def test_fastqfactory():
try:
snaketools.FastQFactory("*", read_tag='error')
assert False
except:
assert True
try:
snaketools.FastQFactory("*", read_tag='[12]')
assert False
except:
assert True
directory = os.path.dirname(
sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz"))
ff = snaketools.FastQFactory(directory + os.sep + "Hm2*gz",
read_tag='R[12]')
assert ff.paired is True
assert ff.tags == ['Hm2_GTGAAA_L005_']
ff = snaketools.FastQFactory(directory + os.sep + "Hm2*gz", read_tag=None)
assert ff.paired is False
assert sorted(ff.tags) == sorted(
['Hm2_GTGAAA_L005_R2_001', 'Hm2_GTGAAA_L005_R1_001'])
def test_file_name_factory():
import glob
def inner_test(ff):
len(ff)
print(ff)
ff.filenames
ff.realpaths
ff.all_extensions
ff.pathnames
ff.extensions
#list
list_files = glob.glob("*.py")
ff = snaketools.FileFactory(list_files)
inner_test(ff)
# glob
ff = snaketools.FileFactory("*py")
inner_test(ff)
directory = os.path.dirname(
sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz"))
ff = snaketools.FastQFactory(directory + "/Hm2*fastq.gz", verbose=True)
assert ff.tags == ['Hm2_GTGAAA_L005']
ff.get_file1(ff.tags[0])
ff.get_file2(ff.tags[0])
assert len(ff) == 1