def string_format(filepattern):
f = []
last = 0
for match in _wildcard_regex.finditer(filepattern):
f.append(filepattern[last:match.start()])
wildcard = match.group("name")
f.append("{{{}}}".format(wildcard))
last = match.end()
f.append(filepattern[last:])
return "".join(f)
def matches(text):
return [(match.group("name"), match.group("constraint"))
for match in _wildcard_regex.finditer(text)]
def matches(text):
return [(match.group('name'), match.group('constraint'))
for match in _wildcard_regex.finditer(text)]
def glob_wildcards(pattern, files=None):
"""
Glob the values of the wildcards by matching the given pattern to the
filesystem.
Returns a named tuple with a list of values for each wildcard.
"""
from snakemake.io import _wildcard_regex, namedtuple, regex
import regex as re
pattern = os.path.normpath(pattern)
first_wildcard = re.search("{[^{]", pattern)
dirname = os.path.dirname(pattern[:first_wildcard.start()]
) if first_wildcard else os.path.dirname(pattern)
if not dirname:
dirname = "."
names = [
match.group('name') for match in _wildcard_regex.finditer(pattern)
]
Wildcards = namedtuple("Wildcards", names)
wildcards = Wildcards(*[list() for name in names])
pattern = regex(pattern)
# work around partial matching bug in python regex module
# by replacing matches for "\" with "[/\0]" (0x0 can't occur in filenames)
pattern = re.sub('\\\\/', '[/\0]', pattern)
cpattern = re.compile(pattern)
def walker(dirname, pattern):
"""finds files/dirs matching `pattern` in `dirname`"""
for dirpath, dirnames, filenames in os.walk(dirname):
dirpath = os.path.normpath(dirpath)
for f in filenames:
if dirpath != ".":
f = os.path.join(dirpath, f)
match = pattern.match(f)
if match:
yield match
for i in range(len(dirnames) - 1, -1, -1):
d = dirnames[i]
if dirpath != ".":
d = os.path.join(dirpath, d)
match = pattern.match(os.path.join(d, ""), partial=True)
if not match:
del dirnames[i]
continue
if match.partial:
continue
yield match
print("searching {}".format(pattern))
if files is None:
for match in walker(dirname, cpattern):
for name, value in match.groupdict().items():
getattr(wildcards, name).append(value)
else:
for f in files:
match = re.match(cpattern, os.normpath(f))
if match:
for name, value in match.groupdict().items():
getattr(wildcards, name).append(value)
print("searching {}: done".format(pattern))
return wildcards