def _get_node_description(name, algorithm, input_files_1, input_files_2 = (), prefix = None, threads = 1):
threads_str = ("%i threads" % (threads,)) if (threads > 1) else None
prefix_str = os.path.basename(prefix) if prefix else None
if prefix_str.endswith(".fasta") or prefix_str.endswith(".fa"):
prefix_str = prefix_str.rsplit(".", 1)[0]
file_desc = describe_paired_files(input_files_1, input_files_2 or ())
info = ", ".join(filter(None, (prefix_str, algorithm, threads_str)))
return "<%s (%s): %s>" % (name, info, file_desc)
def _get_node_description(name,
algorithm,
input_files_1,
input_files_2=(),
prefix=None,
threads=1):
threads_str = ("%i threads" % (threads, )) if (threads > 1) else None
prefix_str = os.path.basename(prefix) if prefix else None
if prefix_str.endswith(".fasta") or prefix_str.endswith(".fa"):
prefix_str = prefix_str.rsplit(".", 1)[0]
file_desc = describe_paired_files(input_files_1, input_files_2 or ())
info = ", ".join(filter(None, (prefix_str, algorithm, threads_str)))
return "<%s (%s): %s>" % (name, info, file_desc)
def __init__(self, parameters):
self._quality_offset = parameters.quality_offset
self._version = parameters.version
self._basename = parameters.basename
self._collapse = parameters.collapse
self._check_fastqs = _are_fastq_checks_required(parameters.version)
if len(parameters.input_files_1) != len(parameters.input_files_2):
raise CmdError("Number of mate 1 files differ from mate 2 files: "
"%i != %i" % (len(parameters.input_files_1),
len(parameters.input_files_2)))
zcat_pair_1 = _build_cat_command(parameters.input_files_1, "uncompressed_input_1")
zcat_pair_2 = _build_cat_command(parameters.input_files_2, "uncompressed_input_2")
zip_pair_1 = _build_zip_command(parameters.output_format, parameters.output_prefix, ".pair1.truncated")
zip_pair_2 = _build_zip_command(parameters.output_format, parameters.output_prefix, ".pair2.truncated")
zip_discarded = _build_zip_command(parameters.output_format, parameters.output_prefix, ".discarded")
adapterrm = parameters.command.finalize()
commands = [adapterrm, zip_pair_1, zip_pair_2]
if parameters.version == VERSION_15:
zip_unaligned = _build_zip_command(parameters.output_format, parameters.output_prefix, ".singleton.truncated")
if parameters.collapse:
zip_aln = _build_zip_command(parameters.output_format, parameters.output_prefix, ".collapsed")
zip_aln_trunc = _build_zip_command(parameters.output_format, parameters.output_prefix, ".collapsed.truncated")
commands += [zip_aln, zip_aln_trunc, zip_unaligned]
else:
commands += [zip_unaligned]
else:
zip_aln = _build_zip_command(parameters.output_format, parameters.output_prefix, ".singleton.aln.truncated")
zip_unaligned = _build_zip_command(parameters.output_format, parameters.output_prefix, ".singleton.unaln.truncated")
commands += [zip_aln, zip_unaligned]
commands += [zip_discarded, zcat_pair_1, zcat_pair_2]
commands = ParallelCmds(commands)
description = "<AdapterRM (PE): %s -> '%s.*'>" \
% (fileutils.describe_paired_files(parameters.input_files_1,
parameters.input_files_2),
parameters.output_prefix)
CommandNode.__init__(self,
command=commands,
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
self._quality_offset = parameters.quality_offset
self._version = parameters.version
self._basename = parameters.basename
self._collapse = parameters.collapse
self._check_fastqs = _are_fastq_checks_required(parameters.version)
if len(parameters.input_files_1) != len(parameters.input_files_2):
raise CmdError(
"Number of mate 1 files differ from mate 2 files: "
"%i != %i" %
(len(parameters.input_files_1), len(parameters.input_files_2)))
zcat_pair_1 = _build_cat_command(parameters.input_files_1,
"uncompressed_input_1")
zcat_pair_2 = _build_cat_command(parameters.input_files_2,
"uncompressed_input_2")
zip_pair_1 = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".pair1.truncated")
zip_pair_2 = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".pair2.truncated")
zip_discarded = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".discarded")
adapterrm = parameters.command.finalize()
commands = [adapterrm, zip_pair_1, zip_pair_2]
if parameters.version == VERSION_15:
zip_unaligned = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.truncated")
if parameters.collapse:
zip_aln = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".collapsed")
zip_aln_trunc = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".collapsed.truncated")
commands += [zip_aln, zip_aln_trunc, zip_unaligned]
else:
commands += [zip_unaligned]
else:
zip_aln = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.aln.truncated")
zip_unaligned = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.unaln.truncated")
commands += [zip_aln, zip_unaligned]
commands += [zip_discarded, zcat_pair_1, zcat_pair_2]
commands = ParallelCmds(commands)
description = "<AdapterRM (PE): %s -> '%s.*'>" \
% (fileutils.describe_paired_files(parameters.input_files_1,
parameters.input_files_2),
parameters.output_prefix)
CommandNode.__init__(self,
command=commands,
description=description,
dependencies=parameters.dependencies)
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__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))
