def _read_pstdata(self):
row = SnpReader._read_fam(self.filename, remove_suffix="dat")
col, col_property = SnpReader._read_map_or_bim(self.filename,
remove_suffix="dat",
add_suffix="map")
if len(row) == 0 or len(col) == 0:
return SnpData(iid=row,
sid=col,
pos=col_property,
val=np.empty([len(row), len(col)]))
datfields = pd.read_csv(self.filename,
delimiter='\t',
header=None,
index_col=False,
skiprows=self.skiprows)
if not np.array_equal(datfields[0], col):
raise Exception(
"Expect snp list in map file to exactly match snp list in dat file"
)
del datfields[0]
del datfields[1]
del datfields[2]
assert len(row) == datfields.shape[
1], "Expect # iids in fam file to match dat file"
val = datfields.values.T
snpdata = SnpData(iid=row, sid=col, pos=col_property, val=val)
return snpdata
def row(self):
"""*same as* :attr:`iid`
"""
if not hasattr(self, "_row"):
_fam = SnpReader._name_of_other_file(self.path,
remove_suffix="bed",
add_suffix="fam")
local_fam = self._storage.open_read(_fam)
self._row = SnpReader._read_fam(local_fam.__enter__(),
remove_suffix="fam")
self._file_dict["fam"] = local_fam
return self._row
def _read_pstdata(self):
row = SnpReader._read_fam(self.filename,remove_suffix="dat")
col, col_property = SnpReader._read_map_or_bim(self.filename,remove_suffix="dat", add_suffix="map")
if len(row)==0 or len(col)==0:
return SnpData(iid=row,sid=col,pos=col_property,val=np.empty([len(row),len(col)]))
datfields = pd.read_csv(self.filename,delimiter = '\t',header=None,index_col=False)
if not np.array_equal(np.array([x.encode('ascii') for x in datfields[0]]), col) : raise Exception("Expect snp list in map file to exactly match snp list in dat file")
del datfields[0]
del datfields[1]
del datfields[2]
assert len(row) == datfields.shape[1], "Expect # iids in fam file to match dat file"
val = datfields.values.T
snpdata = SnpData(iid=row,sid=col,pos=col_property,val=val)
return snpdata
def _run_once(self):
if self._ran_once:
return
self._ran_once = True
if not hasattr(self,"_row"):
self._row = SnpReader._read_fam(self.filename,remove_suffix="bed")
if not hasattr(self,"_col") or not hasattr(self,"_col_property"):
self._col, self._col_property = SnpReader._read_map_or_bim(self.filename,remove_suffix="bed", add_suffix="bim")
self._assert_iid_sid_pos()
if not self.skip_format_check:
self._open_bed()
self._close_bed()
def _run_once(self):
if self._ran_once:
return
self._ran_once = True
if not hasattr(self, "_row"):
self._row = SnpReader._read_fam(self.filename, remove_suffix="bed")
if not hasattr(self, "_col") or not hasattr(self, "_col_property"):
self._col, self._col_property = SnpReader._read_map_or_bim(
self.filename, remove_suffix="bed", add_suffix="bim")
self._assert_iid_sid_pos(check_val=False)
if not self.skip_format_check:
self._open_bed()
self._close_bed()
def row(self):
"""*same as* :attr:`iid`
"""
if not hasattr(self, "_row"):
self._row = SnpReader._read_fam(self.filename, remove_suffix="bed")
return self._row
def row(self):
"""*same as* :attr:`iid`
"""
if not hasattr(self,"_row"):
self._row = SnpReader._read_fam(self.filename,remove_suffix="bed")
return self._row