def main(self):
self.mate.pushLogPrefix("Teaser")
self.log("Init. Creating %d test datasets." % len(self.tests))
try:
self.preprocessTests()
except RuntimeError as e:
self.mate.error("Teaser: " + str(e))
raise SystemExit
force_recreate = self.mate.force_gen
for name in sorted(self.tests, key=lambda k: self.tests[k]["order"]):
if self.mate.run_only != False:
if name not in self.mate.run_only:
self.created_count += 1
self.log("Data set %s is excluded, not creating." % name)
continue
if self.existsTest(self.tests[name]) and not force_recreate:
self.mate.getReport().generateProgress()
self.created_count += 1
self.log("Data set %s already exists, not creating." % name)
continue
try:
self.createTest(self.tests[name])
except RuntimeError as e:
self.mate.error("Teaser: " + str(e))
raise SystemExit
util.enterRootDir()
self.mate.popLogPrefix()
return [name for name in sorted(self.tests, key=lambda k: self.tests[k]["order"])]
def createTest(self, test):
start_time = time.time()
self.mate.getReport().generateProgress()
self.log("")
self.log("Creating test %s" % test["name"])
try:
os.mkdir(test["dir"])
except:
self.log("Failed to create test directory, probably existing")
self.rm(test["dir"] + "/" + test["name"] + ".yaml")
self.rm(test["dir"] + "/mapping_comparison.sam")
self.rm(test["dir"] + "/reads.fastq")
self.rm(test["dir"] + "/reads1.fastq")
self.rm(test["dir"] + "/reads2.fastq")
self.ch(test)
try:
if test["type"] == "simulated_teaser":
if test["sampling"]["enable"]:
self.makeDatasetDS(test)
else:
self.makeDatasetNoDS(test)
elif test["type"] == "simulated_custom" or test["type"] == "real":
self.makeDatasetNoSim(test)
else:
self.mate.error(
"Teaser: Unknown test type '%s' for test '%s'." %
(test["type"], test["name"]))
raise
except RuntimeError as e:
self.mate.error("Teaser: Test creation failed for '%s': %s" %
(test["name"], str(e)))
raise SystemExit
except Exception as e:
self.mate.error(
"Teaser: Test creation failed for '%s' due to an exception: %s"
% (test["name"], str(e)))
self.mate.log_traceback("Teaser Error")
raise SystemExit
end_time = time.time()
test["create_time"] = end_time - start_time
self.log("Took %d seconds for generating %s" %
(test["create_time"], test["name"]))
self.writeYAML(test)
util.enterRootDir()
self.created_count += 1
self.mate.getReport().generateProgress()
def makeDatasetNoSim(self, test):
util.enterRootDir()
if test["import_read_files"] == None or len(
test["import_read_files"]) == 0:
self.mate.error(
"Teaser: No read files given to import for test '%s'" %
test["name"])
test["type"] = None
raise RuntimeError
if test["paired"]:
if len(test["import_read_files"]) != 2:
self.mate.error(
"Teaser: Expected 2 files in field 'import_read_files' for paired-end test '%s', got %d"
% (test["name"], len(test["import_read_files"])))
raise RuntimeError
else:
if len(test["import_read_files"]) != 1:
self.mate.error(
"Teaser: Expected 1 file in field 'import_read_files' for paired-end test '%s', got %d"
% (test["name"], len(test["import_read_files"])))
raise RuntimeError
for filename in test["import_read_files"]:
if not self.isFastq(filename):
self.mate.error(
"Teaser: Unsupported read file type of '%s' for test '%s'. Expected FASTQ."
