Python ElementTree.parse方法代码示例

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
def gerald(pathname):
    LOGGER.info("Parsing gerald config.xml")
    pathname = os.path.expanduser(pathname)
    config_pathname = os.path.join(pathname, 'config.xml')
    config_tree = ElementTree.parse(config_pathname).getroot()

    # parse Summary.htm file
    summary_xml = os.path.join(pathname, 'Summary.xml')
    summary_htm = os.path.join(pathname, 'Summary.htm')
    report_summary = os.path.join(pathname, '..', 'Data',
                                  'reports', 'Summary', )
    if os.path.exists(summary_xml):
        g = Gerald(pathname = pathname, tree=config_tree)
        LOGGER.info("Parsing Summary.xml")
        g.summary = SummaryGA(summary_xml)
        g.eland_results = eland(g.pathname, g)
    elif os.path.exists(summary_htm):
        g = Gerald(pathname=pathname, tree=config_tree)
        LOGGER.info("Parsing Summary.htm")
        g.summary = SummaryGA(summary_htm)
        g.eland_results = eland(g.pathname, g)
    elif os.path.isdir(report_summary):
        g = CASAVA(pathname=pathname, tree=config_tree)
        LOGGER.info("Parsing %s" % (report_summary,))
        g.summary = SummaryHiSeq(report_summary)
        g.eland_results = eland(g.pathname, g)

    # parse eland files
    return g

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
def bustard_from_hiseq(pathname, config_filename):
    b = Bustard()
    b.pathname = pathname
    bustard_config_root = ElementTree.parse(config_filename)
    b.bustard_config = bustard_config_root.getroot()
    add_phasing(b)
    return b

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
 def _initialize_from_file(self, pathname):
     path, name = os.path.split(pathname)
     basename, ext = os.path.splitext(name)
     # the last character of the param base filename should be the
     # lane number
     tree = ElementTree.parse(pathname).getroot()
     self.set_elements(tree)
     self.lane = int(basename[-1])

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
    def _get_flowcell_id_from_flowcellid(self):
        """Extract flowcell id from a Config/FlowcellId.xml file

        :return: flowcell_id or None if not found
        """
        config_dir = os.path.join(self.pathname, 'Config')
        flowcell_id_path = os.path.join(config_dir, 'FlowcellId.xml')
        if os.path.exists(flowcell_id_path):
            flowcell_id_tree = ElementTree.parse(flowcell_id_path)
            return flowcell_id_tree.findtext('Text')

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
def load_pipeline_run_xml(pathname):
    """
    Load and instantiate a Pipeline run from a run xml file

    :Parameters:
      - `pathname` location of an run xml file

    :Returns: initialized PipelineRun object
    """
    tree = ElementTree.parse(pathname).getroot()
    run = PipelineRun(xml=tree)
    return run

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
    def load(self, filename):
        """Load a run xml into this object.

        :Parameters:
          - `filename` location of a run xml file

        :Types:
          - `filename` str
        """
        LOGGER.info("Loading run report from " + filename)
        tree = ElementTree.parse(filename).getroot()
        self.set_elements(tree)

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
    def _get_flowcell_id_from_runinfo(self):
        """Read RunInfo file for flowcell id

        :return: flowcell_id or None if not found
        """
        runinfo = os.path.join(self.pathname, 'RunInfo.xml')
        if os.path.exists(runinfo):
            tree = ElementTree.parse(runinfo)
            root = tree.getroot()
            fc_nodes = root.xpath('/RunInfo/Run/Flowcell')
            if len(fc_nodes) == 1:
                return fc_nodes[0].text

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
def load_ipar_param_tree(paramfile):
    """
    look for a .param file and load it if it is an IPAR tree
    """

    tree = ElementTree.parse(paramfile).getroot()
    run = tree.find('Run')
    if run.attrib.get('Name', None) in SOFTWARE_NAMES:
        return run
    else:
        LOGGER.info("No run found")
        return None

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
def bustard_from_ga2(pathname, config_filename):
    """Initialize bustard class from ga2-era runfolder
    Actually I don't quite remember if it is exactly the GA2s, but
    its after the original runfolder style and before the HiSeq.
    """
    # for version 1.3.2 of the pipeline the bustard version number went down
    # to match the rest of the pipeline. However there's now a nifty
    # new (useful) bustard config file.

    # stub values
    b = Bustard()
    b.pathname = pathname
    b.update_attributes_from_pathname()
    bustard_config_root = ElementTree.parse(config_filename)
    b.bustard_config = bustard_config_root.getroot()
    b.crosstalk = crosstalk_matrix_from_bustard_config(b.pathname,
                                                       b.bustard_config)
    add_phasing(b)

    return b

# 需要导入模块: from htsworkflow.pipelines import ElementTree [as 别名]
# 或者: from htsworkflow.pipelines.ElementTree import parse [as 别名]
 def parse_genomesize(self, pathname):
     """Parse genomesize.xml file
     """
     tree = ElementTree.parse(pathname)
     self.build_map_from_element(tree.getroot())