def __init__(self, trigger_file, outdir):
"""
:param trigger_file:
"""
self._trigger_file = trigger_file
self._outdir = outdir
self._trigger_file_parser = tp(self._trigger_file)
# Should be like Merck_ImmunoSELECT_Unmatched_Report_Template.xlsx
self._template_file = self._trigger_file_parser.getTemplateFilePath()
self._outfile = self._trigger_file_parser.getFinalReportPath(
) + self._trigger_file_parser.getFinalReportName() + '.xlsx'
self._copy_number_file_parser = cnp(
self._trigger_file_parser.getCopyNumberFile())
self._summarysheet_file_parser = ssp(
self._trigger_file_parser.getSummarysheetFile())
self._combined_coverage_file_parser = ccp(
self._trigger_file_parser.getCombinedCoverageFile())
def main(trigger_file, verbose, outdir):
"""
TRIGGER_FILE: The input file to be processed.
:return: None
"""
assert isinstance(trigger_file, str)
if not os.path.isfile(trigger_file):
print("'%s' is not a file" % trigger_file)
sys.exit(1)
if verbose:
print("The input file is %s" % trigger_file)
if not outdir == './':
pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
if verbose:
print("output directory '%s' was created" % outdir)
trigger_file_parser = tp(trigger_file)
report_type = trigger_file_parser.getReportType()
repgen = None
if report_type == 'Merck_ImmunoSELECT_Matched' or report_type == 'Merck ImmunoSELECT Matched':
repgen = mimRepGen(trigger_file, outdir)
elif report_type == 'Merck_ImmunoSELECT_Unmatched' or report_type == 'Merck ImmunoSELECT Unmatched':
repgen = miumRepGen(trigger_file, outdir)
elif report_type == 'Victor ImmunoSELECT Matched' or report_type == 'Victor_ImmunoSELECT_Matched':
repgen = vimRepGen(trigger_file, outdir)
elif report_type == 'Victor ImmunoSELECT Unmatched' or report_type == 'Victor_ImmunoSELECT_Unmatched':
repgen = viumRepGen(trigger_file, outdir)
elif report_type == 'ImmunoSELECT Matched' or report_type == 'ImmunoSELECT_Matched':
repgen = imRepGen(trigger_file, outdir)
elif report_type == 'ImmunoSELECT Unmatched' or report_type == 'ImmunoSELECT_Unmatched':
repgen = iumRepGen(trigger_file, outdir)
elif report_type == 'CancerXOME Matched' or report_type == 'CancerXOME_Matched':
repgen = cxmRepGen(trigger_file, outdir)
elif report_type == 'CancerXOME Unmatched' or report_type == 'CancerXOME_Unmatched':
repgen = cxumRepGen(trigger_file, outdir)
elif report_type == 'Victor CancerXOME Matched' or report_type == 'Victor_CancerXOME_Matched':
repgen = vcxmRepGen(trigger_file, outdir)
elif report_type == 'Victor CancerXOME Unmatched' or report_type == 'Victor_CancerXOME_Unmatched':
repgen = vcxumRepGen(trigger_file, outdir)
else:
print("report type '%s' is not supported" % report_type)
sys.exit(1)
repgen.generateReport()
