def setup_workdir (self): """ Prepare the necessary input files for FastTree. This creates a temporary working area, and writes input alignment files. """ ## Preconditions & preparations: ## Main: # create workdir and filepaths clineapp.ClineApp.setup_workdir (self) self._inalign_path = scratchfile.make_scratch_file (INALIGN_NAME, self._curr_workdir) # write infile workfile infile_hndl = open (self._inalign_path, 'w') AlignIO.write ([self._in_align], infile_hndl, 'fasta')
def setup_workdir(self):
"""
Perpare the necessary input files for mafft.
This creates a temporary working area, and writes the input sequence
file.
"""
# create workdir and input sequence file
clineapp.ClineApp.setup_workdir(self)
self._inseq_path = scratchfile.make_scratch_file("inseq.fasta", self._curr_workdir)
# convert sequences and fill inseq file
inseqs = []
for s in self._inseqs:
assert isinstance(s, SeqRecord.SeqRecord)
inseqs.append(s)
inseq_hndl = open(self._inseq_path, "w")
SeqIO.write(inseqs, inseq_hndl, "fasta")
inseq_hndl.close()