def args(self):
cls = self.parent()[0]
seq = self.threeprime
if determine_read_type(self.input()[0].path, self.read1_suffix,
self.read2_suffix) == 2:
seq = self.fiveprime
return [
"-a", seq,
self.input()[0], "-o",
self.output(), ">",
rreplace(self.input()[0].path, str(cls().suffix[0]),
self.label + self.suffix[1], 1)
]
def requires(self):
cls = self.parent()[0]
source = self.source()[0]
# Ugly hack for 1 -> 2 dependency: works but should be dealt with otherwise
if str(fullclassname(cls)) in ["ratatosk.lib.utils.misc.ResyncMates"]:
rt = determine_read_type(source, self.read1_suffix, self.read2_suffix)
if rt == 1:
self.is_read1 = True
fq1 = source
fq2 = rreplace(source, self.read1_suffix, self.read2_suffix, 1)
elif rt == 2:
self.is_read1 = False
fq1 = rreplace(source, self.read2_suffix, self.read1_suffix, 1)
fq2 = source
retval = [cls(target=[fq1, fq2])]
else:
retval = [cls(target=source)]
if len(self.parent()) > 1:
retval += [cls(target=source) for cls, source in izip(self.parent()[1:], self.source()[1:])]
return retval
def test_determine_read_type(self):
fn = "sample_index1_1.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 1)
fn = "sample_index1_2.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 2)
fn = "4_120924_AC003CCCXX_P001_101_index1_1.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 1)
fn = "4_120924_AC003CCCXX_P001_101_index1_2.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 2)
fn = "P001_101_index3_TGACCA_L001_R1_001.fastq.gz"
rtype = determine_read_type(fn, "_R1_001", "_R2_001")
self.assertEqual(rtype, 1)
fn = "P001_101_index3_TGACCA_L001_R2_001.fastq.gz"
rtype = determine_read_type(fn, "_R1_001", "_R2_001")
self.assertEqual(rtype, 2)
def test_determine_read_type(self):
fn = "sample_index1_1.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 1)
fn = "sample_index1_2.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 2)
fn = "4_120924_AC003CCCXX_P001_101_index1_1.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 1)
fn = "4_120924_AC003CCCXX_P001_101_index1_2.fastq.gz"
rtype = determine_read_type(fn, "_1", "_2")
self.assertEqual(rtype, 2)
fn = "P001_101_index3_TGACCA_L001_R1_001.fastq.gz"
rtype = determine_read_type(fn, "_R1_001", "_R2_001")
self.assertEqual(rtype, 1)
fn = "P001_101_index3_TGACCA_L001_R2_001.fastq.gz"
rtype = determine_read_type(fn, "_R1_001", "_R2_001")
self.assertEqual(rtype, 2)
def args(self):
cls = self.parent()[0]
seq = self.threeprime
if determine_read_type(self.input()[0].path, self.read1_suffix, self.read2_suffix) == 2:
seq = self.fiveprime
return ["-a", seq, self.input()[0], "-o", self.output(), ">", rreplace(self.input()[0].path, str(cls().suffix[0]), self.label + self.suffix[1], 1)]
