def __init__(self, base_dir, *, ff_tmpl='__SFAM__-ff-__FF_NUM__.sto'):
self.base_dir = base_dir
if re.search(r'[^a-zA-Z_.\-*]', ff_tmpl):
raise err.InvalidInputError(
"ff_tmpl contains unexpected characters")
self.ff_tmpl = ff_tmpl
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 get_by_id(cls, aa_str):
"""Return the AminoAcid object by the given single character aa code."""
aa_str = str(aa_str)
aa_obj = None
if len(aa_str) == 1:
aa_obj = cls._aa_by_one[aa_str.upper()]
elif len(aa_str) == 3:
aa_obj = cls._aa_by_three[aa_str.upper()]
else:
raise err.InvalidInputError(
"expected either 1- or 3-character amino acid id (not: '{}')".
format(aa_str))
return aa_obj
def run_alignment(self,
alignment,
*,
column_gap=None,
group_gap=None,
mclachlan=False):
"""Runs `groupsim` against a given alignment."""
# mclachan max score is 5: normalise to 0-1 before storing
maxscore = 5 if mclachlan else 1
fasta_tmp = tempfile.NamedTemporaryFile(mode='w+',
delete=False,
suffix=".fa")
fasta_tmp_filename = fasta_tmp.name
if not column_gap:
column_gap = self.column_gap
if not group_gap:
group_gap = self.group_gap
column_gap = float(column_gap)
group_gap = float(group_gap)
assert (column_gap > 0 and column_gap < 1)
assert (group_gap > 0 and group_gap < 1)
# write out the alignment with funfam numbers appended to sequence ids
# >1ebgB02/127-436|7431
aln_copy = alignment.copy()
for seq in aln_copy.seqs:
if not seq.cluster_id:
raise err.InvalidInputError((
"need to set_cluster_id() on alignment sequences before running groupsim: {}"
).format(seq.__dict__))
seq.set_uid('{}|{}'.format(seq.uid, str(seq.cluster_id)))
source_ids = {s.cluster_id for s in aln_copy.seqs}
# lower-case aa -> gaps
# '.' -> '-'
for s in aln_copy.seqs:
s.set_all_gap_chars(gap_char='-')
s.set_lower_case_to_gap(gap_char='-')
aln_copy.write_fasta(fasta_tmp_filename)
groupsim_args = [
self.python2path, self.groupsim_path, '-c',
str(self.column_gap), '-g',
str(self.group_gap)
]
if mclachlan:
groupsim_args.extend(['-m', self.mclachlan_path])
groupsim_args.append(fasta_tmp_filename)
groupsim_args.extend(source_ids)
groupsim_args = [str(a) for a in groupsim_args]
LOG.debug("running groupsim: sys: %s", " ".join(groupsim_args))
try:
p = Popen(groupsim_args,
stdout=PIPE,
stderr=PIPE,
universal_newlines=True)
groupsim_out, _ = p.communicate()
except CalledProcessError as e:
LOG.error(
'CMD: %s\nCODE: %s\nOUTPUT: %s\nSTDERR: "%s"\nSTDOUT: "%s"\n',
e.cmd, e.returncode, e.output, e.stderr, e.stdout)
raise e
except:
raise FileNotFoundError(
"Encountered unexpected error running GroupSim: `{}`".format(
" ".join(groupsim_args)))
gs_io = io.StringIO(groupsim_out)
res = GroupsimResult.from_io(gs_io, maxscore=maxscore)
return res
