def __init__(self, infile, outfile=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`PLINK` file.
:param str outfile: (optional) output :term:`VCF` file
"""
if not outfile:
outfile = generate_outfile_name(infile, 'vcf')
super().__init__(infile, outfile)
def __init__(self, infile, outfile):
""".. rubric:: constructor
:param str infile: the path of the input file.
:param str outfile: the path of The output file
"""
if not outfile:
outfile = generate_outfile_name(infile, self.output_ext[0])
self.infile = infile
self.outfile = outfile
self._execute_mode = "shell" #"subprocess" # set to shell to call shell() method
self.logger = logger
def test_utils():
assert utils.get_extension("test.fastq") == "fastq"
assert utils.get_extension("test.fastq.gz",
remove_compression=True) == "fastq"
assert utils.get_extension("test") is None
assert utils.generate_outfile_name("test.fastq", "fq") == "test.fq"
assert utils.get_format_from_extension(".bam") == "BAM"
assert utils.get_format_from_extension(".bb") == "BIGBED"
try:
utils.get_format_from_extension(".temp")
assert False
except:
assert True
def __init__(self, infile, outfile):
""".. rubric:: constructor
:param str infile: the path of the input file.
:param str outfile: the path of The output file
"""
if not outfile:
outfile = generate_outfile_name(infile, self.output_ext[0])
self.infile = infile
self.outfile = outfile
# execute mode can be shell or subprocess.
self._execute_mode = "shell"
# The logger to be set to INFO, DEBUG, WARNING, ERROR, CRITICAL
self.logger = logger
def __init__(self, infile, outfile):
""".. rubric:: constructor
:param str infile: The path of the input file.
:param str outfile: The path of The output file
"""
# do not check the existence of the input file because it could be just a prefix
# if os.path.exists(infile) is False:
# msg = "Incorrect input file: %s" % infile
# _log.error(msg)
# raise ValueError(msg)
if not outfile:
outfile = generate_outfile_name(infile, self.output_ext[0])
self.infile = infile
self.outfile = outfile
self.threads = cpu_count()
self._execute_mode = "shell" #"subprocess" # set to shell to call shell() method
self.logger = logger
def test_generate_outfile_name():
assert generate_outfile_name('foo.fasta', 'phylip') == 'foo.phylip'
assert generate_outfile_name('/foo/bar.ext.fasta',
'clustal') == '/foo/bar.ext.clustal'