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'