def finalize(self):
"""Called by the pipeline at the termination of a run. By default,
this function prints the location of the log-file if one was created
during the run (e.g. if there were errors), and a summary of all nodes.
"""
runtime = (self._end_time or 0) - (self._start_time or 0)
if self.states[self.ERROR]:
print_err("Done; but errors were detected ...")
else:
print_info("Done ...")
print_info()
rows = [(" Number of nodes:", sum(self.states)),
(" Number of done nodes:", self.states[self.DONE]),
(" Number of runable nodes:", self.states[self.RUNABLE]),
(" Number of queued nodes:", self.states[self.QUEUED]),
(" Number of outdated nodes:", self.states[self.OUTDATED]),
(" Number of failed nodes:", self.states[self.ERROR]),
(" Pipeline runtime:", _fmt_runtime(round(runtime)))]
for line in text.padded_table(rows):
print_info(line)
print_info()
print_info("Use --list-output-files to view status of output files.")
logfile = pypeline.logger.get_logfile()
if logfile:
print_debug("Log-file located at %r" % (logfile, ))
print_info()
def run(config, args):
if not os.path.exists(config.temp_root):
try:
os.makedirs(config.temp_root)
except OSError, error:
print_err("ERROR: Could not create temp root:\n\t%s" % (error,))
return 1
def finalize(self):
"""Called by the pipeline at the termination of a run. By default,
this function prints the location of the log-file if one was created
during the run (e.g. if there were errors), and a summary of all nodes.
"""
runtime = (self._end_time or 0) - (self._start_time or 0)
if self.states[self.ERROR]:
print_err("Done; but errors were detected ...")
else:
print_info("Done ...")
print_info()
rows = [(" Number of nodes:", sum(self.states)),
(" Number of done nodes:", self.states[self.DONE]),
(" Number of runable nodes:", self.states[self.RUNABLE]),
(" Number of queued nodes:", self.states[self.QUEUED]),
(" Number of outdated nodes:", self.states[self.OUTDATED]),
(" Number of failed nodes:", self.states[self.ERROR]),
(" Pipeline runtime:", _fmt_runtime(round(runtime)))]
for line in text.padded_table(rows):
print_info(line)
print_info()
print_info("Use --list-output-files to view status of output files.")
logfile = pypeline.logger.get_logfile()
if logfile:
print_debug("Log-file located at %r" % (logfile,))
print_info()
def run(config, args):
if not os.path.exists(config.temp_root):
try:
os.makedirs(config.temp_root)
except OSError, error:
print_err("ERROR: Could not create temp root:\n\t%s" % (error, ))
return 1
def main(argv):
try:
config, args = bam_config.parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except bam_config.ConfigError, error:
print_err(error)
return 1
def main(argv):
try:
config, args = bam_config.parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except bam_config.ConfigError, error:
print_err(error)
return 1
def main(argv):
options, paths = parse_args(argv)
records = {}
for root in paths:
if os.path.isdir(root):
filename = os.path.join(root, _FILENAME)
else:
root, filename = os.path.split(root)[0], root
if not os.path.exists(filename):
print_err("ERROR: Could not find SampleSheet file: %r" % filename,
file=sys.stderr)
return 1
for record in read_alignment_records(filename):
libraries = records.setdefault(record["SampleID"], {})
barcodes = libraries.setdefault(record["Index"], [])
record["Lane"] = int(record["Lane"])
path = "%(SampleID)s_%(Index)s_L%(Lane)03i_R{Pair}_*.fastq.gz" % record
record["Path"] = select_path(os.path.join(root, path))
barcodes.append(record)
_print_header(
timestamp=datetime.datetime.now().isoformat(),
full_mkfile=(os.path.basename(sys.argv[0]) != "trim_pipeline"),
sample_tmpl=not bool(records),
minimal=options.minimal)
for (sample, libraries) in records.iteritems():
print "%s:" % sample
print " %s:" % sample
for (library, barcodes) in libraries.iteritems():
print " %s:" % library
for record in barcodes:
print " {FCID}_{Lane}: {Path}".format(**record)
print
print
if not argv:
print_info(
"No directories/files specified, standard makefile printed.",
file=sys.stderr)
print_info("If the reads have associated %s files, these" %
(_FILENAME, ),
file=sys.stderr)
print_info("may be used to generate a preliminary makefile:",
file=sys.stderr)
print_info(" Usage: bam_pipeline mkfile [filename/directory] [...]",
file=sys.stderr)
print_info("Each directory must contain a '%s' file." % _FILENAME,
file=sys.stderr)
else:
print_info(
"Makefile printed. Please check for correctness before running pipeline.",
file=sys.stderr)
return 0
def main(argv):
check_python_version()
check_pysam_module_version()
try:
config, args = parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except RuntimeError, error:
print_err(error)
return 1
def finalize(self):
"""Called by the pipeline at the termination of a run. By default,
this function prints the location of the log-file if one was created
during the run (e.g. if there were errors)."""
logfile = pypeline.logger.get_logfile()
if logfile:
print_debug("Log-file located at %r" % (logfile, ))
if self.states[self.ERROR]:
print_err("Done; but errors were detected ...")
