From: Diane Trout Date: Thu, 29 Jan 2015 18:42:52 +0000 (-0800) Subject: whitespace-cleanup X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=686401da016a696b36a82dca7eecf686b8c58c38 whitespace-cleanup --- diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py index d1a40bd..9fef5d1 100644 --- a/htsworkflow/pipelines/gerald.py +++ b/htsworkflow/pipelines/gerald.py @@ -189,10 +189,10 @@ class CASAVA(Alignment): return None time_element = self.tree.xpath('TIME_STAMP') if len(time_element) == 1: - timetuple = time.strptime( - time_element[0].text.strip(), - "%a %b %d %H:%M:%S %Y") - return datetime(*timetuple[:6]) + timetuple = time.strptime( + time_element[0].text.strip(), + "%a %b %d %H:%M:%S %Y") + return datetime(*timetuple[:6]) return super(CASAVA, self)._get_date() date = property(_get_date) diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py index 03e71f9..52dda08 100644 --- a/htsworkflow/pipelines/ipar.py +++ b/htsworkflow/pipelines/ipar.py @@ -89,7 +89,7 @@ class IPAR(object): else: return runfolder[0].text runfolder_name = property(_get_runfolder_name) - + def _get_software(self): """Return software name""" if self.tree is None: @@ -197,7 +197,7 @@ class IPAR(object): if element.tag == IPAR.RUN: self.tree = element elif element.tag == IPAR.TIMESTAMP: - self.time = int(element.text) + self.time = int(element.text) elif element.tag == IPAR.MATRIX: self.matrix = element.text else: diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index dfc75f4..7acb294 100644 --- a/htsworkflow/pipelines/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -30,7 +30,7 @@ from htsworkflow.pipelines import srf class PipelineRun(object): """Capture "interesting" information about a pipeline run - + :Variables: - `pathname` location of the root of this runfolder - `serialization_filename` read only property containing name of run xml file @@ -46,12 +46,12 @@ class PipelineRun(object): def __init__(self, pathname=None, flowcell_id=None, xml=None): """Initialize a PipelineRun object - + :Parameters: - `pathname` the root directory of this run folder. - `flowcell_id` the flowcell ID in case it can't be determined - `xml` Allows initializing an object from a serialized xml file. - + :Types: - `pathname` str - `flowcell_id` str @@ -74,7 +74,7 @@ class PipelineRun(object): def _get_flowcell_id(self): """Return the flowcell ID - + Attempts to find the flowcell ID through several mechanisms. """ # extract flowcell ID @@ -96,7 +96,7 @@ class PipelineRun(object): 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') @@ -139,9 +139,9 @@ class PipelineRun(object): def _get_run_dirname(self): """Return name of directory to hold result files from one analysis - + For pre-multiplexing runs this is just the cycle range C1-123 - For post-multiplexing runs the "suffix" that we add to + For post-multiplexing runs the "suffix" that we add to differentiate runs will be added to the range. E.g. Unaligned_6mm may produce C1-200_6mm """ @@ -158,7 +158,7 @@ class PipelineRun(object): def get_elements(self): """make one master xml file from all of our sub-components. - + :return: an ElementTree containing all available pipeline run xml compoents. """ @@ -202,10 +202,10 @@ class PipelineRun(object): def _get_serialization_filename(self): """Compute the filename for the run xml file - - Attempts to find the latest date from all of the run + + Attempts to find the latest date from all of the run components. - + :return: filename run_{flowcell id}_{timestamp}.xml :rtype: str """ @@ -219,7 +219,7 @@ class PipelineRun(object): def save(self, destdir=None): """Save a run xml file. - + :param destdir: Directory name to save too, uses current directory if not specified. :type destdir: str @@ -234,10 +234,10 @@ class PipelineRun(object): def load(self, filename): """Load a run xml into this object. - + :Parameters: - `filename` location of a run xml file - + :Types: - `filename` str """ @@ -260,7 +260,7 @@ def load_pipeline_run_xml(pathname): def get_runs(runfolder, flowcell_id=None): """Find all runs associated with a runfolder. - + We end up with multiple analysis runs as we sometimes need to try with different parameters. This attempts to return a list of all the various runs. @@ -367,7 +367,7 @@ def build_hiseq_runs(image_analysis, runs, datadir, runfolder, flowcell_id): p.gerald = gerald.gerald(aligned) runs.append(p) except (IOError, RuntimeError) as e: - LOGGER.error("Exception %s", str(e)) + LOGGER.error("Exception %s", str(e)) LOGGER.error("Skipping run in %s", flowcell_id) return len(runs) - start @@ -543,8 +543,8 @@ def summary_report(runs): for run in runs: # print a run name? report.append('Summary for %s' % (run.serialization_filename,)) - # sort the report - if run.gerald: + # sort the report + if run.gerald: eland_keys = sorted(run.gerald.eland_results.keys()) else: report.append("Alignment not done, no report possible") @@ -831,6 +831,3 @@ def clean_runs(runs, dry_run=True): clean_process = subprocess.Popen(['make', 'clean_intermediate'], cwd=run.image_analysis.pathname,) clean_process.wait() - - -