList = CGData.CGZ.list( path )
for type in cgzList:
for zPath in cgzList[type]:
self.addFile(type, cgzList[type][zPath], zPath, path)
if os.path.isdir(path):
self.scan_dirs([path])
def gen_sql_heatmap(self, id_table, opts):
CGData.log("ClincalTrack SQL " + self.get_name())
features = self.members["clinicalFeature"].features
matrix = self.members["clinicalMatrix"]
# e.g. { 'HER2+': 'category', ...}
explicit_types = dict((f, features[f]['valueType']) for f in features if 'valueType' in features[f])
matrix.feature_type_setup(explicit_types)
for a in self.members['clinicalMatrix'].col_list:
if a in features and "stateOrder" in features[a]:
enums = [x for x in csv.reader(features[a]["stateOrder"], skipinitialspace=True)][0]
i = 0
#do not drop states in stateOrder
for e in enums:
matrix.enum_map[a][e] = enums.index(e)
for e in matrix.enum_map[a]:
if e in enums:
matrix.enum_map[a][e] = enums.index(e)
else:
matrix.enum_map[a][e] = len(enums) + i
i += 1
for a in matrix.gen_sql_heatmap(id_table, features=features):
yield a
class SampleMap(CGData.CGDataSetObject):
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('node_name', str, primary_key=True),
CGData.Column('parent', str),
CGData.Column('child', str)
]
def __init__(self):
CGData.CGDataSetObject.__init__(self)
self.mhash = {}
def read(self, handle):
for line in handle:
tmp = line.rstrip().split('\t')
if not tmp[0] in self.sample_hash:
self.sample_hash[tmp[0]] = {}
if len(tmp) > 1:
self.sample_hash[tmp[0]][tmp[1]] = True
def get_children(self, sample):
out = {}
for a in self.sample_hash.get(sample, {}):
out[a] = True
for c in self.get_children(a):
out[c] = True
return out.keys()
def gen_sql_heatmap(self, id_table, opts):
CGData.log("ClincalTrack SQL " + self.get_name())
features = self.members["clinicalFeature"].features
matrix = self.members["clinicalMatrix"]
# e.g. { 'HER2+': 'category', ...}
explicit_types = dict((f, features[f]['valueType']) for f in features
if 'valueType' in features[f])
matrix.feature_type_setup(explicit_types)
for a in self.members['clinicalMatrix'].col_list:
if a in features and "stateOrder" in features[a]:
enums = [
x for x in csv.reader(features[a]["stateOrder"],
skipinitialspace=True)
][0]
i = 0
#do not drop states in stateOrder
for e in enums:
matrix.enum_map[a][e] = enums.index(e)
for e in matrix.enum_map[a]:
if e in enums:
matrix.enum_map[a][e] = enums.index(e)
else:
matrix.enum_map[a][e] = len(enums) + i
i += 1
for a in matrix.gen_sql_heatmap(id_table, features=features):
yield a
def gen_sql(self, id_table):
CGData.log("ClincalTrack SQL " + self.get_name())
matrix = self.members["clinicalMatrix"]
matrix.feature_type_setup()
features = self.members["clinicalFeature"]
#print features
for a in features:
if "stateOrder" in features[a]:
#print features[a]["stateOrder"][0]
#this weird bit of code is to split on ',', but respect \,
#if you can think of a better way, please replace this
tmp = re.split(r'([^,]),', features[a]["stateOrder"][0])
enums = []
word = True
appending = False
e = 0
while e < len(tmp):
if word:
if appending:
enums[-1] += tmp[e]
else:
enums.append(tmp[e])
word = False
else:
if tmp[e] != "\\":
enums[-1] += tmp[e]
appending = False
else:
enums[-1] += ","
appending = True
word = True
e += 1
#print tmp
#print enums
#print matrix.enum_map[a]
i = 0
for e in matrix.enum_map[a]:
if e in enums:
matrix.enum_map[a][e] = enums.index(e)
else:
matrix.enum_map[a][e] = len(enums) + i
i += 1
#print matrix.enum_map[a]
#print "-=-=-=-=-"
for a in matrix.gen_sql(id_table, skip_feature_setup=True):
yield a
def gen_sql_heatmap(self, id_table, skip_feature_setup=False):
CGData.log( "Writing Clinical %s SQL" % (self.attrs['name']))
if not skip_feature_setup:
self.feature_type_setup()
table_name = self.attrs['name']
yield "drop table if exists clinical_%s;" % ( table_name )
yield """
CREATE TABLE clinical_%s (
\tsampleID int,
\tsampleName ENUM ('%s')""" % ( table_name, "','".join(sortedSamples(self.row_hash.keys())) )
for col in self.col_order:
if ( self.enum_map.has_key( col ) ):
yield ",\n\t`%s` ENUM( '%s' ) default NULL" % (col.strip(), "','".join( sql_fix(a) for a in sorted(self.enum_map[ col ].keys(), lambda x,y: self.enum_map[col][x]-self.enum_map[col][y]) ) )
else:
yield ",\n\t`%s` FLOAT default NULL" % (col.strip())
yield """
) engine 'MyISAM';
"""
for target in sortedSamples(self.row_hash.keys()):
a = []
for col in self.orig_order:
val = self.row_hash[ target ][ self.col_list[ col ] ]
if val is None or val == "null" or len(val) == 0 :
a.append("\\N")
else:
a.append( "'" + sql_fix( val.encode('string_escape') ) + "'" )
yield u"INSERT INTO clinical_%s VALUES ( %d, '%s', %s );\n" % ( table_name, id_table.get( table_name + ':sample_id', target ), sql_fix(target), u",".join(a) )
yield "drop table if exists clinical_%s_colDb;" % ( table_name )
yield CREATE_COL_DB % ( "clinical_" + table_name + "_colDb" )
yield "INSERT INTO clinical_%s_colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', 'on',1);\n" % \
( table_name, 'sampleName', 'sample name', 'sample name', 'sampleName', "clinical_" + table_name, 'coded' )
i = 0;
for name in self.col_order:
filter = 'coded' if self.enum_map.has_key(name) else 'minMax'
yield "INSERT INTO clinical_%s_colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', '%s',1);\n" % \
( table_name, name, name, name, name, "clinical_" + table_name, filter, 'on' if i < 10 else 'off')
i += 1
class DataSubType(CGData.CGDataSetObject):
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('name', str, primary_key=True),
]
def __init__(self):
CGData.CGDataSetObject.__init__(self)
def addFile(self, type, name, path, zipFile=None):
if CGData.has_type(type):
if not type in self:
self[type] = {}
if name in self[type]:
