def __getSolidRunData(self):
"""Get data about SOLiD runs
Internal function to construct SolidRun objects based on the
supplied SOLiD run directory.
"""
if self.solid_run_dir is not None:
logging.debug("Acquiring run information")
for solid_dir in (self.solid_run_dir, self.solid_run_dir + "_2"):
logging.debug("Examining %s" % solid_dir)
run = SolidData.SolidRun(solid_dir)
if not run:
logging.debug("Unable to get run data for %s" % solid_dir)
else:
self.solid_runs.append(run)
if len(self.solid_runs) == 0:
logging.warning("No run data found")
def verify_runs(solid_dirs):
"""Do basic verification checks on SOLiD run directories
For each SOLiD run directory, create a SolidRun object and check for the
expected sample and library directories, and that primary data files
(csfasta and qual) have been assigned and exist.
Returns a UNIX-like status code: 0 indicates that the checks passed,
1 indicates that they failed.
Arguments:
solid_dirs: a list of SOLiD sequencing directory names.
Returns:
0 if the run is verified, 1 if there is a problem.
"""
print "Performing verification"
status = 0
for solid_dir in solid_dirs:
# Initialise
run_status = 0
run = SolidData.SolidRun(solid_dir)
if not run.verify():
run_status = 1
print "%s:" % run.run_name,
if run_status == 0:
print " [PASSED]"
else:
print " [FAILED]"
status = 1
# Completed
print "Overall status:",
if status == 0:
print " [PASSED]"
else:
print " [FAILED]"
return status
# Output spreadsheet name
if options.xls:
spreadsheet = os.path.splitext(os.path.basename(
solid_dirs[0]))[0] + ".xls"
print "Writing spreadsheet %s" % spreadsheet
# Check there's at least one thing to do
if not (options.report or options.layout or options.xls or options.verify
or options.rsync or options.md5sum or options.copy_pattern
or options.gzip_pattern or options.md5_pattern):
options.report = True
# Get the run information
solid_runs = []
for solid_dir in solid_dirs:
run = SolidData.SolidRun(solid_dir)
if not run:
logging.error("Error extracting run data for %s" % solid_dir)
sys.exit(1)
else:
solid_runs.append(run)
# Report the runs
if options.report:
report_run(solid_runs, options.report_paths)
# Report the runs to a spreadsheet
if options.xls:
try:
import Spreadsheet
write_spreadsheet(solid_runs, spreadsheet)
def verify_runs(solid_dirs):
"""Do basic verification checks on SOLiD run directories
For each SOLiD run directory, create a SolidRun object and check for the
expected sample and library directories, and that primary data files
(csfasta and qual) have been assigned and exist.
Returns a UNIX-like status code: 0 indicates that the checks passed,
1 indicates that they failed.
Arguments:
solid_dirs: a list of SOLiD sequencing directory names.
Returns:
0 if the run is verified, 1 if there is a problem.
"""
print "Performing verification"
status = 0
for solid_dir in solid_dirs:
# Initialise
run_status = 0
run = SolidData.SolidRun(solid_dir)
if not run:
# Some error processing the basics
run_status = 1
else:
# Check basic parameters: should have non-zero numbers of
# samples and libraries
if len(run.samples) == 0:
print "No sample data"
run_status = 1
# Determine if run is paired-end
paired_end = SolidData.is_paired_end(run)
# Check libraries in each sample
for sample in run.samples:
if len(sample.libraries) == 0:
print "No libraries for sample %s" % sample.name
run_status = 1
for library in sample.libraries:
# Check csfasta was found
if not library.csfasta:
print "No F3 csfasta for %s/%s" % \
(sample.name,library.name)
run_status = 1
else:
if not os.path.exists(library.csfasta):
print "Missing F3 csfasta for %s/%s" % \
(sample.name,library.name)
run_status = 1
# Check qual was found
if not library.qual:
print "No F3 qual for %s/%s" % \
(sample.name,library.name)
run_status = 1
else:
if not os.path.exists(library.qual):
print "Missing F3 qual for %s/%s" % \
(sample.name,library.name)
run_status = 1
# Paired-end run: check F5 reads
if paired_end:
if not library.csfasta_f5:
print "No F5 csfasta for %s/%s" % \
(sample.name,library.name)
run_status = 1
else:
if not os.path.exists(library.csfasta_f5):
print "Missing F5 csfasta for %s/%s" % \
(sample.name,library.name)
run_status = 1
# Check for F5 qual
if not library.qual_f5:
print "No F5 qual for %s/%s" % \
(sample.name,library.name)
run_status = 1
else:
if not os.path.exists(library.qual_f5):
print "Missing F5 qual for %s/%s" % \
(sample.name,library.name)
run_status = 1
# Completed checks for run
print "%s:" % run.run_name,
if run_status == 0:
print " [PASSED]"
else:
print " [FAILED]"
status = 1
# Completed
print "\nOverall status:",
if status == 0:
print " [PASSED]"
else:
print " [FAILED]"
return status