% (filename, test["name"]))
raise RuntimeError
if test["type"] == "simulated_custom":
self.importDatasetCustom(test)
elif test["type"] == "real":
self.importDatasetReal(test)
self.ch(test)
self.log("Generate dummy alignments")
aligner = fastq2sam.DummyAligner()
conv = fastq2sam.Converter(aligner, "mapping_comparison.sam")
if test["paired"]:
conv.align_pe("reads1.fastq", "reads2.fastq")
# self.mv("enc_reads1.fastq", "reads1.fastq")
# self.mv("enc_reads2.fastq", "reads2.fastq")
else:
conv.align_se("reads.fastq")
# self.mv("enc_reads.fastq", "reads.fastq")
self.mv("enc_mapping_comparison.sam", "mapping_comparison.sam")
self.ch(test)
def createTest(self, test):
start_time = time.time()
self.mate.getReport().generateProgress()
self.log("")
self.log("Creating test %s" % test["name"])
try:
os.mkdir(test["dir"])
except:
self.log("Failed to create test directory, probably existing")
self.rm(test["dir"] + "/" + test["name"] + ".yaml")
self.rm(test["dir"] + "/mapping_comparison.sam")
self.rm(test["dir"] + "/reads.fastq")
self.rm(test["dir"] + "/reads1.fastq")
self.rm(test["dir"] + "/reads2.fastq")
self.ch(test)
try:
if test["type"] == "simulated_teaser":
if test["sampling"]["enable"]:
self.makeDatasetDS(test)
else:
self.makeDatasetNoDS(test)
elif test["type"] == "simulated_custom" or test["type"] == "real":
self.makeDatasetNoSim(test)
else:
self.mate.error("Teaser: Unknown test type '%s' for test '%s'."%(test["type"],test["name"]))
raise
except RuntimeError as e:
self.mate.error("Teaser: Test creation failed for '%s': %s"%(test["name"],str(e)))
raise SystemExit
except Exception as e:
self.mate.error("Teaser: Test creation failed for '%s' due to an exception: %s"%(test["name"],str(e)))
self.mate.log_traceback("Teaser Error")
raise SystemExit
end_time = time.time()
test["create_time"] = end_time - start_time
self.log("Took %d seconds for generating %s" % (test["create_time"], test["name"]))
self.writeYAML(test)
util.enterRootDir()
self.created_count += 1
self.mate.getReport().generateProgress()
def makeDatasetNoSim(self,test):
util.enterRootDir()
if test["import_read_files"] == None or len(test["import_read_files"])==0:
self.mate.error("Teaser: No read files given to import for test '%s'"%test["name"])
test["type"]=None
raise RuntimeError
if test["paired"]:
if len(test["import_read_files"]) != 2:
self.mate.error("Teaser: Expected 2 files in field 'import_read_files' for paired-end test '%s', got %d"%(test["name"],len(test["import_read_files"])))
raise RuntimeError
else:
if len(test["import_read_files"]) != 1:
self.mate.error("Teaser: Expected 1 file in field 'import_read_files' for paired-end test '%s', got %d"%(test["name"],len(test["import_read_files"])))
raise RuntimeError
for filename in test["import_read_files"]:
if not self.isFastq(filename):
self.mate.error("Teaser: Unsupported read file type of '%s' for test '%s'. Expected FASTQ." % (filename,test["name"]) )
raise RuntimeError
if test["type"] == "simulated_custom":
self.importDatasetCustom(test)
elif test["type"] == "real":
self.importDatasetReal(test)
self.ch(test)
self.log("Generate dummy alignments")
aligner = fastq2sam.DummyAligner()
conv = fastq2sam.Converter(aligner, "mapping_comparison.sam")
if test["paired"]:
conv.align_pe("reads1.fastq", "reads2.fastq")
self.mv("enc_reads1.fastq", "reads1.fastq")
self.mv("enc_reads2.fastq", "reads2.fastq")
else:
conv.align_se("reads.fastq")
self.mv("enc_reads.fastq", "reads.fastq")
self.mv("enc_mapping_comparison.sam", "mapping_comparison.sam")
self.ch(test)
def main(self):
self.mate.pushLogPrefix("Teaser")
self.log("Init. Creating %d test datasets." % len(self.tests))
try:
self.preprocessTests()
except RuntimeError as e:
self.mate.error("Teaser: " + str(e))
raise SystemExit
force_recreate = self.mate.force_gen
for name in sorted(self.tests, key=lambda k: self.tests[k]["order"]):
if self.mate.run_only != False:
if name not in self.mate.run_only:
self.created_count += 1
self.log("Data set %s is excluded, not creating." % name)
continue
if self.existsTest(self.tests[name]) and not force_recreate:
self.mate.getReport().generateProgress()
self.created_count += 1
self.log("Data set %s already exists, not creating." % name)
continue
try:
self.createTest(self.tests[name])
except RuntimeError as e:
self.mate.error("Teaser: " + str(e))
raise SystemExit
util.enterRootDir()
self.mate.popLogPrefix()
return [
name for name in sorted(self.tests,
key=lambda k: self.tests[k]["order"])
]