def estimate(run_id, conf):
"""Estimate space needed in directories : hiseq, bcl and fastq
if it has not enough space free send a warning mail
Arguments:
run_id: the run id
conf: configuration dictionary
"""
# retrieve data from RunInfo.xml
run_info = hiseq_run.get_run_info(run_id, conf)
# retrieve count lane
lane_count = run_info.getFlowCellLaneCount()
# retrieve count cycle
cycle_count = 0
for read in run_info.getReads():
cycle_count = cycle_count + read.getNumberCycles()
# retrieve data from runParameters.xml
run_param_path = common.get_run_parameters_path(run_id, conf)
#
# Estimate space needed +10%
#
# Set factor and ratio util
run_factor = lane_count * cycle_count * 1.10
# bcl file : compressed or not, info in runParameters.xml
ratio_bcl = ratio_bcl_compressed(run_param_path)
# quality data for Q30 : compressed or not
ratio_quality = compressed_quality_data(run_param_path)
# for hiseq data
check_space_needed_and_free(run_id, 'hiseq', run_factor, conf)
# for bcl files
check_space_needed_and_free(run_id, 'bcl', run_factor * ratio_bcl * ratio_quality, conf)
# for fastq files
check_space_needed_and_free(run_id, 'fastq', run_factor, conf)
def send_report(run_id, conf):
"""Send a mail with the first base report.
Arguments:
run_id: the run id
conf: configuration dictionary
"""
#
# Retrieve features the current run in RunInfos.xml file
#
run_info = hiseq_run.get_run_info(run_id, conf)
if run_info is None:
return False
# TODO ?? add check sample-sheet if demux step enable
# add warning in report if useful
reads = run_info.getReads()
error_cycles_per_read_not_indexes_count = 0
reads_indexed_count = 0
reads_not_indexed_count = 0
cycles_count = 0
cycles_per_read_not_indexed = 0
for read in reads:
cycles_count += read.getNumberCycles()
if read.isIndexedRead():
reads_indexed_count += 1
else:
reads_not_indexed_count += 1
if cycles_per_read_not_indexed == 0:
cycles_per_read_not_indexed = read.getNumberCycles()
# Check same cycles count for each reads not indexed
error_cycles_per_read_not_indexes_count = cycles_per_read_not_indexed != read.getNumberCycles()
# Identification type run according to data in RunInfos.xml : SR or PE
if reads_not_indexed_count == 1:
type_run_estimated = "SR-" + str(cycles_per_read_not_indexed) + " with " + str(
reads_indexed_count) + " index"
if reads_indexed_count > 1:
type_run_estimated += "es"
elif reads_not_indexed_count == 2:
type_run_estimated = "PE-" + str(cycles_per_read_not_indexed) + " with " + str(
reads_indexed_count) + " index"
if reads_indexed_count > 1:
type_run_estimated += "es"
else:
type_run_estimated = "Undetermined run type (" + str(reads_not_indexed_count) + " reads with " + str(
reads_indexed_count) + " index)"
if reads_indexed_count > 1:
type_run_estimated += "es"
type_run_estimated += ")"
description_run = "Informations about this run:\n"
description_run += "\t- Sequencer: " + common.get_instrument_name(run_id, conf) + ".\n"
description_run += "\t- " + str(run_info.getFlowCellLaneCount()) + " lanes with " + str(
run_info.alignToPhix.size()) + " aligned to Phix.\n"
description_run += "\t- " + str(reads_not_indexed_count) + " read"
if reads_not_indexed_count > 1:
description_run += "s"
description_run += " and " + str(reads_indexed_count) + " index"
if reads_indexed_count > 1:
description_run += "es"
description_run += ".\n"
if error_cycles_per_read_not_indexes_count or cycles_per_read_not_indexed == 0:
description_run += "\t- ERROR : cycles count per read different between reads (" + str(
cycles_count) + " total cycles).\n"
else:
description_run += "\t- " + str(cycles_per_read_not_indexed) + " cycles per read (" + str(
cycles_count) + " total cycles).\n"
description_run += "\t- Estimated run type: " + type_run_estimated + ".\n"
attachment_file = str(hiseq_run.find_hiseq_run_path(run_id, conf)) + '/' + run_id + '/' + common.FIRST_BASE_REPORT_FILE
# If the First base report file exists, send it by email
if common.is_file_readable(attachment_file):
message = 'You will find attached to this message the first base report for the run ' + \
run_id + '.\n\n' + description_run
common.send_msg_with_attachment('[Aozan] First base report for the run ' + type_run_estimated + ' ' + run_id +
' on ' + common.get_instrument_name(run_id, conf),
message, attachment_file, False, conf)
else:
# With other no attachment file
message = 'You will find below the parameters of the run ' + run_id + '.\n\n' + description_run
common.send_msg('[Aozan] New run ' + type_run_estimated + ' ' + run_id + ' on ' +
common.get_instrument_name(run_id, conf), message,
False, conf)
return True