def test_bam_splitter():
'It test bam splitter'
bam_fhand = os.path.join(DATA_DIR, 'seq.bam')
splitter = bam_splitter
dir1 = NamedTemporaryDir()
dir2 = NamedTemporaryDir()
dir3 = NamedTemporaryDir()
new_files = splitter(bam_fhand, [dir1, dir2, dir3])
assert len(new_files) == 2
dir1.close()
dir2.close()
dir3.close()
def test_fastq_splitter():
'It tests the fastq splitter'
fastq = '@seq1\nACTG\n+\nmoco\n@seq2\nGTCA\n+\nhola\n'
file_ = NamedTemporaryFile()
file_.write(fastq)
file_.flush()
splitter = fastq_splitter
dir1 = NamedTemporaryDir()
dir2 = NamedTemporaryDir()
dir3 = NamedTemporaryDir()
new_files = splitter(file_, [dir1, dir2, dir3])
assert len(new_files) == 2
assert open(new_files[0].name).read() == '@seq1\nACTG\n+\nmoco\n'
assert open(new_files[1].name).read() == '@seq2\nGTCA\n+\nhola\n'
dir1.close()
dir2.close()
dir3.close()
def test_re_splitter():
'It tests the general regular expression based splitter'
fastq = '@seq1\nACTG\n+\nmoco\n@seq2\nGTCA\n+\nhola\n'
file_ = NamedTemporaryFile()
file_.write(fastq)
file_.flush()
splitter = create_file_splitter_with_re(expression='^@')
dir1 = NamedTemporaryDir()
dir2 = NamedTemporaryDir()
dir3 = NamedTemporaryDir()
new_files = splitter(file_, [dir1, dir2, dir3])
assert len(new_files) == 2
assert open(new_files[0].name).read() == '@seq1\nACTG\n+\nmoco\n'
assert open(new_files[1].name).read() == '@seq2\nGTCA\n+\nhola\n'
dir1.close()
dir2.close()
dir3.close()
def test_blank_line_splitter():
'It tests the blank line splitter'
fastq = 'hola\n\ncaracola\n\n'
file_ = NamedTemporaryFile()
file_.write(fastq)
file_.flush()
splitter = blank_line_splitter
dir1 = NamedTemporaryDir()
dir2 = NamedTemporaryDir()
dir3 = NamedTemporaryDir()
new_files = splitter(file_, [dir1, dir2, dir3])
assert len(new_files) == 2
assert open(new_files[0].name).read() == 'hola\n\n'
assert open(new_files[1].name).read() == 'caracola\n\n'
dir1.close()
dir2.close()
dir3.close()