CGData.error("Duplicate %s file %s" % (type, name))
self[type][name] = CGData.light_load(path, zipFile)
CGData.log("FOUND: " + type + "\t" + name + "\t" + path)
else:
CGData.warn("Unknown file type: %s" % (path))
def addFile(self, type, name, path, zipFile=None):
if CGData.has_type(type):
if not type in self:
self[type] = {}
if name in self[type]:
CGData.error("Duplicate %s file %s" % (type, name))
self[type][name] = CGData.light_load(path, zipFile)
CGData.log("FOUND: " + type + "\t" + name + "\t" + path)
else:
CGData.warn("Unknown file type: %s" % (path))
class Assembly(CGData.CGObjectBase):
"""
Blank Class to represent Genome Assemblies
"""
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('name', str, primary_key=True),
]
def append(self, probe):
for attr in self.child_type.core_attr:
if not hasattr(probe, attr):
raise CGData.FormatException("Missing %s" % (attr))
if self.chrom_map is None:
self.chrom_map = {}
if not probe.chrom in self.chrom_map:
self.chrom_map[probe.chrom] = {}
if not probe.name in self.chrom_map[probe.chrom]:
self.chrom_map[probe.chrom][probe.name] = [probe]
else:
self.chrom_map[probe.chrom][probe.name].append(probe)
def gen_sql(self, id_table):
gmatrix = self.members[ 'genomicMatrix' ]
pmap = self.members[ 'probeMap' ].get( assembly="hg18" ) # BUG: hard coded to only producing HG18 tables
if pmap is None:
CGData.error("Missing HG18 %s" % ( self.members[ 'probeMap'].get_name() ))
return
table_base = self.get_name()
CGData.log("Writing Track %s" % (table_base))
clinical_table_base = self.members[ "clinicalMatrix" ].get_name()
yield "INSERT into raDb( name, sampleTable, clinicalTable, columnTable, aliasTable, shortLabel, expCount, dataType, platform, profile, security) VALUES ( '%s', '%s', '%s', '%s', '%s', '%s', '%d', '%s', '%s', '%s', '%s');\n" % \
( "genomic_" + table_base, "sample_" + table_base,
"clinical_" + clinical_table_base, "clinical_" + clinical_table_base + "_colDb",
"genomic_" + table_base + "_alias",
table_base,
len(gmatrix.get_sample_list()),
'bed 15',
gmatrix.attrs[':dataSubType'],
'localDb',
'public',
)
# write out the sample table
yield "drop table if exists sample_%s;" % ( table_base )
yield """
CREATE TABLE sample_%s (
id int,
sampleName varchar(255)
) engine 'MyISAM';
""" % ( table_base )
for sample in gmatrix.get_sample_list():
yield "INSERT INTO sample_%s VALUES( %d, '%s' );\n" % ( table_base, id_table.get( 'sample_id', sample), sample )
# write out the BED table
yield "drop table if exists %s;" % ( "genomic_" + table_base )
yield CREATE_BED % ( "genomic_" + table_base )
sample_ids = []
for sample in gmatrix.get_sample_list():
sample_ids.append( str( id_table.get( 'sample_id', sample ) ) )
missingProbeCount = 0
for probe_name in gmatrix.get_probe_list():
exp_ids = ','.join( sample_ids )
row = gmatrix.get_row_vals( probe_name )
exps = ','.join( str(a) for a in row )
probe = pmap.get( probe_name )
if probe is not None:
istr = "insert into %s(chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) values ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s' );\n" % \
( "genomic_%s" % (table_base), probe.chrom, probe.chrom_start, probe.chrom_end, probe.strand, sql_fix(probe_name), len(sample_ids), exp_ids, exps )
yield istr
else:
missingProbeCount += 1
CGData.log("%s Missing probes %d" % (table_base, missingProbeCount))
def gen_sql(self):
if "compiler.mode" in self.params and self.params[ "compiler.mode" ] == "scan":
return
log( "Writing SQL" )
if not os.path.exists(self.out_dir):
os.makedirs(self.out_dir)
self.id_table = CGIDTable()
for rtype in self.compile_matrix:
if issubclass( CGData.get_type( rtype ), CGData.CGSQLObject ):
for rname in self.compile_matrix[ rtype ]:
shandle = self.compile_matrix[ rtype ][ rname ].gen_sql( self.id_table )
if shandle is not None:
ohandle = open( os.path.join( self.out_dir, "%s.%s.sql" % (rtype, rname ) ), "w" )
for line in shandle:
ohandle.write( line )
ohandle.close()
#tell the object to unload data, so we don't continually allocate over the compile
self.compile_matrix[ rtype ][ rname ].unload()
def gen_sql_heatmap(self, id_table, features=None):
CGData.log( "Writing Clinical %s SQL" % (self['name']))
if features == None:
self.feature_type_setup()
features = {}
features['sampleName'] = { 'shortTitle': ['Sample name'], 'longTitle': ['Sample name'], 'visibility': ['on'], 'priority': [100.0] }
table_name = self['name'].replace(".","_")
clinical_table = 'clinical_' + table_name
yield "DROP TABLE IF EXISTS %s;\n" % ( clinical_table )
yield "DELETE codes FROM codes, colDb WHERE codes.feature = colDb.id AND colDb.clinicalTable = '%s';\n" % clinical_table
yield "DELETE FROM colDb WHERE clinicalTable = '%s';\n" % clinical_table
# colDb
i = 0;
for name in self.col_order:
shortLabel = name if name not in features or 'shortTitle' not in features[name] else features[name]['shortTitle'][0]
longLabel = name if name not in features or 'longTitle' not in features[name] else features[name]['longTitle'][0]
filter = 'coded' if self.enum_map.has_key(name) else 'minMax'
visibility = ('on' if i < 10 else 'off') if name not in features or 'visibility' not in features[name] else features[name]['visibility'][0]
priority = 1 if name not in features or 'priority' not in features[name] else float(features[name]['priority'][0])
yield "INSERT INTO colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', '%s', %f);" % \
( sql_fix(name), sql_fix(shortLabel), sql_fix(longLabel), sql_fix(name), clinical_table, filter, visibility, priority)
yield "SET @col%d=LAST_INSERT_ID();\n" % i
i += 1
# codes
i = 0;
values = {}
for col in self.col_order:
if ( self.enum_map.has_key( col ) ):
values[col] = {}
j = 0
for a in sorted(self.enum_map[ col ].keys(), lambda x,y: self.enum_map[col][x]-self.enum_map[col][y]):
