def col_property(self):
"""*same as* :attr:`pos`
"""
if not hasattr(self, "_col_property"):
self._col, self._col_property = SnpReader._read_map_or_bim(
self.filename, remove_suffix="bed", add_suffix="bim")
return self._col_property
def col(self):
"""*same as* :attr:`sid`
"""
if not hasattr(self, "_col"):
self._col, self._col_property = SnpReader._read_map_or_bim(
self.filename,
remove_suffix="pgen",
add_suffix="bim",
max_filesize=1E9)
return self._col
def run_once(self):
if (self._ran_once):
return
self._ran_once = True
self._iid = SnpReader._read_fam(self.dat_filename,remove_suffix="dat")
self._sid, self._pos = SnpReader._read_map_or_bim(self.dat_filename,remove_suffix="dat", add_suffix="map")
self._assert_iid_sid_pos()
return self
def _read_pstdata(self):
col, col_property = SnpReader._read_map_or_bim(self.filename,remove_suffix="ped", add_suffix="map")
ped = np.loadtxt(self.filename, dtype='str', comments=None)
row = ped[:,0:2]
snpsstr = ped[:,6::]
inan=snpsstr==self.missing
snps = np.zeros((snpsstr.shape[0],snpsstr.shape[1]/2))
for i in xrange(snpsstr.shape[1]//2):
snps[inan[:,2*i],i]=np.nan
vals=snpsstr[~inan[:,2*i],2*i:2*(i+1)]
snps[~inan[:,2*i],i]+=(vals==vals[0,0]).sum(1)
snpdata = SnpData(iid=row,sid=col,pos=col_property,val=snps)
return snpdata
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(datfields[0],dtype="string"), 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.as_matrix().T
snpdata = SnpData(iid=row,sid=col,pos=col_property,val=val)
return snpdata
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(datfields[0],dtype="string"), 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.as_matrix().T
snpdata = SnpData(iid=row,sid=col,pos=col_property,val=val)
return snpdata
def _read_pstdata(self):
col, col_property = SnpReader._read_map_or_bim(self.filename,
remove_suffix="ped",
add_suffix="map")
ped = np.loadtxt(self.filename, dtype='str', comments=None)
row = ped[:, 0:2]
snpsstr = ped[:, 6::]
inan = snpsstr == self.missing
snps = np.zeros((snpsstr.shape[0], snpsstr.shape[1] / 2))
for i in xrange(snpsstr.shape[1] // 2):
snps[inan[:, 2 * i], i] = np.nan
vals = snpsstr[~inan[:, 2 * i], 2 * i:2 * (i + 1)]
snps[~inan[:, 2 * i], i] += (vals == vals[0, 0]).sum(1)
snpdata = SnpData(iid=row, sid=col, pos=col_property, val=snps)
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
self._row = SnpReader._read_fam(self.filename,remove_suffix="bed")
self._col, self._col_property = SnpReader._read_map_or_bim(self.filename,remove_suffix="bed", add_suffix="bim")
self._assert_iid_sid_pos()
bedfile = SnpReader._name_of_other_file(self.filename,"bed","bed")
self._filepointer = open(bedfile, "rb")
mode = self._filepointer.read(2)
if mode != 'l\x1b': raise Exception('No valid binary BED file')
mode = self._filepointer.read(1) #\x01 = SNP major \x00 = individual major
if mode != '\x01': raise Exception('only SNP-major is implemented')
logging.info("bed file is open {0}".format(bedfile))
def run_once(self):
if (self._ran_once):
return
self._ran_once = True
self._sid, self._pos = SnpReader._read_map_or_bim(self.basefilename,remove_suffix="bed", add_suffix="map")
pedfile = SnpReader._name_of_other_file(self.basefilename,remove_suffix="ped", add_suffix="ped")
ped = np.loadtxt(pedfile,dtype = 'str',comments=None)
self._iid = ped[:,0:2]
self._assert_iid_sid_pos()
snpsstr = ped[:,6::]
inan=snpsstr==self.missing
self._snps = np.zeros((snpsstr.shape[0],snpsstr.shape[1]/2))
for i in xrange(snpsstr.shape[1]/2):
self._snps[inan[:,2*i],i]=np.nan
vals=snpsstr[~inan[:,2*i],2*i:2*(i+1)]
self._snps[~inan[:,2*i],i]+=(vals==vals[0,0]).sum(1)
