def write_bcl2fastq_samplesheet(samplesheet, samplesheet_path, conf):
try:
# Write CSV samplesheet file in BCL2FASTQ2 format
writer = SampleSheetCSVWriter(samplesheet_path)
writer.setVersion(2)
writer.writer(samplesheet)
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error while writing Bcl2fastq samplesheet: " + samplesheet_path, exp.getMessage(), conf)
return False
def update_samplesheet(samplesheet, run_id, lane_count, conf):
common.log("INFO", "Flowcell lane count: " + str(lane_count), conf)
try:
# Replace index sequence shortcuts by sequences
SampleSheetUtils.replaceIndexShortcutsBySequences(samplesheet, load_index_sequences(conf))
# Set the lane field if does not set
SampleSheetUtils.duplicateSamplesIfLaneFieldNotSet(samplesheet, lane_count)
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error while updating samplesheet for run " + run_id, exp.getMessage(), conf)
return False
def load_samplesheet(run_id, input_run_data_path, samplesheet_filename, conf):
""" Load the samplesheet.
Arguments:
run id: The run id
input_run_data_path: The input run data path
samplesheet_filename: samplesheet filename
conf: configuration dictionary
Return:
a Samplesheet object and the original path of the samplesheet
"""
run_info_path = input_run_data_path + '/RunInfo.xml'
if not os.path.isfile(run_info_path):
error("no RunInfo.xml file found for run " + run_id,
"No RunInfo.xml file found for run " + run_id + ': ' + run_info_path + '.\n', conf)
return None, None
run_info = RunInfo.parse(run_info_path)
flow_cell_id = run_info.getFlowCell()
common.log("INFO", "Flowcell id: " + flow_cell_id, conf)
common.log("INFO", "Samplesheet format: " + str(conf[BCL2FASTQ_SAMPLESHEET_FORMAT_KEY]), conf)
try:
if common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xls', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xls',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'csv', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'csv',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xlsx', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xlsx',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'command', conf):
action_error_msg = 'Error while creating Bcl2fastq CSV samplesheet file'
if not common.is_conf_key_exists(BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY, conf):
error(action_error_msg + ' for run ' + run_id, action_error_msg + ' the command is empty.', conf)
return None, None
input_samplesheet_generated_path = conf[TMP_PATH_KEY] + '/' + samplesheet_filename + 'generated.csv'
cmd = conf[
BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY] + ' ' + run_id + ' ' + quote(input_samplesheet_generated_path)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error(action_error_msg + ' for run ' + run_id,
action_error_msg + '.\nCommand line:\n' + cmd, conf)
if not os.path.exists(input_samplesheet_generated_path):
error(action_error_msg + ' for run ' + run_id,
action_error_msg + ', the external command did not create Bcl2fastq CSV file:\n' + cmd, conf)
return None, None
# Load CSV samplesheet file
samplesheet = SampleSheetCSVReader(input_samplesheet_generated_path).read()
# Remove generated samplesheet
os.unlink(input_samplesheet_generated_path)
return samplesheet, None
else:
error('Error while creating Bcl2fastq CSV samplesheet file for run ' + run_id,
'No method to get Bcl2fastq samplesheet file has been defined. Please, set the ' +
'"bcl2fastq.samplesheet.format" property.\n',
conf)
return None, None
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error reading samplesheet: " + samplesheet_filename, exp.getMessage(), conf)
return None, None
return samplesheet, None
else:
error('Error while creating Bcl2fastq CSV samplesheet file for run ' + run_id,
'No method to get Bcl2fastq samplesheet file has been defined. Please, set the ' +
'"bcl2fastq.samplesheet.format" property.\n',
conf)
return None, None
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error reading samplesheet: " + samplesheet_filename, exp.getMessage(), conf)
return None, None
except Exception, exp:
print StringUtils.stackTraceToString(exp)
error("Error reading samplesheet: " + samplesheet_filename, exp.getMessage(), conf)
return None, None
return None, None
def update_samplesheet(samplesheet, run_id, lane_count, conf):
common.log("INFO", "Flowcell lane count: " + str(lane_count), conf)
try:
# Replace index sequence shortcuts by sequences
SampleSheetUtils.replaceIndexShortcutsBySequences(samplesheet, load_index_sequences(conf))