yield "INSERT INTO codes(feature,ordering,value) VALUES (@col%d, %d, '%s'); SET @val%d_%d=LAST_INSERT_ID();\n" % (i, j, sql_fix(a), i, j)
values[col][a] = "@val%d_%d" % (i, j)
j += 1
i += 1
yield "CREATE TABLE %s (sampleID INT NOT NULL UNIQUE" % clinical_table
for col in self.col_order:
if col == 'sampleName':
yield ",\n\tsampleName INT UNSIGNED NOT NULL UNIQUE"
else:
if self.enum_map.has_key(col):
yield ",\n\t`%s` INT UNSIGNED DEFAULT NULL" % (col.strip())
else:
yield ",\n\t`%s` FLOAT DEFAULT NULL" % (col.strip())
yield """
) engine 'MyISAM';
"""
for target in sortedSamples(self.row_hash.keys()):
a = []
for col,orig in zip(self.col_order, self.orig_order):
if col == 'sampleName':
val = target
else:
val = self.row_hash[ target ][ self.col_list[ orig ] ]
if val is None or val.upper() in NULL_VALUES:
a.append("\\N")
else:
if col in self.enum_map:
a.append(values[col][val])
else:
a.append(val)
yield u"INSERT INTO %s VALUES ( %d, %s );\n" % ( clinical_table, id_table.get( table_name + ':sample_id', target ), u",".join(a) )
def link_objects(self):
"""
Scan found object records and determine if the data they link to is
avalible
"""
omatrix = {}
for otype in self.set_hash:
if issubclass( CGData.get_type( otype ), CGData.CGGroupMember ):
gmap = {}
for oname in self.set_hash[ otype ]:
oobj = self.set_hash[ otype ][ oname ]
if oobj.get_group() not in gmap:
if issubclass(CGData.get_type(otype), CGData.CGGroupMemberSQL):
gmap[ oobj.get_group() ] = CGData.CGGroupBaseSQL( oobj.get_group() )
else:
gmap[ oobj.get_group() ] = CGData.CGGroupBase( oobj.get_group() )
gmap[ oobj.get_group() ].put( oobj )
omatrix[ otype ] = gmap
else:
omatrix[ otype ] = self.set_hash[ otype ]
# Now it's time to check objects for their dependencies
ready_matrix = {}
for stype in omatrix:
for sname in omatrix[ stype ]:
sobj = omatrix[ stype ][ sname ]
lmap = sobj.get_link_map()
is_ready = True
for ltype in lmap:
if not omatrix.has_key( ltype ):
warn( "%s missing data type %s" % (sname, ltype) )
is_ready = False
else:
for lname in lmap[ ltype ]:
if not omatrix[ltype].has_key( lname ):
warn( "%s %s missing data %s %s" % ( stype, sname, ltype, lname ) )
is_ready = False
if not sobj.is_link_ready():
warn( "%s %s not LinkReady" % ( stype, sname ) )
elif is_ready:
if not stype in ready_matrix:
ready_matrix[ stype ] = {}
ready_matrix[ stype ][ sname ] = sobj
for rtype in ready_matrix:
log( "READY %s: %s" % ( rtype, ",".join(ready_matrix[rtype].keys()) ) )
for dType in ready_matrix:
log("Found %s %d" % (dType, len(ready_matrix[dType])))
merge_children = {}
for merge_type in CGData.MERGE_OBJECTS:
mtype = CGData.get_type( merge_type )
select_types = mtype.typeSet
select_set = {}
try:
for stype in select_types:
select_set[ stype ] = ready_matrix[ stype ]
if stype not in merge_children:
merge_children[stype] = {}
except KeyError:
error("missing data type %s" % (stype) )
continue
mobjlist = self.set_enumerate( mtype, select_set )
for mobj in mobjlist:
if merge_type not in ready_matrix:
ready_matrix[ merge_type ] = {}
for cType in mobj:
merge_children[cType][mobj[cType].get_name()] = True
ready_matrix[ merge_type ][ mobj.get_name() ] = mobj
self.compile_matrix = {}
for sType in ready_matrix:
self.compile_matrix[sType] = {}
for name in ready_matrix[sType]:
if sType not in merge_children or name not in merge_children[sType]:
self.compile_matrix[sType][name] = ready_matrix[sType][name]
log("After Merge")
for dType in ready_matrix:
log("Found %s %d" % (dType, len(self.compile_matrix[dType])))
#!/usr/bin/env python
#note: this script assumes that the first alias in the probeMap aliaslist
#is a HUGO gene name...
import CGData
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.load(sys.argv[1])
#load the probeMap
probeMap = CGData.load(sys.argv[2])
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
matrix.remap(probeMap, skip_missing=True)
matrix.add_history("Transformed from probespace %s to HUGO" %
(probeMap.get_name()))
matrix.attrs[":probeMap"] = "hugo"
#output the matrix
matrix.store(sys.argv[3])
import CGData
import CGData.NumpyMatrix
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.NumpyMatrix.NumpyMatrix()
matrixHandle = open(sys.argv[1])
matrix.read(matrixHandle)
matrixHandle.close()
#load the probeMap
probeMap = CGData.load( sys.argv[2] )
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
valid_map = {}
for alt in probeMap.get_probes():
valid_map[alt.aliases[0]] = True
if alt.name in matrix.get_row_names():
matrix.row_rename(alt.name, alt.aliases[0])
remove_list = []
for name in matrix.get_row_names():
if not name in valid_map:
def gen_sql_heatmap(self, id_table):
#scan the children
# XXX Handling of sql for children is broken if the child may appear
# as part of multiple merge objects, such as TrackGenomic and TrackClinical.
# A disgusting workaround for clinicalMatrix is to prevent the TrackGenomic from calling
# it for gen_sql.
clinical = self.members.pop("clinicalMatrix")
for line in CGData.CGMergeObject.sql_pass(self, id_table, method="heatmap"):
yield line
self.members["clinicalMatrix"] = clinical
gmatrix = self.members[ 'genomicMatrix' ]
pmap = self.members[ 'probeMap' ].get( assembly="hg18" ) # BUG: hard coded to only producing HG18 tables
if pmap is None:
CGData.error("Missing HG18 %s" % ( self.members[ 'probeMap'].get_name() ))
return
table_base = self.get_name()
CGData.log("Writing Track %s" % (table_base))
clinical_table_base = self.members[ "clinicalMatrix" ].get_name()
yield "INSERT into raDb( name, sampleTable, clinicalTable, columnTable, aliasTable, shortLabel, longLabel, expCount, dataType, platform, profile, security) VALUES ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%d', '%s', '%s', '%s', '%s');\n" % \
