comparison scaffold_wrapper.py @ 1:0d0cbb69a03f draft

Uploaded

0:e9981e6af666

                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print open(tmp_stderr_name, "r").read(64000)
        print open(tmp_stdout_name, "r").read(64000)


def delete_file(path):
    if os.path.exists(path):
        try:

def build_samples(samples_file):
    group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"])
    samples_description = ""
    for sample_name, sample_data in group_data.iteritems():
        files = sample_data["inputs"]
        mudpit = sample_data["group_data"]["mudpit"]
        category = sample_data["group_data"]["category"]
        samples_description += """<BiologicalSample database="database" name="%s" mudpit="%s" category="%s">\n""" % (sample_name, mudpit, category)
        for (name, path, ext) in files:

    output_path = options.output
    template_parameters["output_path"] = output_path

    # Prepare and create driver file
    driver_contents = Template(template).substitute(template_parameters)
    print driver_contents
    driver_path = os.path.abspath("driver.xml")
    open(driver_path, "w").write(driver_contents)

    # Run Scaffold
    execute("ScaffoldBatch3 '%s'" % driver_path)

1:0d0cbb69a03f

                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print((open(tmp_stderr_name, "r").read(64000)))
        print((open(tmp_stdout_name, "r").read(64000)))


def delete_file(path):
    if os.path.exists(path):
        try:

def build_samples(samples_file):
    group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"])
    samples_description = ""
    for sample_name, sample_data in list(group_data.items()):
        files = sample_data["inputs"]
        mudpit = sample_data["group_data"]["mudpit"]
        category = sample_data["group_data"]["category"]
        samples_description += """<BiologicalSample database="database" name="%s" mudpit="%s" category="%s">\n""" % (sample_name, mudpit, category)
        for (name, path, ext) in files:

    output_path = options.output
    template_parameters["output_path"] = output_path

    # Prepare and create driver file
    driver_contents = Template(template).substitute(template_parameters)
    print(driver_contents)
    driver_path = os.path.abspath("driver.xml")
    open(driver_path, "w").write(driver_contents)

    # Run Scaffold
    execute("ScaffoldBatch3 '%s'" % driver_path)