def test_pair_fastqs_empty_files(self):
"""pair_fastqs: handle set of FASTQs with 'empty' pairs
"""
fastqs = [self.empty_r1,
self.empty_r2]
self.assertEqual(pair_fastqs(fastqs),
([],[self.empty_r1,self.empty_r2]))
def test_pair_fastqs_no_pairs(self):
"""pair_fastqs: handle set of FASTQ with no pairs
"""
fastqs = [self.fastq2_r2,
self.fastq1_r1,]
self.assertEqual(pair_fastqs(fastqs),
([],[self.fastq1_r1,self.fastq2_r2]))
def test_pair_fastqs_unpaired(self):
"""pair_fastqs: handle paired and unpaired FASTQs
"""
fastqs = [self.fastq2_r2,
self.fastq1_r1,
self.fastq2_r1,]
self.assertEqual(pair_fastqs(fastqs),
([(self.fastq2_r1,self.fastq2_r2),],
[self.fastq1_r1,]))
def test_pair_fastqs(self):
"""pair_fastqs: pair up a set of FASTQs
"""
fastqs = [self.fastq2_r2,
self.fastq1_r1,
self.fastq2_r1,
self.fastq1_r2,]
self.assertEqual(pair_fastqs(fastqs),
([(self.fastq1_r1,self.fastq1_r2),
(self.fastq2_r1,self.fastq2_r2)],
[]))
# Input Fastqs
fastqs = args.fastqs
# Well list file
if args.well_list_file is not None:
well_list = ICell8WellList(args.well_list_file)
else:
well_list = None
# Number of cores
nprocs = args.nprocessors
print "%d processor%s will be used" % (nprocs,
('s' if nprocs != 1 else ''))
# Pair up Fastq files
fastqs, unpaired = pair_fastqs(fastqs)
if unpaired:
print "Unpaired Fastqs specified:"
for fq in unpaired:
print "- %s" % fq
logging.fatal("Unpaired Fastqs specified")
sys.exit(1)
# Only need R1 Fastqs
fastqs = [pair[0] for pair in fastqs]
# Set up a working directory
if args.temporary_directory is not None:
tmpdir = os.path.abspath(args.temporary_directory)
else:
try:
def main():
# Handle the command line
p = argparse.ArgumentParser()
p.add_argument("fastqs",
nargs='*',
metavar="FASTQ_R1 FASTQ_R2",
help="FASTQ file pairs")
p.add_argument("-w",
"--well-list",
dest="well_list_file",
default=None,
help="iCell8 'well list' file")
p.add_argument("-m",
"--mode",
dest="splitting_mode",
default="barcodes",
choices=["barcodes", "batch", "none"],
help="how to split the input FASTQs: 'barcodes' "
"(one FASTQ pair per barcode), 'batch' (one or "
"more FASTQ pairs with fixed number of reads not "
"exceeding BATCH_SIZE), or 'none' (output all "
"reads to a single FASTQ pair) (default: "
"'barcodes')")
p.add_argument("-s",
"--size",
type=int,
dest="batch_size",
default=DEFAULT_BATCH_SIZE,
help="number of reads per batch in 'batch' mode "
"(default: %d)" % DEFAULT_BATCH_SIZE)
p.add_argument("-b",
"--basename",
default="icell8",
help="basename for output FASTQ files (default: "
"'icell8')")
p.add_argument("-o",
"--outdir",
dest="out_dir",
default=None,
help="directory to write output FASTQ files to "
"(default: current directory)")
p.add_argument("-d",
"--discard-unknown-barcodes",
dest='discard_unknown_barcodes',
action='store_true',
help="discard reads with barcodes which don't "
"match any of those in the WELL_LIST_FILE "
"(default: keep all reads)")
p.add_argument("-q",
"--quality-filter",
dest='quality_filter',
action='store_true',
help="filter reads by barcode and UMI quality "
"(default: don't filter reads on quality)")
p.add_argument("-c",
"--compress",
action='store_true',
help="output compressed .gz FASTQ files")
args = p.parse_args()
# Convert quality cutoffs to character encoding
barcode_quality_cutoff = chr(INLINE_BARCODE_QUALITY_CUTOFF + 33)
umi_quality_cutoff = chr(UMI_QUALITY_CUTOFF + 33)
# Get well list and expected barcodes
well_list_file = args.well_list_file
if well_list_file is not None:
well_list_file = os.path.abspath(args.well_list_file)
well_list = ICell8WellList(well_list_file)
expected_barcodes = set(well_list.barcodes())
print "%d expected barcodes" % len(expected_barcodes)
# Filtering on barcode
do_check_barcodes = args.discard_unknown_barcodes
if do_check_barcodes and well_list_file is None:
logging.fatal("-d/--discard-unknown-barcodes: need to supply a "
"well list file")
sys.exit(1)
# Filter on barcode and UMI quality
do_quality_filter = args.quality_filter
# Splitting mode
splitting_mode = args.splitting_mode
batch_size = args.batch_size
# Count barcodes and rejections
assigned = 0
unassigned = 0
filtered = 0
barcode_list = set()
filtered_counts = {}
# Input Fastqs
fastqs = pair_fastqs([fq for fq in args.fastqs])[0]
# Output Fastqs
output_fqs = BufferedOutputFiles(base_dir=args.out_dir)
if args.out_dir is not None:
out_dir = os.path.abspath(args.out_dir)
mkdir(out_dir)
else:
out_dir = os.getcwd()