( "genomic_" + table_base, "sample_" + table_base,
"clinical_" + clinical_table_base, "clinical_" + clinical_table_base + "_colDb",
"genomic_" + table_base + "_alias",
sql_fix(gmatrix.attrs['shortTitle']),
sql_fix(gmatrix.attrs['longTitle']),
len(gmatrix.get_sample_list()),
self.format,
gmatrix.attrs[':dataSubType'],
'localDb',
'public',
)
# write out the sample table
yield "drop table if exists sample_%s;" % ( table_base )
yield """
CREATE TABLE sample_%s (
id int,
sampleName varchar(255)
) engine 'MyISAM';
""" % ( table_base )
from CGData.ClinicalMatrix import sortedSamples
for sample in sortedSamples(gmatrix.get_sample_list()):
yield "INSERT INTO sample_%s VALUES( %d, '%s' );\n" % ( table_base, id_table.get( clinical_table_base + ':sample_id', sample), sample )
yield "drop table if exists genomic_%s_alias;" % ( table_base )
yield """
CREATE TABLE genomic_%s_alias (
name varchar(255),
alias varchar(255)
) engine 'MyISAM';
""" % ( table_base )
for pset in pmap:
for probe in pset:
for alias in probe.aliases:
yield "insert into genomic_%s_alias( name, alias ) values( '%s', '%s' );\n" % (table_base, sql_fix(probe.name), sql_fix(alias))
# write out the BED table
yield "drop table if exists %s;" % ( "genomic_" + table_base )
yield CREATE_BED % ( "genomic_" + table_base + "_tmp")
sample_ids = []
samples = gmatrix.get_sample_list()
# sort samples by sample_id, and retain the sort order for application to the genomic data, below
tmp=sorted(zip(samples, range(len(samples))), cmp=lambda x,y: id_table.get(clinical_table_base + ':sample_id', x[0]) - id_table.get( clinical_table_base + ':sample_id', y[0]))
samples, order = map(lambda t: list(t), zip(*tmp))
for sample in samples:
sample_ids.append( str( id_table.get( clinical_table_base + ':sample_id', sample ) ) )
exp_ids = ','.join( sample_ids )
missingProbeCount = 0
for probe_name in gmatrix.get_probe_list():
# get the genomic data and rearrange to match the sample_id order
tmp = gmatrix.get_row_vals( probe_name )
row = map(lambda i: tmp[order[i]], range(len(tmp)))
pset = pmap.get( probe_name )
if pset is not None:
for probe in pset:
istr = "insert into %s(chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) values ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', %s );\n" % \
( "genomic_%s_tmp" % (table_base), probe.chrom, probe.chrom_start, probe.chrom_end, probe.strand, sql_fix(probe_name), len(sample_ids), exp_ids, self.scores(row) )
yield istr
else:
missingProbeCount += 1
yield "create table genomic_%s like genomic_%s_tmp;" % (table_base, table_base)
yield "insert into genomic_%s select * from genomic_%s_tmp order by chrom, chromStart;" % (table_base, table_base)
yield "drop table genomic_%s_tmp;" % table_base
CGData.log("%s Missing probes %d" % (table_base, missingProbeCount))
#!/usr/bin/env python #note: this script assumes that the first alias in the probeMap aliaslist #is a HUGO gene name... import CGData import sys # matrixProbeRemap.py <matrixFile> <probeFile> #load the matrix matrix = CGData.load( sys.argv[1] ) #load the probeMap probeMap = CGData.load( sys.argv[2] ) #remove null probes from the matrix matrix.remove_null_probes() #remap the matrix using the probe map matrix.remap( probeMap, skip_missing=True ) matrix.add_history( "Transformed from probespace %s to HUGO" % (probeMap.get_name() ) ) matrix.attrs[":probeMap"] = "hugo" #output the matrix matrix.store( sys.argv[3] )
def link_objects(self):
"""
Scan found object records and determine if the data they link to is
avalible
"""
omatrix = {}
for otype in self.set_hash:
if issubclass(CGData.get_type(otype), CGData.CGGroupMember):
gmap = {}
for oname in self.set_hash[otype]:
oobj = self.set_hash[otype][oname]
if oobj.get_group() not in gmap:
gmap[oobj.get_group()] = CGData.CGGroupBase(
oobj.get_group())
gmap[oobj.get_group()].put(oobj)
omatrix[otype] = gmap
else:
omatrix[otype] = self.set_hash[otype]
# Now it's time to check objects for their dependencies
ready_matrix = {}
for stype in omatrix:
for sname in omatrix[stype]:
sobj = omatrix[stype][sname]
lmap = sobj.get_link_map()
is_ready = True
for ltype in lmap:
if not omatrix.has_key(ltype):
warn("%s missing data type %s" % (sname, ltype))
is_ready = False
else:
for lname in lmap[ltype]:
if not omatrix[ltype].has_key(lname):
warn("%s %s missing data %s %s" %
(stype, sname, ltype, lname))
is_ready = False
if not sobj.is_link_ready():
warn("%s %s not LinkReady" % (stype, sname))
elif is_ready:
if not stype in ready_matrix:
ready_matrix[stype] = {}
ready_matrix[stype][sname] = sobj
for rtype in ready_matrix:
log("READY %s: %s" % (rtype, ",".join(ready_matrix[rtype].keys())))
for dType in ready_matrix:
log("Found %s %d" % (dType, len(ready_matrix[dType])))
merge_children = {}
for merge_type in CGData.MERGE_OBJECTS:
mtype = CGData.get_type(merge_type)
select_types = mtype.typeSet
select_set = {}
try:
for stype in select_types:
select_set[stype] = ready_matrix[stype]
if stype not in merge_children:
merge_children[stype] = {}
except KeyError:
error("missing data type %s" % (stype))
continue
mobjlist = self.set_enumerate(mtype, select_set)
for mobj in mobjlist:
if merge_type not in ready_matrix:
ready_matrix[merge_type] = {}
for cType in mobj:
merge_children[cType][mobj[cType].get_name()] = True
ready_matrix[merge_type][mobj.get_name()] = mobj
self.compile_matrix = {}
for sType in ready_matrix:
self.compile_matrix[sType] = {}
for name in ready_matrix[sType]:
if sType not in merge_children or name not in merge_children[
sType]:
self.compile_matrix[sType][name] = ready_matrix[sType][
name]
log("After Merge")
for dType in ready_matrix:
log("Found %s %d" % (dType, len(self.compile_matrix[dType])))
def gen_sql_heatmap(self, id_table):