else:
print_info("Done ...")
def finalize(self):
"""Called by the pipeline at the termination of a run. By default,
this function prints the location of the log-file if one was created
during the run (e.g. if there were errors)."""
logfile = pypeline.logger.get_logfile()
if logfile:
print_debug("Log-file located at %r" % (logfile,))
if self.states[self.ERROR]:
print_err("Done; but errors were detected ...")
else:
print_info("Done ...")
def main(argv):
options, paths = parse_args(argv)
records = {}
for root in paths:
if os.path.isdir(root):
filename = os.path.join(root, _FILENAME)
else:
root, filename = os.path.split(root)[0], root
if not os.path.exists(filename):
print_err("ERROR: Could not find SampleSheet file: %r" % filename,
file=sys.stderr)
return 1
for record in read_alignment_records(filename):
libraries = records.setdefault(record["SampleID"], {})
barcodes = libraries.setdefault(record["Index"], [])
record["Lane"] = int(record["Lane"])
path = "%(SampleID)s_%(Index)s_L%(Lane)03i_R{Pair}_*.fastq.gz" \
% record
record["Path"] = select_path(os.path.join(root, path))
barcodes.append(record)
is_trim_pipeline = os.path.basename(sys.argv[0]) == "trim_pipeline"
print_header(full_mkfile=not is_trim_pipeline,
sample_tmpl=not bool(records),
minimal=options.minimal)
for (sample, libraries) in records.iteritems():
print("%s:" % sample)
print(" %s:" % sample)
for (library, barcodes) in libraries.iteritems():
print(" %s:" % library)
for record in barcodes:
print(" {FCID}_{Lane}: {Path}".format(**record))
print()
print()
if not argv:
print_info("No directories/files specified, standard makefile printed.", file = sys.stderr)
print_info("If the reads have associated %s files, these" % (_FILENAME,), file = sys.stderr)
print_info("may be used to generate a preliminary makefile:", file = sys.stderr)
print_info(" Usage: bam_pipeline mkfile [filename/directory] [...]", file = sys.stderr)
print_info("Each directory must contain a '%s' file." % _FILENAME, file = sys.stderr)
else:
print_info("Makefile printed. Please check for correctness before running pipeline.", file = sys.stderr)
return 0
" std.out." % basename)
print_info(" -- %s run [...] -- Run pipeline on provided "
"makefiles." % basename)
def main(argv):
check_python_version()
check_pysam_module_version()
try:
config, args = parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except RuntimeError, error:
print_err(error)
return 1
commands = ("makefile", "mkfile", "run", "dry_run", "dry-run", "dryrun")
if (len(args) == 0) or (args[0] not in commands):
_print_usage()
return 1
elif args[0] in ("mkfile", "makefile"):
return epicreatemkfile.main(args[1:])
elif not args[1:]:
_print_usage()
print_err("\nPlease specify at least one makefile!")
return 1
return run(config, args[1:])
if __name__ == '__main__':
sys.exit(main(sys.argv[1:]))
files.add(os.path.abspath(fpath))
else:
files.add(os.path.abspath(root_filename))
return (files - mkfiles) - frozenset(pipeline.list_output_files())
def run(config, args):
if not os.path.exists(config.temp_root):
try:
os.makedirs(config.temp_root)
except OSError, error:
print_err("ERROR: Could not create temp root:\n\t%s" % (error,))
return 1
if not os.access(config.temp_root, os.R_OK | os.W_OK | os.X_OK):
print_err("ERROR: Insufficient permissions for temp root: '%s'" % (config.temp_root,))
return 1
# Init worker-threads before reading in any more data
pipeline = Pypeline(config)
try:
print_info("Building BAM pipeline ...", file=sys.stderr)
makefiles = read_makefiles(config, args)
except (MakefileError, pypeline.yaml.YAMLError, IOError), error:
print_err(
"Error reading makefiles:",
"\n %s:\n " % (error.__class__.__name__,),
"\n ".join(str(error).split("\n")),
file=sys.stderr,
)
def main(argv):
try:
config, args = parse_config(argv)
except ConfigError, error:
print_err(error)
return 1
def main(argv):
try:
config, args = parse_config(argv)
except ConfigError, error:
print_err(error)
return 1
fpath = os.path.join(dirpath, filename)
files.add(os.path.abspath(fpath))
return files - pipeline.list_output_files()
def main(argv):
try:
config, args = parse_config(argv)
except ConfigError, error:
print_err(error)
return 1
if not args or ("help" in args):
return 0
elif (len(args) < 2) and ("mkfile" not in args and "makefile" not in args):
print_err("\nPlease specify at least one makefile!")
return 1
commands = select_commands(args.pop(0))
if any((cmd in ("makefile", "mkfile")) for (cmd, _) in commands):
return mkfile.main(args[1:])
if not os.path.exists(config.temp_root):
try:
os.makedirs(config.temp_root)
except OSError, error:
print_err("ERROR: Could not create temp root:\n\t%s" % (error, ))
return 1
if not os.access(config.temp_root, os.R_OK | os.W_OK | os.X_OK):
print_err("ERROR: Insufficient permissions for temp root: '%s'" %
