def __init__(self, source, target, cmds, remove=False):
self.source = listify(source)
self.target = listify(target)
self.cmds = listify(cmds)
if remove:
rm_cmd = "rm -f {0}".format(" ".join(self.target))
self.cmds = [rm_cmd] + self.cmds
def __init__(self, taxon, chr, pos, ref_allele, alt_allele, profile):
self.taxon = taxon
self.chr = chr
self.pos = pos
self.ref_nt = listify(ref_allele)
self.ref_allele = listify(ref_allele)
self.alt_allele = listify(alt_allele)
self.update(profile)
def __init__(self, taxon, chr, pos, ref_allele, alt_allele, profile):
self.taxon = taxon
self.chr = chr
self.pos = pos
self.ref_nt = listify(ref_allele)
self.ref_allele = listify(ref_allele)
self.alt_allele = listify(alt_allele)
self.update(profile)
def __init__(self, source, target, cmds, id, remove=False):
self.id = id
self.source = listify(source)
self.target = listify(target)
self.cmds = listify(cmds)
if remove:
rm_cmd = "rm -f {0}".format(" ".join(self.target))
self.cmds = [rm_cmd] + self.cmds
def wrapper(*args, **kwargs):
assert outfile in kwargs, "You need to specify `outfile=` on function call"
if infile in kwargs:
infilename = listify(kwargs[infile])
for x in infilename:
assert op.exists(
x), "The specified infile `{0}` does not exist".format(x)
outfilename = kwargs[outfile]
if need_update(infilename, outfilename):
return func(*args, **kwargs)
else:
msg = "File `{0}` exists. Computation skipped.".format(outfilename)
logging.debug(msg)
outfilename = listify(outfilename)
for x in outfilename:
assert op.exists(
x), "Something went wrong, `{0}` not found".format(x)
return outfilename
def wrapper(*args, **kwargs):
assert outfile in kwargs, \
"You need to specify `outfile=` on function call"
if infile in kwargs:
infilename = listify(kwargs[infile])
for x in infilename:
assert op.exists(x), \
"The specified infile `{0}` does not exist".format(x)
outfilename = kwargs[outfile]
if need_update(infilename, outfilename):
return func(*args, **kwargs)
else:
msg = "File `{0}` exists. Computation skipped." \
.format(outfilename)
logging.debug(msg)
outfilename = listify(outfilename)
for x in outfilename:
assert op.exists(x), \
"Something went wrong, `{0}` not found".format(x)
return outfilename
def normalize_axes(axes):
axes = listify(axes)
for ax in axes:
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
ax.set_axis_off()
def normalize_axes(axes):
axes = listify(axes)
for ax in axes:
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
ax.set_axis_off()
def __init__(self, target, args):
for x in args:
x = listify(x)
self.append(Process(target=target, args=x))
def add(self, source, target, cmds, remove=False):
self.ndeps += 1
d = Dependency(source, target, cmds, self.ndeps, remove=remove)
self.append(d)
self.targets |= set(listify(target))
def add(self, source, target, cmds, remove=False):
self.ndeps += 1
d = Dependency(source, target, cmds, self.ndeps, remove=remove)
self.append(d)
self.targets |= set(listify(target))
def __init__(self, target, args):
for x in args:
x = listify(x)
self.append(Process(target=target, args=x))
def __init__(self, source, target, cmds):
self.source = listify(source)
self.target = listify(target)
self.cmds = listify(cmds)
