def load_snakemake_params():
global is_snakemake_child
if PARAMETER_PASSING_ENVVAR not in os.environ:
return
is_snakemake_child = lambda: True
import json, collections
from snakemake.io import Namedlist
import builtins
options = json.load(open(os.environ[PARAMETER_PASSING_ENVVAR]))
# Unset the parameter file var not to pass to children.
del os.environ[PARAMETER_PASSING_ENVVAR]
for varname, value in options.items():
if not isinstance(value, int):
nl = Namedlist()
for k, v in value:
nl.append(v)
if k is not None:
nl.add_name(k)
value = nl
setattr(builtins, varname, value)
def recursive_format(ruleinfo):
"""Expand wildcards within ruleinfo
This is not fully implemented!
At this time, only `input` and `output` are expanded within
`params`.
"""
args = {}
for name in ['input', 'output']:
attr = getattr(ruleinfo, name)
if attr is None:
continue
nlist = Namedlist()
for item in flatten(attr[0]):
nlist.append(item)
for key, item in attr[1].items():
nlist.append(item)
nlist.add_name(key)
args[name] = nlist
for key, value in ruleinfo.params[1].items():
if not isinstance(value, str):
continue
value = partial_format(value, **args)
ruleinfo.params[1][key] = value
def make_namedlist(self, item, first_lvl=True):
if isinstance(item, list):
return Namedlist(item)
elif isinstance(item, dict):
return Namedlist(fromdict={
k: self.make_namedlist(v, False)
for k, v in item.items()
})
elif isinstance(item, (str, int, float)):
if first_lvl:
return Namedlist([item])
else:
return item
return Namedlist([])
def listfiles(pattern, restriction=None, omit_value=None):
"""
Yield a tuple of existing filepaths for the given pattern.
Wildcard values are yielded as the second tuple item.
Arguments
pattern -- a filepattern.
Wildcards are specified in snakemake syntax, e.g. "{id}.txt"
"""
pattern = os.path.normpath(pattern)
first_wildcard = re.search("{[^{]", pattern)
if first_wildcard:
dirname = os.path.dirname(pattern[:first_wildcard.start()])
if not dirname:
dirname = "."
else:
dirname = os.path.dirname(pattern)
pattern = re.compile(regex(pattern))
for dirpath, dirnames, filenames in os.walk(dirname):
for f in chain(filenames, dirnames):
if dirpath != ".":
f = os.path.join(dirpath, f)
match = re.match(pattern, f)
if match and len(match.group()) == len(f):
wildcards = Namedlist(fromdict=match.groupdict())
if restriction is not None:
invalid = any(omit_value not in v and v != wildcards[k]
for k, v in restriction.items())
if not invalid:
yield f, wildcards
else:
yield f, wildcards
def _to_iofile(self, files):
def cleanup(f):
prefix = self.rule.workflow.default_remote_prefix
# remove constraints and turn this into a plain string
cleaned = strip_wildcard_constraints(f)
modified_by = get_flag_value(f, PATH_MODIFIER_FLAG)
if (
self.rule.workflow.default_remote_provider is not None
and f.startswith(prefix)
and not is_flagged(f, "local")
):
cleaned = f[len(prefix) + 1 :]
cleaned = IOFile(cleaned, rule=self.rule)
else:
cleaned = IOFile(AnnotatedString(cleaned), rule=self.rule)
cleaned.clone_remote_object(f)
if modified_by is not None:
cleaned.flags[PATH_MODIFIER_FLAG] = modified_by
return cleaned
files = Namedlist(files, custom_map=cleanup)
return files
def load_snakemake_params():
global is_snakemake_child
if PARAMETER_PASSING_ENVVAR not in os.environ:
return
is_snakemake_child = lambda: True
import json, collections
from snakemake.io import Namedlist
import builtins
options = json.load(open(os.environ[PARAMETER_PASSING_ENVVAR]))
# Unset the parameter file var not to pass to children.
del os.environ[PARAMETER_PASSING_ENVVAR]
for varname, value in options.items():
if not isinstance(value, int):
nl = Namedlist()
for k, v in value:
nl.append(v)
if k is not None:
nl.add_name(k)
value = nl
setattr(builtins, varname, value)
def listfiles(pattern, restriction=None, omit_value=None):
"""Yield a tuple of existing filepaths for the given pattern.
Wildcard values are yielded as the second tuple item.
Args:
pattern (str): a filepattern. Wildcards are specified in snakemake syntax, e.g. "{id}.txt"
restriction (dict): restrict to wildcard values given in this dictionary
omit_value (str): wildcard value to omit
Yields:
tuple: The next file matching the pattern, and the corresponding wildcards object
"""
pattern = os.path.normpath(pattern)
first_wildcard = re.search("{[^{]", pattern)
if first_wildcard:
dirname = os.path.dirname(pattern[: first_wildcard.start()])
if not dirname:
dirname = "."
else:
dirname = os.path.dirname(pattern)
pattern = re.compile(regex(pattern))
for dirpath, dirnames, filenames in os.walk(dirname):
for f in chain(filenames, dirnames):
if dirpath != ".":
f = os.path.normpath(os.path.join(dirpath, f))
match = re.match(pattern, f)
if match:
wildcards = Namedlist(fromdict=match.groupdict())
if restriction is not None:
invalid = any(
omit_value not in v and v != wildcards[k]
for k, v in restriction.items()
)
if not invalid:
yield f, wildcards
else:
yield f, wildcards
