def start(self, primerFile, samplesFile, verbose=True, debug=False):
"""
Start preprocessing double barcoded Illumina sequencing run, perform
"""
self.verbose = verbose
try:
res1 = res2 = 0
if primerFile is not None:
# read in primer sequences if present
prTable = primerTable(primerFile)
if verbose:
sys.stdout.write("primer table length P5 Primer (expanded) Sequences:%s, P7 Primer (expanded) Sequences:%s\n" % (len(prTable.getP5sequences()), len(prTable.getP7sequences())))
res1 = self.validatePrimer(prTable, debug)
if samplesFile is not None:
# read in sample sheet
sTable = sampleTable(samplesFile)
if verbose:
sys.stdout.write("sample table length: %s, and %s projects.\n" % (sTable.getSampleNumber(), len(sTable.getProjectList())))
res2 = self.validateSample(sTable, debug)
if res1 == 0 and res2 == 0:
sys.stderr.write("Validation confirmed, files are ok\n")
return 0
else:
sys.stderr.write("Failed validation\n")
return 1
except (KeyboardInterrupt, SystemExit):
self.clean()
sys.stderr.write("%s unexpectedly terminated\n" % (__name__))
return 1
except:
self.clean()
if not debug:
sys.stderr.write("A fatal error was encountered. trying turning on debug\n")
if debug:
sys.stderr.write("".join(traceback.format_exception(*sys.exc_info())))
return 1
def start(self, fastq_file1, fastq_file2, output_prefix, primerFile, primerMaxDiff=4, primerEndMatch=4, insertionSite='TA', batchsize=10000, uncompressed=False, output_unidentified=False, minQ=None, minL=0, verbose=True, debug=False, test=False):
"""
Start preprocessing double barcoded Illumina sequencing run, perform
"""
self.verbose = verbose
try:
# read in primer sequences if present
prTable = primerTable(primerFile)
if verbose:
sys.stdout.write("primer table length P5 Primer Sequences:%s, P7 Primer Sequences:%s, Linker sequences:%s\n" % (len(prTable.getP5sequences()), len(prTable.getP7sequences()), len(prTable.getLinkersequences())))
# validate assumptions
# v = validateApp()
# if v.validatePrimer(prTable, debug) != 0:
# sys.stderr.write("Failed validation\n")
# self.clean()
# return 1
# setup output files
identified_count = 0
unidentified_count = 0
self.run_out = {}
self.run_out["Identified"] = IlluminaTwoReadOutput(output_prefix, uncompressed)
if output_unidentified:
self.run_out["Unidentified"] = IlluminaTwoReadOutput(output_prefix+"_Unidentified", uncompressed)
# establish and open the Illumina run
self.run = TwoReadIlluminaRun(fastq_file1, fastq_file2)
self.run.open()
lasttime = time.time()
while 1:
# get next batch of reads
reads = self.run.next(batchsize)
if len(reads) == 0:
break
# process individual reads
for read in reads:
read.checkLinker(prTable, 0, primerMaxDiff, primerEndMatch)
read.assignPrimer(prTable, 0, primerMaxDiff, primerEndMatch)
if minQ is not None:
read.trimRead(minQ, minL)
if read.goodRead is True:
identified_count += 1
self.run_out["Identified"].addRead(read.getFastq())
else:
unidentified_count += 1
if output_unidentified:
self.run_out["Unidentified"].addRead(read.getFastq())
# Write out reads
for key in self.run_out:
self.run_out[key].writeReads()
if self.verbose:
sys.stderr.write("processed %s total reads, %s Reads/second, %s identified reads(%s%%), %s unidentified reads\n" % (self.run.count(), round(self.run.count()/(time.time() - lasttime), 0), identified_count, round((float(identified_count)/float(self.run.count()))*100, 1), unidentified_count))
if test: # exit after the first batch to test the inputs
break
if self.verbose:
sys.stdout.write("%s reads processed in %s minutes, %s (%s%%) identified\n\n" % (self.run.count(), round((time.time()-lasttime)/(60), 2), identified_count, round((float(identified_count)/float(self.run.count()))*100, 1)))
self.clean()
return 0
except (KeyboardInterrupt, SystemExit):
self.clean()
sys.stderr.write("%s unexpectedly terminated\n" % (__name__))
return 1
except:
self.clean()
if not debug:
sys.stderr.write("A fatal error was encountered. trying turning on debug\n")
if debug:
sys.stderr.write("".join(traceback.format_exception(*sys.exc_info())))
return 1