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()
class DataSubType(CGData.CGDataSetObject):
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('name', str, primary_key=True),
]
def __init__(self):
CGData.CGDataSetObject.__init__(self)
class Assembly(CGData.CGObjectBase):
"""
Blank Class to represent Genome Assemblies
"""
DATA_FORM = CGData.TABLE
COLS = [
CGData.Column('name', str, primary_key=True),
]
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
