def test_gzipped(self):
forward_gzip_fp = self.forward_fp + ".gz"
subprocess.check_call(["gzip", self.forward_fp])
reverse_gzip_fp = self.reverse_fp + ".gz"
subprocess.check_call(["gzip", self.reverse_fp])
index_gzip_fp = self.index_fp + ".gz"
subprocess.check_call(["gzip", self.index_fp])
main([
self.barcode_fp,
forward_gzip_fp,
reverse_gzip_fp,
"--i1-fastq",
index_gzip_fp,
"--output-dir",
self.output_dir,
"--revcomp",
])
self.assertEqual(
set(os.listdir(self.output_dir)),
set((
"SampleA_R1.fastq",
"SampleA_R2.fastq",
"SampleB_R1.fastq",
"SampleB_R2.fastq",
)))
def test_regular(self):
main([
self.barcode_fp, self.forward_fp, self.reverse_fp,
"--i1-fastq", self.index_fp,
"--output-dir", self.output_dir,
"--manifest-file", self.manifest_fp,
"--total-reads-file", self.total_reads_fp,
"--revcomp",
])
self.assertEqual(
set(os.listdir(self.output_dir)), set((
"SampleA_R1.fastq", "SampleA_R2.fastq",
"SampleB_R1.fastq", "SampleB_R2.fastq",
)))
with open(self.manifest_fp) as f:
self.assertEqual(next(f), "sample-id,absolute-filepath,direction\n")
for line in f:
sample_id, fp, direction = line.split(",", 3)
self.assertIn(direction, ["forward\n", "reverse\n"])
self.assertIn(sample_id, ["SampleA", "SampleB"])
with open(self.total_reads_fp) as f:
self.assertEqual(next(f), "SampleID\tNumReads\n")
self.assertEqual(next(f), "SampleA\t1\n")
self.assertEqual(next(f), "SampleB\t1\n")
self.assertEqual(next(f), "unassigned\t1\n")
def test_regular(self):
main([
"--forward-reads", self.forward_fp,
"--reverse-reads", self.reverse_fp,
"--index-reads", self.index_fp,
"--barcode-file", self.barcode_fp,
"--output-dir", self.output_dir,
"--summary-file", self.summary_fp,
])
with open(self.summary_fp) as f:
res = json.load(f)
self.assertEqual(res["data"], {"SampleA": 1, "SampleB": 1})
def test_gzipped(self):
forward_gzip_fp = self.forward_fp + ".gz"
subprocess.check_call(["gzip", self.forward_fp])
reverse_gzip_fp = self.reverse_fp + ".gz"
subprocess.check_call(["gzip", self.reverse_fp])
index_gzip_fp = self.index_fp + ".gz"
subprocess.check_call(["gzip", self.index_fp])
main([
self.barcode_fp, forward_gzip_fp, reverse_gzip_fp,
"--i1-fastq", index_gzip_fp,
"--output-dir", self.output_dir,
"--revcomp",
])
self.assertEqual(
set(os.listdir(self.output_dir)), set((
"SampleA_R1.fastq", "SampleA_R2.fastq",
"SampleB_R1.fastq", "SampleB_R2.fastq",
)))
def test_regular(self):
main([
"--forward-reads",
self.forward_fp,
"--reverse-reads",
self.reverse_fp,
"--index-reads",
self.index_fp,
"--barcode-file",
self.barcode_fp,
"--output-dir",
self.output_dir,
"--summary-file",
self.summary_fp,
])
with open(self.summary_fp) as f:
res = json.load(f)
self.assertEqual(res["data"], {
"SampleA": 1,
"SampleB": 1,
"unassigned": 1
})
def test_regular(self):
main([
self.barcode_fp,
self.forward_fp,
self.reverse_fp,
"--i1-fastq",
self.index_fp,
"--output-dir",
self.output_dir,
"--manifest-file",
self.manifest_fp,
"--total-reads-file",
self.total_reads_fp,
"--revcomp",
])
self.assertEqual(
set(os.listdir(self.output_dir)),
set((
"SampleA_R1.fastq",
"SampleA_R2.fastq",
"SampleB_R1.fastq",
"SampleB_R2.fastq",
)))
with open(self.manifest_fp) as f:
self.assertEqual(next(f),
"sample-id,absolute-filepath,direction\n")
for line in f:
sample_id, fp, direction = line.split(",", 3)
self.assertIn(direction, ["forward\n", "reverse\n"])
self.assertIn(sample_id, ["SampleA", "SampleB"])
with open(self.total_reads_fp) as f:
self.assertEqual(next(f), "SampleID\tNumReads\n")
self.assertEqual(next(f), "SampleA\t1\n")
self.assertEqual(next(f), "SampleB\t1\n")
self.assertEqual(next(f), "unassigned\t1\n")
#!/usr/bin/env python from dnabclib.main import main main()