#scan the children
# XXX Handling of sql for children is broken if the child may appear
# as part of multiple merge objects, such as TrackGenomic and TrackClinical.
# A disgusting workaround for clinicalMatrix is to prevent the TrackGenomic from calling
# it for gen_sql.
clinical = self.members.pop("clinicalMatrix")
for line in CGData.CGMergeObject.sql_pass(self, id_table, method="heatmap"):
yield line
self.members["clinicalMatrix"] = clinical
gmatrix = self.members[ 'genomicMatrix' ]
pmap = self.members[ 'probeMap' ].lookup( assembly="hg18" ) # BUG: hard coded to only producing HG18 tables
if pmap is None:
CGData.error("Missing HG18 %s" % ( self.members[ 'probeMap'].get_name() ))
return
table_base = self.get_name()
CGData.log("Writing Track %s" % (table_base))
clinical_table_base = self.members[ "clinicalMatrix" ].get_name()
other = {}
for attr in ['wrangler', 'wrangling_procedure', 'url', 'citation', 'description']:
if attr in gmatrix:
other[attr] = gmatrix[attr]
if 'dataProducer' in gmatrix:
other['author_list'] = gmatrix['dataProducer']
if 'articleTitle' in gmatrix:
other['article_title'] = gmatrix['articleTitle']
other['version'] = gmatrix.get('version', "")
datetime.datetime.strptime(other['version'], "%Y-%m-%d") #if the version isn't properly formatted, though exception
if 'owner' in gmatrix:
other['owner'] = gmatrix['owner']
other['colNormalization'] = gmatrix.get('colNormalization', False)
if not isinstance(other['colNormalization'], bool):
other['colNormalization'] = False
other['redistribution'] = gmatrix.get('redistribution', False)
if not isinstance(other['redistribution'], bool):
other['redistribution'] = False
other['security'] = gmatrix.get('security', "public")
if other['security'] not in [ "public", "private" ]:
other['security'] = "public"
yield "DELETE from raDb where name = '%s';\n" % ("genomic_" + table_base)
yield "INSERT into raDb( name, sampleTable, clinicalTable, columnTable, aliasTable, shortLabel, longLabel, expCount, dataType, platform, profile, security, priority, gain, groupName, wrangler, url, article_title, citation, author_list, wrangling_procedure, other) VALUES ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%d', '%s', '%s', '%s', '%s', %f, %f, '%s', %s, %s, %s, %s, %s, %s, '%s');\n" % \
( "genomic_" + table_base, "sample_" + table_base,
"clinical_" + clinical_table_base, "colDb",
"genomic_" + table_base + "_alias",
sql_fix(gmatrix['shortTitle']),
sql_fix(gmatrix['longTitle']),
len(gmatrix.get_sample_list()),
self.format,
dataSubTypeMap[gmatrix[':dataSubType']] if gmatrix[':dataSubType'] in dataSubTypeMap else gmatrix[':dataSubType'],
'localDb',
'public',
float(gmatrix.get('priority', 1.0)),
float(gmatrix.get('gain', 1.0)),
sql_fix(gmatrix.get('groupTitle', 'Misc.')),
"'%s'"%sql_fix(gmatrix['wrangler']) if 'wrangler' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['url']) if 'url' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['articleTitle']) if 'articleTitle' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['citation']) if 'citation' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['dataProducer']) if 'dataProducer' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['wrangling_procedure']) if 'wrangling_procedure' in gmatrix else '\N',
sql_fix(json.dumps(other)),
)
# write out the sample table
yield "drop table if exists sample_%s;" % ( table_base )
yield """
CREATE TABLE sample_%s (
id int,
sampleName varchar(255)
) engine 'MyISAM';
""" % ( table_base )
from CGData.ClinicalMatrix import sortedSamples
for sample in sortedSamples(gmatrix.get_sample_list()):
yield "INSERT INTO sample_%s VALUES( %d, '%s' );\n" % ( table_base, id_table.get( clinical_table_base + ':sample_id', sample), sql_fix(sample) )
yield "drop table if exists genomic_%s_alias;" % ( table_base )
yield """
CREATE TABLE genomic_%s_alias (
name varchar(255),
alias varchar(255)
) engine 'MyISAM';
""" % ( table_base )
for probe in pmap.get_probes():
for alias in probe.aliases:
yield "insert into genomic_%s_alias( name, alias ) values( '%s', '%s' );\n" % (table_base, sql_fix(probe.name), sql_fix(alias))
# write out the BED table
yield "drop table if exists %s;" % ( "genomic_" + table_base )
yield CREATE_BED % ( "genomic_" + table_base + "_tmp")
sample_ids = []
samples = gmatrix.get_sample_list()
# sort samples by sample_id, and retain the sort order for application to the genomic data, below
tmp=sorted(zip(samples, range(len(samples))), cmp=lambda x,y: id_table.get(clinical_table_base + ':sample_id', x[0]) - id_table.get( clinical_table_base + ':sample_id', y[0]))
samples, order = map(lambda t: list(t), zip(*tmp))
for sample in samples:
sample_ids.append( str( id_table.get( clinical_table_base + ':sample_id', sample ) ) )
exp_ids = ','.join( sample_ids )
missingProbeCount = 0
for probe_name in gmatrix.get_probe_list():
# get the genomic data and rearrange to match the sample_id order
tmp = gmatrix.get_row_vals( probe_name )
row = map(lambda i: tmp[order[i]], range(len(tmp)))
pset = pmap.lookup( probe_name )
if pset is not None:
for probe in pset:
istr = "insert into %s(chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) values ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', %s );\n" % \
( "genomic_%s_tmp" % (table_base), probe.chrom, probe.chrom_start-1, probe.chrom_end, probe.strand, sql_fix(probe_name), len(sample_ids), exp_ids, self.scores(row) )
yield istr
else:
missingProbeCount += 1
yield "# sort file by chrom position\n"
yield "create table genomic_%s like genomic_%s_tmp;\n" % (table_base, table_base)
yield "insert into genomic_%s select * from genomic_%s_tmp order by chrom, chromStart;\n" % (table_base, table_base)
yield "drop table genomic_%s_tmp;\n" % table_base
CGData.log("%s Missing probes %d" % (table_base, missingProbeCount))
#!/usr/bin/env python
import sys
import CGData
import CGData.Compiler
c = CGData.Compiler.BrowserCompiler()
c.scan_dirs(sys.argv[1:])
linkSpace = {}
for type in c.set_hash:
if issubclass( CGData.get_type( type ), CGData.CGDataMatrixObject ):
for name in c.set_hash[type]:
current = "%s:%s" % (type,name)
x_link = c.set_hash[type][name].get_x_namespace()
y_link = c.set_hash[type][name].get_y_namespace()
if x_link is not None:
if x_link not in linkSpace:
linkSpace[x_link] = {}
linkSpace[x_link][current] = True
print "%s x_link %s" % (current, x_link)
if y_link is not None:
if y_link not in linkSpace:
linkSpace[y_link] = {}
linkSpace[y_link][current] = True
print "%s y_link %s" % (current, y_link)
for ns in linkSpace:
s = linkSpace[ns].keys()
def gen_sql(self, id_table, skip_feature_setup=False):
CGData.log( "Gen %s SQL" % (self.attrs['name']))
if not skip_feature_setup:
self.feature_type_setup()
table_name = self.attrs['name']
yield "drop table if exists clinical_%s;" % ( table_name )
yield """
CREATE TABLE clinical_%s (
\tsampleID int,
\tsampleName ENUM ('%s')""" % ( table_name, "','".join(sortedSamples(self.row_hash.keys())) )
for col in self.col_order:
if ( self.enum_map.has_key( col ) ):
yield ",\n\t`%s` ENUM( '%s' ) default NULL" % (col.strip(), "','".join( sql_fix(a) for a in self.enum_map[ col ].keys() ) )
else:
yield ",\n\t`%s` FLOAT default NULL" % (col.strip())
yield """
) engine 'MyISAM';
"""
for target in sortedSamples(self.row_hash.keys()):
a = []
for col in self.orig_order:
val = self.row_hash[ target ][ self.col_list[ col ] ]
#print target, col, val
if val is None or val == "null" or len(val) == 0 :
a.append("\\N")
else:
#a.append( "'" + sql_fix(val) + "'" )
a.append( "'" + sql_fix( val.encode('string_escape') ) + "'" )
yield u"INSERT INTO clinical_%s VALUES ( %d, '%s', %s );\n" % ( table_name, id_table.get( 'sample_id', target ), sql_fix(target), u",".join(a) )
#yield u"INSERT INTO clinical_%s VALUES ( %d, %s );\n" % ( table_name, id_table.get( 'sample_id', target ), u",".join(a) )
yield "drop table if exists clinical_%s_colDb;" % ( table_name )
yield CREATE_COL_DB % ( "clinical_" + table_name + "_colDb" )
"""
`id` int(10) unsigned NOT NULL default '0',
`name` varchar(255) default NULL,
`shortLabel` varchar(255) default NULL,
`longLabel` varchar(255) default NULL,
`valField` varchar(255) default NULL,
`clinicalTable` varchar(255) default NULL,
`priority` float default NULL,
`filterType` varchar(255) default NULL,
`visibility` varchar(255) default NULL,
`groupName` varchar(255) default NULL,
PRIMARY KEY (`id`),
KEY `name` (`name`)
"""
yield "INSERT INTO clinical_%s_colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', 'on',1);\n" % \
( table_name, 'sampleName', 'sample name', 'sample name', 'sampleName', "clinical_" + table_name, 'coded' )
i = 0;
for name in self.col_order:
filter = 'coded' if self.enum_map.has_key(name) else 'minMax'
yield "INSERT INTO clinical_%s_colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', '%s',1);\n" % \
( table_name, name, name, name, name, "clinical_" + table_name, filter, 'on' if i < 10 else 'off')
i += 1
def gen_sql_heatmap(self, id_table, opts):
