def __init__(self, lims_sample): """ Wrapper around the genologics Sample class Args: lims_sample (genologics.Sample): the sample instance to extend """ self.lims = lims_sample self._apptag = ApplicationTag(self.lims.udf['Sequencing Analysis'])
def set_missingreads(lims_sample, force=False): """Set the 'Reads Missing (M)' UDF base on app tag.""" raw_apptag = lims_sample.udf['Sequencing Analysis'] app_tag = ApplicationTag(raw_apptag) target_amount = app_tag.reads missing_reads = lims_sample.udf.get('Reads missing (M)') if not force and missing_reads is not None: log.warn("missing reads already set: %s", missing_reads) else: lims_sample.udf['Reads missing (M)'] = target_amount log.info("updating reads missing") lims_sample.put()
def apptag_wgs(): raw_tag = 'WGSPCFC030' return ApplicationTag(raw_tag)
def apptag_focused_exome(): raw_tag = 'EFTSXTR020' return ApplicationTag(raw_tag)
def apptag_rml(): raw_tag = 'RMLP10R150' return ApplicationTag(raw_tag)
def apptag_metagenome(): raw_tag = 'METPCFR020' return ApplicationTag(raw_tag)
def apptag_external_wgs(): raw_tag = 'WGXCUSR000' return ApplicationTag(raw_tag)
def apptag_external(): raw_tag = 'EXXCUSR000' return ApplicationTag(raw_tag)
def apptag_rna(): raw_tag = 'RNLPOAR030' return ApplicationTag(raw_tag)
def apptag_microbial(): raw_tag = 'MWGNXTR003' return ApplicationTag(raw_tag)
def apptag_wes(): raw_tag = 'EXOSXTR100' return ApplicationTag(raw_tag)