def split_path(cls, path):
"""
Returns information about a cluster based on the path (filename).
"""
re_file = re.compile(r'(?P<sfam_id>[0-9.]+)' # 1.10.8.10
# - or __
r'(?P<join_char>-|__)'
# ff
r'(?P<cluster_type>\w+)'
# - or __
r'(?:-|__)'
# 1234
r'(?P<cluster_num>[0-9]+)'
# .reduced (optional)
r'(?P<desc>.*?)'
# .sto (optional)
r'(?P<suffix>\.\w+)?$')
basename = os.path.basename(path)
m = re_file.match(basename)
if m:
info = m.groupdict()
info['path'] = os.path.dirname(path)
return info
raise err.NoMatchesError(
'failed to parse cluster details from filename "{}"'.format(
basename))
def search_by_domain_id(self, domain_id):
"""Return the filename of the FunFam alignment containing the domain id."""
if not is_valid_domain_id(domain_id):
raise err.InvalidInputError('{} is not a valid domain id'.format(
repr(domain_id)))
# replace template placeholders with '*'
glob_path = re.sub(r'__([A-Z_]+)__', '*', self.ff_tmpl)
grep_args = (self.grep_path, '--include', glob_path, '-l',
'^' + domain_id, '-R', self.base_dir)
LOG.debug("search_by_domain_id: sys: " + " ".join(grep_args))
try:
# note: this returns bytes (not strings)
grep_out = subprocess.check_output(grep_args).decode('ascii')
except subprocess.CalledProcessError as e:
if e.returncode == 1:
# grep telling us it didn't find any matches
raise err.NoMatchesError(
'failed to find domain id {} with cmd {}'.format(
domain_id, str(e.cmd)))
else:
LOG.error(
'CMD: {}\nCODE: {}\nOUTPUT: {}\nSTDERR: "{}"\nSTDOUT: "{}"\n'
.format(e.cmd, e.returncode, e.output, e.stderr, e.stdout))
raise
except:
raise FileNotFoundError(
"Encountered error trying to find domain_id '{}' (grep: `{}`)".
format(domain_id, " ".join(grep_args)))
ff_files = grep_out.splitlines()
if len(ff_files) == 0:
raise FileNotFoundError(
"Failed to find FunFam alignment for domain_id '{}' (grep: `{}`)"
.format(domain_id, " ".join(grep_args)))
elif len(ff_files) > 1:
raise err.GeneralError(
"Found more than one FunFam file ({}) containing the domain id '{}' (grep: `{}`):\n{}\n"
.format(
len(ff_files),
domain_id,
" ".join(grep_args),
"\n".join(ff_files),
))
LOG.debug("search_by_domain_id: found funfam alignment {}".format(
repr(ff_files[0])))
return ff_files[0]
def funfam_id_from_file(self, ff_file):
"""Extracts a FunfamID from the file name (based on the ff_tmpl)"""
ff_re = self.ff_tmpl
ff_re = ff_re.replace('__SFAM__', r'(?P<sfam_id>[0-9\.]+)')
ff_re = ff_re.replace('__FF_NUM__', r'(?P<ff_num>[0-9]+)')
filename = os.path.basename(ff_file)
m = re.match(ff_re, filename)
if not m:
raise err.NoMatchesError(
"failed to match template '{}' against filename '{}'".format(
ff_re, filename))
ff_id = FunfamID(sfam_id=m.group('sfam_id'),
cluster_num=int(m.group('ff_num')))
return ff_id