def __init__(
self,
input_file_1,
input_file_2,
output_prefix,
collapse=True,
threads=1,
options={},
dependencies=(),
):
cmd = _get_common_parameters(threads=threads, options=options)
# Prefix for output files, to ensure that all end up in temp folder
cmd.set_option("--basename", "%(TEMP_OUT_BASENAME)s")
output_tmpl = output_prefix + ".%s.gz"
cmd.set_kwargs(
TEMP_OUT_BASENAME=os.path.basename(output_prefix),
OUT_SETTINGS=output_prefix + ".settings",
OUT_READS_1=output_tmpl % ("pair1.truncated", ),
OUT_READS_2=output_tmpl % ("pair2.truncated", ),
OUT_SINGLETON=output_tmpl % ("singleton.truncated", ),
OUT_DISCARDED=output_tmpl % ("discarded", ),
)
if collapse:
cmd.set_option("--collapse")
cmd.set_kwargs(
OUT_COLLAPSED=output_tmpl % ("collapsed", ),
OUT_COLLAPSED_TRUNC=output_tmpl % ("collapsed.truncated", ),
)
cmd.set_option("--file1", "%(IN_READS_1)s")
cmd.set_option("--file2", "%(IN_READS_2)s")
cmd.set_kwargs(IN_READS_1=input_file_1, IN_READS_2=input_file_2)
apply_options(cmd, options)
CommandNode.__init__(
self,
command=cmd.finalize(),
threads=threads,
description="<AdapterRM (PE): %s -> '%s.*'>" % (
fileutils.describe_paired_files(input_file_1, input_file_2),
output_prefix,
),
dependencies=dependencies,
)
def __init__(self, parameters):
command = parameters.command.finalize()
self._multi_file_input = len(parameters.input_files_1) > 1
if self._multi_file_input:
cat_1 = _build_cat_command(parameters.input_files_1, "uncompressed_input_1")
cat_2 = _build_cat_command(parameters.input_files_2, "uncompressed_input_2")
command = ParallelCmds((command, cat_1, cat_2))
CommandNode.__init__(self,
command=command,
threads=parameters.threads,
description="<AdapterRM (PE): %s -> '%s.*'>"
% (fileutils.describe_paired_files(parameters.input_files_1,
parameters.input_files_2),
parameters.output_prefix),
dependencies=parameters.dependencies)
def _get_node_description(name, input_files_1, input_files_2=(),
algorithm=None, prefix=None, threads=1):
info = []
if prefix is not None:
prefix = os.path.basename(prefix)
if prefix.endswith(".fasta") or prefix.endswith(".fa"):
prefix = prefix.rsplit(".", 1)[0]
info.append(prefix)
if algorithm is not None:
info.append(algorithm)
if threads > 1:
info.append("%i threads" % (threads,))
file_desc = describe_paired_files(input_files_1, input_files_2 or ())
return "<%s (%s): %s>" % (name, ", ".join(info), file_desc)
def _get_node_description(name, input_files_1, input_files_2=None,
algorithm=None, prefix=None, threads=1):
info = []
if prefix is not None:
prefix = os.path.basename(prefix)
if prefix.endswith(".fasta") or prefix.endswith(".fa"):
prefix = prefix.rsplit(".", 1)[0]
info.append(prefix)
if algorithm is not None:
info.append(algorithm)
if threads > 1:
info.append("%i threads" % (threads,))
file_desc = describe_paired_files(input_files_1, input_files_2 or ())
return "<%s (%s): %s>" % (name, ", ".join(info), file_desc)
def test_describe_paired_files__different_path_and_files():
files_1 = ("foo/1_abc", "bar/2_def")
files_2 = ("zed/3_ghi", "not/4_jkl")
expected = "2 pair(s) of files"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__same_path__similar_files__too_different():
files_1 = ("foo/1a_abc", "foo/1a_def")
files_2 = ("foo/2b_ghi", "foo/2b_jkl")
expected = "2 pair(s) of files in 'foo'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__same_path__different_file_lens():
files_1 = ("foo/1_a", "foo/2_de")
files_2 = ("foo/3_g", "foo/4_jk")
expected = "2 pair(s) of files in 'foo'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__identical_files():
fpath = "/var/foo/bar"
ftuple = (fpath,)
assert_equal(describe_paired_files(ftuple, ftuple), repr(fpath))
def test_describe_paired_files__same_path__similar_files__different_prefixes():
files_1 = ("foo/1_abc", "foo/1_def")
files_2 = ("foo/2_ghi", "foo/2_jkl")
expected = "'foo/[12]_???'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__different_path_and_files():
files_1 = ("foo/1_abc", "bar/2_def")
files_2 = ("zed/3_ghi", "not/4_jkl")
expected = "2 pair(s) of files"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__single_file():
fpath = "/var/foo/bar"
assert_equal(describe_paired_files((fpath,), ()), repr(fpath))
def test_describe_paired_files__same_path__different_file_lens():
files_1 = ("foo/1_a", "foo/2_de")
files_2 = ("foo/3_g", "foo/4_jk")
expected = "2 pair(s) of files in 'foo'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__same_path__similar_files__too_different():
files_1 = ("foo/1a_abc", "foo/1a_def")
files_2 = ("foo/2b_ghi", "foo/2b_jkl")
expected = "2 pair(s) of files in 'foo'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__same_path__similar_files__different_prefixes():
files_1 = ("foo/1_abc", "foo/1_def")
files_2 = ("foo/2_ghi", "foo/2_jkl")
expected = "'foo/[12]_???'"
result = describe_paired_files(files_1, files_2)
assert_equal(result, expected)
def test_describe_paired_files__identical_files():
fpath = "/var/foo/bar"
ftuple = (fpath, )
assert_equal(describe_paired_files(ftuple, ftuple), repr(fpath))
def test_describe_paired_files__single_file():
fpath = "/var/foo/bar"
assert_equal(describe_paired_files((fpath, ), ()), repr(fpath))