basename = args.basename
# Compress outputs?
if args.compress:
fastq_ext = "fastq.gz"
else:
fastq_ext = "fastq"
# Iterate over pairs of Fastqs
for fastq_pair in fastqs:
# Iterate over read pairs from the Fastqs
print "-- %s\n %s" % fastq_pair
print " Starting at %s" % time.ctime()
start_time = time.time()
for i, read_pair in enumerate(ICell8FastqIterator(*fastq_pair),
start=1):
# Deal with read pair
if (i % 100000) == 0:
print " Examining read pair #%d (%s)" % \
(i,time.ctime())
inline_barcode = read_pair.barcode
barcode_list.add(inline_barcode)
# Initial assignment
assign_to = inline_barcode
# Apply quality filtering
if do_quality_filter:
if not pass_quality_filter(read_pair.barcode_quality,
barcode_quality_cutoff):
assign_to = "failed_barcode"
elif not pass_quality_filter(read_pair.umi_quality,
umi_quality_cutoff):
assign_to = "failed_umi"
else:
filtered += 1
# Check barcode is valid
if do_check_barcodes:
if inline_barcode not in expected_barcodes:
assign_to = "unassigned"
unassigned += 1
else:
assigned += 1
logging.debug("%s" % '\t'.join([
assign_to, inline_barcode, read_pair.umi,
read_pair.min_barcode_quality, read_pair.min_umi_quality
]))
# Post filtering counts
if assign_to == inline_barcode:
try:
filtered_counts[inline_barcode] += 1
except KeyError:
filtered_counts[inline_barcode] = 1
# Reassign read pair to appropriate output files
if splitting_mode == "batch":
# Output to a batch-specific file pair
batch_number = filtered / batch_size
assign_to = "B%03d" % batch_number
elif splitting_mode == "none":
# Output to a single file pair
assign_to = "filtered"
# Write read pair
fq_r1 = "%s_R1" % assign_to
fq_r2 = "%s_R2" % assign_to
if fq_r1 not in output_fqs:
try:
# Try to reopen file and append
output_fqs.open(fq_r1, append=True)
except KeyError:
# Open new file
output_fqs.open(
fq_r1,
"%s.%s.r1.%s" % (basename, assign_to, fastq_ext))
output_fqs.write(fq_r1, "%s" % read_pair.r1)
if fq_r2 not in output_fqs:
try:
# Try to reopen file and append
output_fqs.open(fq_r2, append=True)
except KeyError:
# Open new file
output_fqs.open(
fq_r2,
"%s.%s.r2.%s" % (basename, assign_to, fastq_ext))
output_fqs.write(fq_r2, "%s" % read_pair.r2)
print " Finished at %s" % time.ctime()
print " (Took %.0fs)" % (time.time() - start_time)
# Close output files
output_fqs.close()
# Summary output to screen
total_reads = assigned + unassigned
print "Summary:"
print "--------"
print "Number of barcodes : %d" % len(barcode_list)
if do_check_barcodes:
print "Number of expected barcodes: %d/%d" % \
(len(filtered_counts.keys()),
len(expected_barcodes))
print "Total reads : %d" % total_reads
if do_quality_filter:
print "Total reads (filtered) : %d" % filtered
if do_check_barcodes:
print "Total reads (assigned) : %d" % assigned
print "Unassigned reads : %d" % unassigned
