def test_merge_unaligned_folder(self):
"""Merging Unaligned folders and comparing the results with the expected
"""
self.logger.info("Merging Unaligned folders")
merge_demux_results(self.fc_dir)
self.logger.info("Testing the merging of Flowcell_demux_summary.xml")
self.assertTrue(self._compare_flowcell_demux_summary(),
"The resulting file Flowcell_demux_summary.xml is not as expected.")
self.logger.info("Testing the merging of Demultiplex_Stats.htm")
self.assertTrue(self._compare_demultiplex_stats(),
"The resulting file Demultiplex_Stats.htm is not as expected.")
self.logger.info("Testing the merging of Undemultiplexed_stats.metrics")
self.assertTrue(self._compare_undemultiplexed_stats(),
"The resulting file Undemultiplexed_stats.metrics is not as expected")
def process_second_read(*args, **kwargs):
"""Processing to be performed after all reads have been sequenced
"""
dname, config = args[0:2]
logger2.info("The instrument has finished dumping on directory %s" % dname)
utils.touch_indicator_file(os.path.join(dname, "second_read_processing_started.txt"))
_update_reported(config["msg_db"], dname)
fastq_dir = None
# Do bcl -> fastq conversion and demultiplexing using Casava1.8+
if kwargs.get("casava", False):
if not kwargs.get("no_casava_processing", False):
logger2.info("Generating fastq.gz files for {:s}".format(dname))
_generate_fastq_with_casava(dname, config)
# Merge demultiplexing results into a single Unaligned folder
utils.merge_demux_results(dname)
#Move the demultiplexing results
if config.has_key('mfs_dir'):
fc_id = os.path.basename(dname)
cl = ["rsync", \
"--checksum", \
"--recursive", \
"--links", \
"-D", \
"--partial", \
"--progress", \
"--prune-empty-dirs", \
os.path.join(dname, 'Unaligned'), \
os.path.join(config.get('mfs_dir'), fc_id)
]
logger2.info("Synching Unaligned folder to MooseFS for run {}".format(fc_id))
logdir = os.path.join(config.get('log_dir'), os.getcwd())
rsync_out = os.path.join(logdir,"rsync_transfer.out")
rsync_err = os.path.join(logdir,"rsync_transfer.err")
with open(rsync_out, 'a') as ro:
with open(rsync_err, 'a') as re:
try:
ro.write("-----------\n{}\n".format(" ".join(cl)))
re.write("-----------\n{}\n".format(" ".join(cl)))
subprocess.check_call(cl, stdout=ro, stderr=re)
except subprocess.CalledProcessError, e:
logger2.error("rsync transfer of Unaligned results FAILED")
def test_merge_unaligned_folder(self):
"""Merging Unaligned folders and comparing the results with the expected
"""
self.logger.info("Merging Unaligned folders")
merge_demux_results(self.fc_dir)
self.logger.info("Testing the merging of Flowcell_demux_summary.xml")
self.assertTrue(
self._compare_flowcell_demux_summary(),
"The resulting file Flowcell_demux_summary.xml is not as expected."
)
self.logger.info("Testing the merging of Demultiplex_Stats.htm")
self.assertTrue(
self._compare_demultiplex_stats(),
"The resulting file Demultiplex_Stats.htm is not as expected.")
self.logger.info(
"Testing the merging of Undemultiplexed_stats.metrics")
self.assertTrue(
self._compare_undemultiplexed_stats(),
"The resulting file Undemultiplexed_stats.metrics is not as expected"
)
