#######################################################################
# Imports
#######################################################################
import optparse
from auto_process_ngs import stats
#######################################################################
# Main script
#######################################################################
if __name__ == '__main__':
# Process command line
p = optparse.OptionParser(
usage="%prog [OPTIONS] STATS_INFO_FILE",
version="%prog " + __version__,
description="Summarise the per sample stats for each lane "
"for an Illumina sequencing run, using the data from "
"STATS_INFO_FILE (typically called 'statistics.info' and "
"found in the top-level directory of sequencing runs "
"processed using auto_process.py.")
options, args = p.parse_args()
if len(args) == 0:
stats_file = "statistics.info"
elif len(args) > 1:
p.error("expects a single argument (statistics file)")
else:
stats_file = args[0]
stats.report_per_lane_stats(stats_file)
#######################################################################
# Imports
#######################################################################
import optparse
from auto_process_ngs import stats
#######################################################################
# Main script
#######################################################################
if __name__ == '__main__':
# Process command line
p = optparse.OptionParser(usage="%prog [OPTIONS] STATS_INFO_FILE",
version="%prog "+__version__,
description="Summarise the per sample stats for each lane "
"for an Illumina sequencing run, using the data from "
"STATS_INFO_FILE (typically called 'statistics.info' and "
"found in the top-level directory of sequencing runs "
"processed using auto_process.py.")
options,args = p.parse_args()
if len(args) == 0:
stats_file = "statistics.info"
elif len(args) > 1:
p.error("expects a single argument (statistics file)")
else:
stats_file = args[0]
stats.report_per_lane_stats(stats_file)
if not options.force:
stats = TabFile.TabFile(filen=filein,first_line_is_header=True)
else:
logging.warning("--force specified, statistics will be regenerated")
if stats is None:
# (Re)create statistics from raw files
try:
illumina_data = IlluminaData.IlluminaData(args[0],
unaligned_dir=options.unaligned_dir)
except IlluminaData.IlluminaDataError,ex:
logging.error("Failed to get data from %s: %s" % (args[0],ex))
sys.exit(1)
# Generate statistics for fastq files
stats = fastq_statistics(illumina_data,n_processors=options.n)
stats.write(options.stats_file,include_header=True)
print "Statistics written to %s" % options.stats_file
# Per-lane sequencer statistics
if illumina_data.lanes == [None]:
print "No lane information: per-lane statistics not generated"
else:
auto_process_stats.report_per_lane_stats(options.stats_file,
options.per_lane_stats_file)
print "Per-lane sequencer stats written to %s" % \
options.per_lane_stats_file
# Summary of per-lane sequencer stats
per_lane_stats_summary
seqstats = sequencer_stats(stats)
seqstats.write(seq_stats_file,include_header=True)
print "Summary of per-lane sequencer stats written to %s" % \
seq_stats_file
