def __init__(self, name, data, workdir=None, mapfile=None):
self.name = name
self.data = os.path.abspath(os.path.expanduser(data))
self.mainparams = _MainParams()
self.extraparams = _ExtraParams()
self.clumppparams = _ClumppParams()
self.asyncs = []
## check that bpp is installed and in path
for binary in ['structure']:
if not subprocess.call("type " + binary,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE) == 0:
raise IPyradWarningExit(MISSING_IMPORTS)
## make workdir if it does not exist
if workdir:
self.workdir = os.path.abspath(os.path.expanduser(workdir))
else:
self.workdir = OPJ(os.path.abspath('.'), "analysis-structure")
if not os.path.exists(self.workdir):
os.makedirs(self.workdir)
## check that strfile exists, print and parse some info from it
with open(data) as ifile:
lines = ifile.readlines()
self.ntaxa = len(lines) // 2
self.nsites = len(lines[0].strip().split()[1:])
self.labels = [i.split('\t')[0].strip() for i in lines][::2]
self.popdata = [i.split('\t')[1] for i in lines][::2]
self.popflag = [i.split('\t')[2] for i in lines][::2]
self.locdata = [i.split('\t')[3] for i in lines][::2]
self.phenotype = [i.split('\t')[4] for i in lines][::2]
#self.extra = [i.split('\t')[5] for i in lines][::2] #default extracols=0
del lines
## if mapfile then parse it to an array
if mapfile:
with open(mapfile) as inmap:
maparr = np.genfromtxt(inmap)[:, [0, 3]].astype(np.uint64)
spans = np.zeros((maparr[-1, 0], 2), np.uint64)
spans = get_spans(maparr, spans)
self.maparr = spans
self.nsites = spans.shape[0]
else:
self.maparr = None
def __init__(self, name, strfile, workdir=None, mapfile=None):
self.name = name
self.strfile = os.path.realpath(strfile)
self.mainparams = _MainParams()
self.extraparams = _ExtraParams()
self.clumppparams = _ClumppParams()
self.asyncs = []
## make workdir if it does not exist
if workdir:
self.workdir = os.path.realpath(workdir)
else:
self.workdir = os.path.join(os.path.curdir, "analysis-structure")
if not os.path.exists(self.workdir):
os.makedirs(self.workdir)
## check that strfile exists, print and parse some info from it
with open(strfile) as ifile:
lines = ifile.readlines()
self.ntaxa = len(lines) // 2
self.nsites = len(lines[0].strip().split()[1:])
self.labels = [i.split('\t')[0].strip() for i in lines][::2]
self.popdata = [i.split('\t')[1] for i in lines][::2]
self.popflag = [i.split('\t')[2] for i in lines][::2]
del lines
## if mapfile then parse it to an array
if mapfile:
with open(mapfile) as inmap:
maparr = np.genfromtxt(inmap)[:, [0, 3]].astype(np.uint64)
spans = np.zeros((maparr[-1, 0], 2), np.uint64)
spans = get_spans(maparr, spans)
self.maparr = spans
self.nsites = spans.shape[0]
else:
self.maparr = None
def __init__(self,
data,
name="test",
workdir="analysis-treemix",
imap=None,
mapfile=None,
minmap=None,
*args,
**kwargs):
## path attributes
self.name = name
self.data = data
self.mapfile = mapfile
## if not imap then it will be set to 1
if imap:
self.imap = imap
## if not minmap then none
if minmap:
self.minmap = minmap
## params dict
self.params = Params()
self.params.k = 0
self.params.m = 0
self.params.g = (None, None)
self.params.bootstrap = 0
self.params.cormig = 0
self.params.climb = 0
self.params.noss = 0
self.params.seed = np.random.randint(0, int(1e9))
self.params.root = None
self.params.se = 0
self.params.global_ = 0
## if mapfile then parse it to an array
if self.mapfile:
with open(self.mapfile) as inmap:
maparr = np.genfromtxt(inmap)[:, [0, 3]].astype(np.uint64)
spans = np.zeros((maparr[-1, 0], 2), np.uint64)
spans = get_spans(maparr, spans)
self.maparr = spans
self.nsites = spans.shape[0]
else:
self.maparr = None
## make workdir if it does not exist
if workdir:
self.workdir = os.path.abspath(os.path.expanduser(workdir))
else:
self.workdir = OPJ(os.path.curdir, "analysis-structure")
if not os.path.exists(self.workdir):
os.makedirs(self.workdir)
## set params
notparams = set(["workdir", "name", "data", "minmap", "imap"])
for key in set(kwargs.keys()) - notparams:
self.params[key] = kwargs[key]
## check binary
self._get_binary()
## results files
self.files = Params()
self.files.cov = OPJ(self.workdir, self.name + ".cov.gz")
self.files.covse = OPJ(self.workdir, self.name + ".covse.gz")
self.files.edges = OPJ(self.workdir, self.name + ".edges.gz")
self.files.llik = OPJ(self.workdir, self.name + ".llik")
self.files.modelcov = OPJ(self.workdir, self.name + ".modelcov.gz")
self.files.treeout = OPJ(self.workdir, self.name + ".treeout.gz")
self.files.vertices = OPJ(self.workdir, self.name + ".vertices.gz")
## results
self.results = Params()
self.results.tree = ""
self.results.admixture = []
self.results.cov = []
self.results.covse = []
self.results.modelcov = []