def hmmbuild(alignment, outfile, name=None, **kwargs):
unlink_file = False
if isinstance(alignment, str): msafile = alignment
elif isinstance(alignment, MultipleSeqAlignment):
msafile = AlignmentUtils.mktmp(alignment)
if not msafile: return False
unlink_file = True
else:
print 'Alignment must be either a filename or an instance of MultipleSeqAlignment'
return False
if not name: name = FilenameParser.strip_ext(os.path.basename(outfile))
ret = run_cline(HMMBuildCommandline(input=msafile,
out=outfile,
n=name,
cpu=cpu_count,
seed=0,
**kwargs),
_msg='Unable to build HMM profile')
if unlink_file: os.unlink(msafile)
return ret
def hmmbuild(alignment, outfile, name=None, **kwargs):
msafile = AlignmentUtils.mktmp(alignment)
if not name: name = FilenameParser.strip_ext(outfile)
return run_cline(HMMBuildCommandline(input=msafile, out=outfile,
n=name, cpu=cpu_count, seed=0, **kwargs),
_msg = 'Unable to build HMM profile')
