def __init__(self,
csv=None,
iso_format=True,
origin=date(1970, 1, 1),
delimiter='_',
field=-1,
ft2path=None,
Rpath=None,
java=None,
tmpfile='anchre-tmp',
beast_xml_template=None):
self.csv = csv
self.iso_format = iso_format
self.origin = origin
self.delimiter = delimiter
self.field = field
# paths to binaries
self.ft2path = ft2path
self.Rpath = Rpath
self.java = java
self.pyphy = PyPhy(os.getcwd(), 1) # instance of HyPhy
self.beauti = Beauti(beast_xml_template)
# if given, parse dates from csv
self.dates = {}
if self.csv is not None:
self.parse_date_csv()
# store sequence records
self.fasta = {}
self.last_date = None
self.tmp = tempfile.gettempdir()
self.tmpfile = os.path.join(self.tmp, tmpfile)
self.test()