#scan the children
# XXX Handling of sql for children is broken if the child may appear
# as part of multiple merge objects, such as TrackGenomic and TrackClinical.
# A disgusting workaround for clinicalMatrix is to prevent the TrackGenomic from calling
# it for gen_sql.
clinical = self.members.pop("clinicalMatrix")
for line in CGData.CGMergeObject.sql_pass(self, id_table, method="heatmap"):
yield line
self.members["clinicalMatrix"] = clinical
gmatrix = self.members[ 'genomicMatrix' ]
pmap = self.members[ 'probeMap' ].lookup( assembly="hg18" ) # BUG: hard coded to only producing HG18 tables
if pmap is None:
CGData.error("Missing HG18 %s" % ( self.members[ 'probeMap'].get_name() ))
return
savedownsample = 'save-ds' in opts and opts['save-ds']
table_base = self.get_name().replace(".", "_")
CGData.log("Writing Track %s" % (table_base))
clinical_table_base = self.members[ "clinicalMatrix" ].get_name().replace(".", "_")
other = {}
for attr in ['wrangler', 'wrangling_procedure', 'url', 'citation', 'description']:
if attr in gmatrix:
other[attr] = gmatrix[attr]
if 'dataProducer' in gmatrix:
other['author_list'] = gmatrix['dataProducer']
if 'articleTitle' in gmatrix:
other['article_title'] = gmatrix['articleTitle']
##TO DO, the version info should be the lastest of genomic and clinical, currently only check genomic
cVersion= self.members[ 'clinicalMatrix' ].get('version',"")
gVersion= self.members[ 'genomicMatrix' ].get('version',"")
dG= makeDate(gVersion)
dC= makeDate(cVersion)
if dC == None:
other['version'] = gVersion
elif dG<dC:
other['version'] = cVersion
else:
other['version'] = gVersion
datetime.datetime.strptime(other['version'], "%Y-%m-%d") #if the version isn't properly formatted, though exception
if 'owner' in gmatrix:
other['owner'] = gmatrix['owner']
other['colNormalization'] = gmatrix.get('colNormalization', False)
if not isinstance(other['colNormalization'], bool):
other['colNormalization'] = False
other['redistribution'] = gmatrix.get('redistribution', False)
if not isinstance(other['redistribution'], bool):
other['redistribution'] = False
security = gmatrix.get('security', "public")
if security not in [ "public", "private" ]:
security = "public"
if savedownsample:
yield "SET @ds=(SELECT downSampleTable FROM raDb WHERE name = '%s');\n" % ("genomic_" + table_base)
yield "DELETE from raDb where name = '%s';\n" % ("genomic_" + table_base)
yield "INSERT into raDb( name, downSampleTable, sampleTable, clinicalTable, columnTable, aliasTable, shortLabel, longLabel, expCount, dataType, platform, profile, security, priority, gain, groupName, wrangler, url, article_title, citation, author_list, wrangling_procedure, other) VALUES ( '%s', %s, '%s', '%s', '%s', '%s', '%s', '%s', '%d', '%s', '%s', '%s', '%s', %f, %f, '%s', %s, %s, %s, %s, %s, %s, '%s');\n" % \
( "genomic_" + table_base,
"@ds" if savedownsample else "NULL",
"sample_" + table_base,
"clinical_" + clinical_table_base, "colDb",
"genomic_" + table_base + "_alias",
sql_fix(gmatrix['shortTitle']),
sql_fix(gmatrix['longTitle']),
len(gmatrix.get_sample_list()),
self.format,
dataSubTypeMap[gmatrix[':dataSubType']] if gmatrix[':dataSubType'] in dataSubTypeMap else gmatrix[':dataSubType'],
'localDb',
security,
float(gmatrix.get('priority', 1.0)),
float(gmatrix.get('gain', 1.0)),
sql_fix(gmatrix.get('groupTitle', 'Misc.')),
"'%s'"%sql_fix(gmatrix['wrangler']) if 'wrangler' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['url']) if 'url' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['articleTitle']) if 'articleTitle' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['citation']) if 'citation' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['dataProducer']) if 'dataProducer' in gmatrix else '\N',
"'%s'"%sql_fix(gmatrix['wrangling_procedure']) if 'wrangling_procedure' in gmatrix else '\N',
sql_fix(json.dumps(other)),
)
if 'no-genomic-matrix' in opts and opts['no-genomic-matrix']:
return
# write out the sample table
yield "drop table if exists sample_%s;" % ( table_base )
yield """
CREATE TABLE sample_%s (
id int,
sampleName varchar(255)
) engine 'MyISAM';
""" % ( table_base )
from CGData.ClinicalMatrix import sortedSamples
for sample in sortedSamples(gmatrix.get_sample_list()):
yield "INSERT INTO sample_%s VALUES( %d, '%s' );\n" % ( table_base, id_table.get( clinical_table_base + ':sample_id', sample), sql_fix(sample) )
yield "drop table if exists genomic_%s_alias;" % ( table_base )
yield """
CREATE TABLE genomic_%s_alias (
name varchar(255),
alias varchar(255)
) engine 'MyISAM';
""" % ( table_base )
for probe in pmap.get_probes():
for alias in probe.aliases:
yield "insert into genomic_%s_alias( name, alias ) values( '%s', '%s' );\n" % (table_base, sql_fix(probe.name), sql_fix(alias))
# write out the BED table
yield "drop table if exists %s;" % ( "genomic_" + table_base )
yield CREATE_BED % ( "genomic_" + table_base + "_tmp")
sample_ids = []
samples = gmatrix.get_sample_list()
