def test_builder__add_multiple_values_multiple_times():
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(("file_a",))
assert_equal(kwargs, {"IN_FILE_01": "file_a"})
kwargs = builder.add_multiple_values(("file_b",))
assert_equal(kwargs, {"IN_FILE_02": "file_b"})
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(IN_FILE_01)s", "%(IN_FILE_02)s"])
def test_builder__add_multiple_values_with_template():
values = ("file_a", "file_b")
expected = {"OUT_BAM_1": "file_a", "OUT_BAM_2": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values, template="OUT_BAM_%i")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(OUT_BAM_1)s", "%(OUT_BAM_2)s"])
def test_builder__add_multiple_values():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values)
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(IN_FILE_01)s", "%(IN_FILE_02)s"])
def test_builder__add_multiple_values_with_template():
values = ("file_a", "file_b")
expected = {"OUT_BAM_1": "file_a", "OUT_BAM_2": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values, template="OUT_BAM_%i")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(OUT_BAM_1)s", "%(OUT_BAM_2)s"])
def __init__(self, d_bam, dependencies):
aux_r = os.path.join(os.path.dirname(gccorrect.__file__), 'model_gc.R')
dest = os.path.join(d_bam.bam_output,
'%s_GC_Model.txt' % (str(d_bam.bam_name)))
plot_dest = os.path.splitext(dest)[0] + '.pdf'
infiles = [''.join(n.output_files) for n in dependencies]
builder = AtomicCmdBuilder(("Rscript", "%(AUX_R)s"))
builder.add_value('%(OUT_FILEPATH)s')
builder.add_value('%(OUT_PLOT)s')
builder.add_multiple_values(infiles)
builder.set_kwargs(AUX_R=aux_r,
OUT_FILEPATH=dest,
OUT_PLOT=plot_dest,
CHECK_VERSION=Rscript_VERSION)
cmd = builder.finalize()
d_bam.opts['BamInfo']['--GCmodel'] = dest
description = "<CreateGCModel: '%s' -> '%s'" % (d_bam.bam_temp_local,
dest)
CommandNode.__init__(self,
description=description,
command=cmd,
dependencies=dependencies)
