def __init__(
self,
records,
analysis,
max_guidetrees=10,
tmpdir=None,
datatype=None,
verbosity=0,
):
self.analysis = optioncheck(analysis, ['ml', 'nj',
'TreeCollection'])
self.max_guidetrees = max_guidetrees
self.records = records
self.datatype = datatype or records[0].datatype
self.verbosity = verbosity
optioncheck(self.datatype, ['protein', 'dna'])
self.tmpdir = tmpdir or records[0].tmpdir
directorymake(self.tmpdir)
self.concats = {}
self.history = []
self.populate_cache()
def __init__(
self,
records=None,
input_dir=None,
file_format='fasta',
datatype=None,
tmpdir='/tmp',
calc_distances=False,
compression=None,
analysis=None,
):
self.tmpdir = directorymake(tmpdir)
if records:
self.records = records
self.datatype = datatype or records[0].datatype
optioncheck(self.datatype, ['dna', 'protein'])
for rec in records:
rec.tmpdir = self.tmpdir
elif input_dir:
directorycheck(input_dir)
self.datatype = optioncheck(datatype, ['dna', 'protein'])
optioncheck(file_format, ['fasta', 'phylip'])
self.records = self.read_files(input_dir, file_format, compression)
else:
print 'Provide a list of records, or the path to a set of alignments'
if not self.records:
raise NoRecordsError(file_format, input_dir, compression)
if calc_distances:
self.calc_distances()
self.taxon_set = TaxonSet()