# sort samples by sample_id, and retain the sort order for application to the genomic data, below
tmp=sorted(zip(samples, range(len(samples))), cmp=lambda x,y: id_table.get(clinical_table_base + ':sample_id', x[0]) - id_table.get( clinical_table_base + ':sample_id', y[0]))
samples, order = map(lambda t: list(t), zip(*tmp))
for sample in samples:
sample_ids.append( str( id_table.get( clinical_table_base + ':sample_id', sample ) ) )
exp_ids = ','.join( sample_ids )
missingProbeCount = 0
for probe_name in gmatrix.get_probe_list():
# get the genomic data and rearrange to match the sample_id order
tmp = gmatrix.get_row_vals( probe_name )
row = map(lambda i: tmp[order[i]], range(len(tmp)))
pset = pmap.lookup( probe_name )
if pset is not None:
for probe in pset:
istr = "insert into %s(bin, chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) values ( %d, '%s', '%s', '%s', '%s', '%s', '%s', '%s', %s );\n" % \
( "genomic_%s_tmp" % (table_base), Binner.calcBin(probe.chrom_start, probe.chrom_end), probe.chrom, probe.chrom_start-1, probe.chrom_end, probe.strand, sql_fix(probe_name), len(sample_ids), exp_ids, self.scores(row) )
yield istr
else:
missingProbeCount += 1
yield "# sort file by chrom position\n"
yield "create table genomic_%s like genomic_%s_tmp;\n" % (table_base, table_base)
yield "insert into genomic_%s(bin, chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) select bin, chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores from genomic_%s_tmp order by chrom, chromStart;\n" % (table_base, table_base)
yield "drop table genomic_%s_tmp;\n" % table_base
CGData.log("%s Missing probes %d" % (table_base, missingProbeCount))
def gen_sql_heatmap(self, id_table, features=None):
CGData.log("Writing Clinical %s SQL" % (self['name']))
if features == None:
self.feature_type_setup()
features = {}
features['sampleName'] = {
'shortTitle': ['Sample name'],
'longTitle': ['Sample name'],
'visibility': ['on'],
'priority': [1]
}
table_name = self['name']
clinical_table = 'clinical_' + table_name
yield "DROP TABLE IF EXISTS %s;\n" % (clinical_table)
yield "DELETE codes FROM codes, colDb WHERE codes.feature = colDb.id AND colDb.clinicalTable = '%s';\n" % clinical_table
yield "DELETE FROM colDb WHERE clinicalTable = '%s';\n" % clinical_table
# colDb
i = 0
for name in self.col_order:
shortLabel = name if name not in features or 'shortTitle' not in features[
name] else features[name]['shortTitle'][0]
longLabel = name if name not in features or 'longTitle' not in features[
name] else features[name]['longTitle'][0]
filter = 'coded' if self.enum_map.has_key(name) else 'minMax'
visibility = (
'on' if i < 10 else
'off') if name not in features or 'visibility' not in features[
name] else features[name]['visibility'][0]
priority = 1 if name not in features or 'priority' not in features[
name] else float(features[name]['priority'][0])
yield "INSERT INTO colDb(name, shortLabel,longLabel,valField,clinicalTable,filterType,visibility,priority) VALUES( '%s', '%s', '%s', '%s', '%s', '%s', '%s', %f);" % \
( sql_fix(name), sql_fix(shortLabel), sql_fix(longLabel), sql_fix(name), clinical_table, filter, visibility, priority)
yield "SET @col%d=LAST_INSERT_ID();\n" % i
i += 1
# codes
i = 0
values = {}
for col in self.col_order:
if (self.enum_map.has_key(col)):
values[col] = {}
j = 0
for a in sorted(
self.enum_map[col].keys(), lambda x, y: self.enum_map[
col][x] - self.enum_map[col][y]):
yield "INSERT INTO codes(feature,ordering,value) VALUES (@col%d, %d, '%s'); SET @val%d_%d=LAST_INSERT_ID();\n" % (
i, j, sql_fix(a), i, j)
values[col][a] = "@val%d_%d" % (i, j)
j += 1
i += 1
yield "CREATE TABLE %s (sampleID INT NOT NULL UNIQUE" % clinical_table
for col in self.col_order:
if col == 'sampleName':
yield ",\n\tsampleName INT UNSIGNED NOT NULL UNIQUE"
else:
if self.enum_map.has_key(col):
yield ",\n\t`%s` INT UNSIGNED DEFAULT NULL" % (col.strip())
else:
yield ",\n\t`%s` FLOAT DEFAULT NULL" % (col.strip())
yield """
) engine 'MyISAM';
"""
for target in sortedSamples(self.row_hash.keys()):
a = []
for col, orig in zip(self.col_order, self.orig_order):
if col == 'sampleName':
val = target
else:
val = self.row_hash[target][self.col_list[orig]]
if val is None or val.upper() in NULL_VALUES:
a.append("\\N")
else:
if col in self.enum_map:
a.append(values[col][val])
else:
a.append(val)
yield u"INSERT INTO %s VALUES ( %d, %s );\n" % (
clinical_table, id_table.get(table_name + ':sample_id',
target), u",".join(a))
import CGData
import CGData.NumpyMatrix
import sys
# matrixProbeRemap.py <matrixFile> <probeFile>
#load the matrix
matrix = CGData.NumpyMatrix.NumpyMatrix()
matrixHandle = open(sys.argv[1])
matrix.read(matrixHandle)
matrixHandle.close()
#load the probeMap
probeMap = CGData.load(sys.argv[2])
#remove null probes from the matrix
matrix.remove_null_probes()
#remap the matrix using the probe map
valid_map = {}
for alt in probeMap.get_probes():
valid_map[alt.aliases[0]] = True
if alt.name in matrix.get_row_names():
matrix.row_rename(alt.name, alt.aliases[0])
remove_list = []
for name in matrix.get_row_names():
if not name in valid_map:
def gen_sql_heatmap(self, id_table):
