def test_qual_02(self):
# test quality filtering with reduced threshold
with Capturing() as output:
main(
[barcodes_qual, '-f', barcodes_qual, '--qual-filter', '-p', '2'])
desc, seqs, __, quals = list(zip(*grouper(output, 4)))
self.assertEqual(len(seqs), 5)
def test_02(self):
# filter barcode file using itself; get back only the most common
# barcode
with Capturing() as output:
main([barcodes, '-f', barcodes, '--match-filter'])
desc, seqs, __, quals = list(zip(*grouper(output, 4)))
self.assertSetEqual(set(seqs), {most_common})
def test_count(self):
outdir = mkoutdir(self)
read_counts = path.join(outdir, 'counts.csv')
main([barcodes, '-f', barcodes,
'--qual-filter',
'-o', path.join(outdir, 'filtered.fastq'),
'--read-counts', read_counts])
with open(read_counts) as f:
reader = csv.reader(f)
fname, input, output = next(reader)
self.assertEqual(input, '15000')
self.assertEqual(output, '14729')
def test_empty(self):
# test filtering of empty fastq
# with Capturing() as output:
outdir = mkoutdir(self)
read_counts = path.join(outdir, 'counts.csv')
main([empty, '-f', empty,
'-o', path.join(outdir, 'filtered.fastq'),
'--read-counts', read_counts])
with open(read_counts) as f:
reader = csv.reader(f)
fname, input, output = next(reader)
self.assertEqual(input, '0')
self.assertEqual(output, '0')
def test_04(self):
# --invert option removes all instances of the most common bc
with Capturing() as output:
main([barcodes, '-f', barcodes, '--invert', '--match-filter'])
desc, seqs, __, quals = list(zip(*grouper(output, 4)))
self.assertNotIn(most_common, set(seqs))
def test_03(self):
# --head returns the specified number of records
with Capturing() as output:
main([barcodes, '-f', barcodes, '--head', '10'])
desc, seqs, __, quals = list(zip(*grouper(output, 4)))
self.assertEqual(len(seqs), 10)
def test_01(self):
with Capturing() as output:
# because main() is called in the same global context in
# each test, '-q' silences logging for all invocations.
main([barcodes, '-c', '-q'])
self.assertEqual(output[0].split('\t')[0], most_common)
def test_qual_dual(self):
# test quality filtering with defaults
with Capturing() as output:
main([dual_qual1, dual_qual2, '-f', dual_qual1, '--qual-filter'])
desc, seqs, __, quals = list(zip(*grouper(output, 4)))
self.assertEqual(len(seqs), 5)
def test_05(self):
# test warning when recovery is below --min-pct-assignment
with Capturing() as output:
main([barcodes, '-f', barcodes, '--min-pct-assignment', '100'])
def test_02(self):
# filter barcode file using itself; get back only the most common barcode
with Capturing() as output:
main([dual1, dual2, '-f', dual1])
desc, seqs, __, quals = zip(*grouper(output, 4))
self.assertSetEqual(set(seqs), {most_common_dual.split('+')[0]})
#!/usr/bin/env python
import sys
from barcodecop.barcodecop import main
if __name__ == '__main__':
sys.exit(main(sys.argv[1:]))