def mafft_wrapper(work_msa):
app = Applications.MafftCommandline(
input=work_msa.input_fasta,
clustalout=True,
)
stdout, stderr = app()
work_msa.output_aln.write_text(stdout)
def __call__(self):
"""Calls the underlying alignment method.
First, validate method, command, and outpath arguments as valid.
Next, call the underlying method using BioPython commandline
wrapper or internal method and handle stdout/stderr.
"""
# Either delegate call to BioPython or run internal method
if self.method == 'Mafft':
cmdline = Applications.MafftCommandline(self.cmd,
input=self.inpath,
**self.kwargs)
try:
stdout, stderr = cmdline() # Need to log stderr eventually
except ApplicationError: # Raised if subprocess return code != 0
print(
"Failed to run MAFFT") # Should process better eventually
with open(self.outpath, 'w') as o:
o.write(stdout)
elif self.method == 'Generic':
pass # To be implemented