# scan the children
# XXX Handling of sql for children is broken if the child may appear
# as part of multiple merge objects, such as TrackGenomic and TrackClinical.
# A disgusting workaround for clinicalMatrix is to prevent the TrackGenomic from calling
# it for gen_sql.
clinical = self.members.pop("clinicalMatrix")
for line in CGData.CGMergeObject.sql_pass(self, id_table, method="heatmap"):
yield line
self.members["clinicalMatrix"] = clinical
gmatrix = self.members["genomicMatrix"]
pmap = self.members["probeMap"].lookup(assembly="hg18") # BUG: hard coded to only producing HG18 tables
if pmap is None:
CGData.error("Missing HG18 %s" % (self.members["probeMap"].get_name()))
return
table_base = self.get_name()
CGData.log("Writing Track %s" % (table_base))
clinical_table_base = self.members["clinicalMatrix"].get_name()
other = {}
for attr in ["wrangler", "wrangling_procedure", "url", "citation", "description"]:
if attr in gmatrix:
other[attr] = gmatrix[attr]
if "dataProducer" in gmatrix:
other["author_list"] = gmatrix["dataProducer"]
if "articleTitle" in gmatrix:
other["article_title"] = gmatrix["articleTitle"]
other["version"] = gmatrix.get("version", "")
datetime.datetime.strptime(
other["version"], "%Y-%m-%d"
) # if the version isn't properly formatted, though exception
if "owner" in gmatrix:
other["owner"] = gmatrix["owner"]
other["colNormalization"] = gmatrix.get("colNormalization", False)
if not isinstance(other["colNormalization"], bool):
other["colNormalization"] = False
other["redistribution"] = gmatrix.get("redistribution", False)
if not isinstance(other["redistribution"], bool):
other["redistribution"] = False
other["security"] = gmatrix.get("security", "public")
if other["security"] not in ["public", "private"]:
other["security"] = "public"
yield "DELETE from raDb where name = '%s';\n" % ("genomic_" + table_base)
yield "INSERT into raDb( name, sampleTable, clinicalTable, columnTable, aliasTable, shortLabel, longLabel, expCount, dataType, platform, profile, security, priority, gain, groupName, wrangler, url, article_title, citation, author_list, wrangling_procedure, other) VALUES ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%d', '%s', '%s', '%s', '%s', %f, %f, '%s', %s, %s, %s, %s, %s, %s, '%s');\n" % (
"genomic_" + table_base,
"sample_" + table_base,
"clinical_" + clinical_table_base,
"colDb",
"genomic_" + table_base + "_alias",
sql_fix(gmatrix["shortTitle"]),
sql_fix(gmatrix["longTitle"]),
len(gmatrix.get_sample_list()),
self.format,
dataSubTypeMap[gmatrix[":dataSubType"]]
if gmatrix[":dataSubType"] in dataSubTypeMap
else gmatrix[":dataSubType"],
"localDb",
"public",
float(gmatrix.get("priority", 1.0)),
float(gmatrix.get("gain", 1.0)),
sql_fix(gmatrix.get("groupTitle", "Misc.")),
"'%s'" % sql_fix(gmatrix["wrangler"]) if "wrangler" in gmatrix else "\N",
"'%s'" % sql_fix(gmatrix["url"]) if "url" in gmatrix else "\N",
"'%s'" % sql_fix(gmatrix["articleTitle"]) if "articleTitle" in gmatrix else "\N",
"'%s'" % sql_fix(gmatrix["citation"]) if "citation" in gmatrix else "\N",
"'%s'" % sql_fix(gmatrix["dataProducer"]) if "dataProducer" in gmatrix else "\N",
"'%s'" % sql_fix(gmatrix["wrangling_procedure"]) if "wrangling_procedure" in gmatrix else "\N",
sql_fix(json.dumps(other)),
)
# write out the sample table
yield "drop table if exists sample_%s;" % (table_base)
yield """
CREATE TABLE sample_%s (
id int,
sampleName varchar(255)
) engine 'MyISAM';
""" % (
table_base
)
from CGData.ClinicalMatrix import sortedSamples
for sample in sortedSamples(gmatrix.get_sample_list()):
yield "INSERT INTO sample_%s VALUES( %d, '%s' );\n" % (
table_base,
id_table.get(clinical_table_base + ":sample_id", sample),
sql_fix(sample),
)
yield "drop table if exists genomic_%s_alias;" % (table_base)
yield """
CREATE TABLE genomic_%s_alias (
name varchar(255),
alias varchar(255)
) engine 'MyISAM';
""" % (
table_base
)
for probe in pmap.get_probes():
for alias in probe.aliases:
yield "insert into genomic_%s_alias( name, alias ) values( '%s', '%s' );\n" % (
table_base,
sql_fix(probe.name),
sql_fix(alias),
)
# write out the BED table
yield "drop table if exists %s;" % ("genomic_" + table_base)
yield CREATE_BED % ("genomic_" + table_base + "_tmp")
sample_ids = []
samples = gmatrix.get_sample_list()
# sort samples by sample_id, and retain the sort order for application to the genomic data, below
tmp = sorted(
zip(samples, range(len(samples))),
cmp=lambda x, y: id_table.get(clinical_table_base + ":sample_id", x[0])
- id_table.get(clinical_table_base + ":sample_id", y[0]),
)
samples, order = map(lambda t: list(t), zip(*tmp))
for sample in samples:
sample_ids.append(str(id_table.get(clinical_table_base + ":sample_id", sample)))
exp_ids = ",".join(sample_ids)
missingProbeCount = 0
for probe_name in gmatrix.get_probe_list():
# get the genomic data and rearrange to match the sample_id order
tmp = gmatrix.get_row_vals(probe_name)
row = map(lambda i: tmp[order[i]], range(len(tmp)))
pset = pmap.lookup(probe_name)
if pset is not None:
for probe in pset:
istr = (
"insert into %s(chrom, chromStart, chromEnd, strand, name, expCount, expIds, expScores) values ( '%s', '%s', '%s', '%s', '%s', '%s', '%s', %s );\n"
% (
"genomic_%s_tmp" % (table_base),
probe.chrom,
probe.chrom_start - 1,
probe.chrom_end,
probe.strand,
sql_fix(probe_name),
len(sample_ids),
exp_ids,
self.scores(row),
)
)
yield istr
else:
missingProbeCount += 1
yield "# sort file by chrom position\n"
yield "create table genomic_%s like genomic_%s_tmp;\n" % (table_base, table_base)
yield "insert into genomic_%s select * from genomic_%s_tmp order by chrom, chromStart;\n" % (
table_base,
table_base,
)
yield "drop table genomic_%s_tmp;\n" % table_base
CGData.log("%s Missing probes %d" % (table_base, missingProbeCount))
class ProbeMap(CGData.CGDataSetObject, CGData.CGGroupMember):
child_type = Probe
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('name', str, primary_key=True),
CGData.Column('chrom', str),
CGData.Column('chrom_start', str),
CGData.Column('chrom_end', int),
CGData.Column('strand', str)
]
def __init__(self):
CGData.CGDataSetObject.__init__(self)
self.gene_map = None
self.chrom_map = None
def read(self, handle):
self.gene_map = {}
self.chrom_map = {}
read = csv.reader(handle, delimiter="\t")
for line in read:
self.gene_map[line[0]] = line[1].split(',')
try:
self.append(
Probe(line[0], line[2], int(line[3]), int(line[4]),
line[5], self.gene_map[line[0]]))
except ValueError:
"""location int conversion failed, ignore silently"""
pass
def append(self, probe):
for attr in self.child_type.core_attr:
if not hasattr(probe, attr):
raise CGData.FormatException("Missing %s" % (attr))
if self.chrom_map is None:
self.chrom_map = {}
if not probe.chrom in self.chrom_map:
self.chrom_map[probe.chrom] = {}
if not probe.name in self.chrom_map[probe.chrom]:
self.chrom_map[probe.chrom][probe.name] = [probe]
else:
self.chrom_map[probe.chrom][probe.name].append(probe)
def write(self, handle):
for chrom in self.chrom_map:
for probeName in self.chrom_map[chrom]:
probes = self.chrom_map[chrom][probeName]
for probe in probes:
handle.write("%s\n" % ("\t".join([
probe.name, ",".join(probe.aliases), probe.chrom,
str(probe.chrom_start),
str(probe.chrom_end), probe.strand
])))
# XXX need a better name. What does this return?
def lookup(self, item):
if self.gene_map is None:
self.load()
for chrome in self.chrom_map:
if item in self.chrom_map[chrome]:
return self.chrom_map[chrome][item]
return None
def row_iter(self):
if self.gene_map is None:
self.load()
for chrome in self.chrom_map:
for probe in self.chrom_map[chrome]:
pset = self.chrom_map[chrome][probe]
for p in pset:
yield (p.name, p.chrom, p.chrom_start, p.chrom_end,
p.strand)
# XXX I have no idea what this is returning. What is a pset?
def get_probes(self):
if self.gene_map is None:
self.load()
for chrome in self.chrom_map:
for probeSet in self.chrom_map[chrome]:
for probe in self.chrom_map[chrome][probeSet]:
yield probe
