def test_group_fastqs_by_name_with_R3_and_index_read(self):
"""
group_fastqs_by_name: R1, R2 and R3 fastqs with index reads
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB1_S1_R3_001.fastq.gz",
"/data/PJB1_S1_I1_001.fastq.gz",
"/data/PJB2_S2_R1_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz",
"/data/PJB2_S2_R3_001.fastq.gz",
"/data/PJB2_S2_I1_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs),
[[
"/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB1_S1_R3_001.fastq.gz",
"/data/PJB1_S1_I1_001.fastq.gz",
],
[
"/data/PJB2_S2_R1_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz",
"/data/PJB2_S2_R3_001.fastq.gz",
"/data/PJB2_S2_I1_001.fastq.gz",
]])
def test_group_fastqs_by_name_PE_with_index_read_pair(self):
"""
group_fastqs_by_name: paired-end fastqs with index read pair
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB1_S1_I1_001.fastq.gz",
"/data/PJB1_S1_I2_001.fastq.gz",
"/data/PJB2_S2_R1_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz",
"/data/PJB2_S2_I1_001.fastq.gz",
"/data/PJB2_S2_I2_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs),
[[
"/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB1_S1_I1_001.fastq.gz",
"/data/PJB1_S1_I2_001.fastq.gz",
],
[
"/data/PJB2_S2_R1_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz",
"/data/PJB2_S2_I1_001.fastq.gz",
"/data/PJB2_S2_I2_001.fastq.gz",
]])
def test_group_fastqs_by_name_SE(self):
"""
group_fastqs_by_name: single-end fastqs
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB2_S2_R1_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs),
[["/data/PJB1_S1_R1_001.fastq.gz",],
["/data/PJB2_S2_R1_001.fastq.gz",]])
def test_group_fastqs_by_name_unpaired_R2(self):
"""
group_fastqs_by_name: handle unpaired R2 fastqs
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs),
[["/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz"],
["/data/PJB2_S2_R2_001.fastq.gz",]])
def test_group_fastqs_by_name_mixed_SE_and_PE(self):
"""
group_fastqs_by_name: mixture of single- and paired-end fastqs
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB2_S2_R1_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs),
[["/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz"],
["/data/PJB2_S2_R1_001.fastq.gz",]])
def test_group_fastqs_by_name_PE(self):
"""
group_fastqs_by_name: paired-end fastqs
"""
fastqs = ("/data/PJB1_S1_R1_001.fastq.gz",
"/data/PJB1_S1_R2_001.fastq.gz",
"/data/PJB2_S2_R1_001.fastq.gz",
"/data/PJB2_S2_R2_001.fastq.gz")
self.assertEqual(group_fastqs_by_name(fastqs), [[
"/data/PJB1_S1_R1_001.fastq.gz", "/data/PJB1_S1_R2_001.fastq.gz"
], ["/data/PJB2_S2_R1_001.fastq.gz", "/data/PJB2_S2_R2_001.fastq.gz"]])
extra_files.add(ff)
else:
# Look for a metadata file based on Fastqs
for fq in inputs:
info_file = locate_project_info_file(os.path.dirname(fq))
if info_file:
break
# Filter out index reads
inputs = [fq for fq in inputs
if not fastq_attrs(fq).is_index_read]
if not inputs:
logger.fatal("No Fastqs found")
sys.exit(1)
# Report what was found
for fqs in group_fastqs_by_name(inputs,fastq_attrs=fastq_attrs):
print("%s:" % fastq_attrs(fqs[0]).sample_name)
for fq in fqs:
print(" %s" % fq)
print("Located %s Fastq%s" % (len(inputs),
's' if len(inputs) != 1 else ''))
if info_file:
print("Located project metadata in %s%s" % (info_file,
" (will be ignored)"
if args.ignore_metadata
else ''))
else:
print("Unable to locate project metadata")
# Set up environment
envmodules = dict()