def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args, (["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"],))
assert_equal(kwargs, {"IN_FILE": "/in/file",
"OUT_FILE": "/out/file",
"set_cwd": True})
was_called.append(True)
with Monkeypatch("paleomix.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd=True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE="/out/file",
IN_FILE="/in/file")
builder.finalize()
assert was_called
def test_builder__add_option__overwrite():
builder = AtomicCmdBuilder("find")
builder.add_option("-name", "*.txt")
builder.add_option("-or")
builder.add_option("-name", "*.bat")
assert_equal(builder.call, ["find", "-name",
"*.txt", "-or", "-name", "*.bat"])
def test_builder__add_option__overwrite():
builder = AtomicCmdBuilder("find")
builder.add_option("-name", "*.txt")
builder.add_option("-or")
builder.add_option("-name", "*.bat")
assert_equal(builder.call,
["find", "-name", "*.txt", "-or", "-name", "*.bat"])
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock(object):
def __init__(self, *args, **kwargs):
assert_equal(args,
(["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"], ))
assert_equal(kwargs, {
"IN_FILE": "/in/file",
"OUT_FILE": "/out/file",
"set_cwd": True
})
was_called.append(True)
with Monkeypatch("paleomix.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd=True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE="/out/file", IN_FILE="/in/file")
builder.finalize()
assert was_called
def __init__(
self,
reference,
infile,
bedfile,
outfile,
mpileup_options={},
bcftools_options={},
dependencies=(),
):
mpileup = AtomicCmdBuilder(
("bcftools", "mpileup", "%(IN_BAMFILE)s"),
IN_BAMFILE=infile,
IN_INTERVALS=bedfile,
OUT_STDOUT=AtomicCmd.PIPE,
CHECK_VERSION=BCFTOOLS_VERSION,
)
# Ignore read-groups for pileup
mpileup.add_option("--ignore-RG")
# Reference sequence (FASTA)
mpileup.add_option("--fasta-ref", reference)
# Output compressed VCF
mpileup.add_option("--output-type", "u")
if bedfile:
mpileup.set_option("--regions-file", "%(IN_INTERVALS)s")
apply_options(mpileup, mpileup_options)
genotype = AtomicCmdBuilder(
("bcftools", "call", "-"),
IN_STDIN=mpileup,
IN_BAMFILE=infile,
OUT_STDOUT=outfile,
CHECK_VERSION=BCFTOOLS_VERSION,
)
genotype.set_option("--output-type", "z")
apply_options(genotype, bcftools_options)
CommandNode.__init__(
self,
description="<GenotypeRegions: '%s' -> '%s'>" % (
infile,
outfile,
),
command=ParallelCmds([mpileup.finalize(),
genotype.finalize()]),
dependencies=dependencies,
)
def test_builder__pop_option__last_option():
builder = AtomicCmdBuilder("find")
builder.add_option("-size", "0", fixed=False)
builder.add_option("-size", "1", fixed=False)
builder.pop_option("-size")
assert_equal(builder.call, ["find", "-size", "0"])
def test_builder__pop_option__last_option():
builder = AtomicCmdBuilder("find")
builder.add_option("-size", "0", fixed=False)
builder.add_option("-size", "1", fixed=False)
builder.pop_option("-size")
assert_equal(builder.call, ["find", "-size", "0"])
