def test_extract_paired_reads_4_output_files():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# actual output files...
outfile1 = utils.get_temp_filename('out_pe')
outfile2 = utils.get_temp_filename('out_se')
script = 'extract-paired-reads.py'
args = [infile, '-p', outfile1, '-s', outfile2]
utils.runscript(script, args)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_interleave_read_stdout():
# create input files
infile1 = utils.get_test_data('paired-slash1.fq.1')
infile2 = utils.get_test_data('paired-slash1.fq.2')
# correct output
ex_outfile = utils.get_test_data('paired-slash1.fq')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2]
(stats, out, err) = utils.runscript(script, args)
with open(outfile, 'w') as ofile:
ofile.write(out)
n = 0
for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_extract_paired_reads_3_output_dir():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# output directory
out_dir = utils.get_temp_filename('output')
script = 'extract-paired-reads.py'
args = [infile, '-d', out_dir]
utils.runscript(script, args)
outfile1 = os.path.join(out_dir, 'paired-mixed.fa.pe')
outfile2 = os.path.join(out_dir, 'paired-mixed.fa.se')
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_split_paired_reads_3_output_files_right():
# test input file
infile = utils.get_test_data('paired.fq')
ex_outfile1 = utils.get_test_data('paired.fq.1')
ex_outfile2 = utils.get_test_data('paired.fq.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fq.1')
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('yyy', output_dir)
script = 'split-paired-reads.py'
args = ['-2', outfile2, '-d', output_dir, infile]
utils.runscript(script, args)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
def test_extract_paired_reads_3_output_dir():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# output directory
out_dir = utils.get_temp_filename('output')
script = 'extract-paired-reads.py'
args = [infile, '-d', out_dir]
utils.runscript(script, args)
outfile1 = os.path.join(out_dir, 'paired-mixed.fa.pe')
outfile2 = os.path.join(out_dir, 'paired-mixed.fa.se')
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_extract_paired_reads_4_output_files():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# actual output files...
outfile1 = utils.get_temp_filename('out_pe')
outfile2 = utils.get_temp_filename('out_se')
script = 'extract-paired-reads.py'
args = [infile, '-p', outfile1, '-s', outfile2]
utils.runscript(script, args)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_split_paired_reads_1_fa():
# test input file
infile = utils.get_test_data('paired.fa')
ex_outfile1 = utils.get_test_data('paired.fa.1')
ex_outfile2 = utils.get_test_data('paired.fa.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fa.1')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fa.2', in_dir)
script = 'split-paired-reads.py'
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_split_paired_reads_3_output_files_right():
# test input file
infile = utils.get_test_data('paired.fq')
ex_outfile1 = utils.get_test_data('paired.fq.1')
ex_outfile2 = utils.get_test_data('paired.fq.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fq.1')
output_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('yyy', output_dir)
script = 'split-paired-reads.py'
args = ['-2', outfile2, '-d', output_dir, infile]
utils.runscript(script, args)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
def test_extract_paired_reads_2_fq():
# test input file
infile = utils.get_test_data('paired-mixed.fq')
ex_outfile1 = utils.get_test_data('paired-mixed.fq.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fq.se')
# actual output files...
outfile1 = utils.get_temp_filename('paired-mixed.fq.pe')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fq.se', in_dir)
script = 'extract-paired-reads.py'
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name, (r.name, q.name, n)
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
def test_interleave_read_stdout():
# create input files
infile1 = utils.get_test_data('paired-slash1.fq.1')
infile2 = utils.get_test_data('paired-slash1.fq.2')
# correct output
ex_outfile = utils.get_test_data('paired-slash1.fq')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2]
(stats, out, err) = utils.runscript(script, args)
with open(outfile, 'w') as ofile:
ofile.write(out)
n = 0
for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_split_paired_reads_1_fa():
# test input file
infile = utils.get_test_data('paired.fa')
ex_outfile1 = utils.get_test_data('paired.fa.1')
ex_outfile2 = utils.get_test_data('paired.fa.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fa.1')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fa.2', in_dir)
script = 'split-paired-reads.py'
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_interleave_reads_broken_fq():
# test input files
infile1 = utils.get_test_data('paired-broken.fq.1')
infile2 = utils.get_test_data('paired-broken.fq.2')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
assert status == 1
assert 'ERROR: Input files contain different number of records.' in err
def test_interleave_reads_broken_fq_5():
# test input files
infile1 = utils.get_test_data('paired-broken4.fq.1')
infile2 = utils.get_test_data('paired-broken4.fq.2')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
assert status == 1
assert "ERROR: This doesn't look like paired data!" in err
def test_interleave_reads_broken_fq_5():
# test input files
infile1 = utils.get_test_data('paired-broken4.fq.1')
infile2 = utils.get_test_data('paired-broken4.fq.2')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
assert status == 1
assert "ERROR: This doesn't look like paired data!" in err
def test_interleave_reads_broken_fq():
# test input files
infile1 = utils.get_test_data('paired-broken.fq.1')
infile2 = utils.get_test_data('paired-broken.fq.2')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
status, out, err = utils.runscript(script, args, fail_ok=True)
assert status == 1
assert 'ERROR: Input files contain different number of records.' in err
def test_interleave_reads_no_reformat():
infile1 = utils.get_test_data('paired.fq.1')
infile2 = utils.get_test_data('paired.malformat.fq.2')
ex_outfile = utils.get_test_data('paired.malformat.fq')
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '--no-reformat', '-o', outfile]
utils.runscript(script, args)
r = open(ex_outfile).read()
q = open(outfile).read()
assert r == q, (r, q)
def test_interleave_reads_no_reformat():
infile1 = utils.get_test_data('paired.fq.1')
infile2 = utils.get_test_data('paired.malformat.fq.2')
ex_outfile = utils.get_test_data('paired.malformat.fq')
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '--no-reformat', '-o', outfile]
utils.runscript(script, args)
r = open(ex_outfile).read()
q = open(outfile).read()
assert r == q, (r, q)
def test_read_bundler():
infile = utils.get_test_data('unclean-reads.fastq')
records = [r for r in khmer.ReadParser(infile)]
bundle = khmer.utils.ReadBundle(*records)
raw_seqs = (
'GGTTGACGGGGNNNAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGANNNCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
)
cleaned_seqs = (
'GGTTGACGGGGAAAAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGAAAACCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
)
assert bundle.num_reads == 2
assert bundle.total_length == 200
for read, raw_seq, clean_seq in zip(bundle.reads, raw_seqs, cleaned_seqs):
assert read.sequence == raw_seq
assert read.cleaned_seq == clean_seq
def test_read_bundler():
infile = utils.get_test_data('unclean-reads.fastq')
records = [r for r in khmer.ReadParser(infile)]
bundle = khmer.utils.ReadBundle(*records)
raw_seqs = (
'GGTTGACGGGGNNNAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGANNNCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
)
cleaned_seqs = (
'GGTTGACGGGGAAAAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGATTTCCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
'GGTTGACGGGGCTCAGGGGGCGGCTGACTCCGAGAGACAGCAGCCGCAGCTGTCGTCAGGGGAAAACCG'
'GGGCGGAGGCCGCAGACGCGAGTGGTGGAGG',
)
assert bundle.num_reads == 2
assert bundle.total_length == 200
for read, raw_seq, clean_seq in zip(bundle.reads, raw_seqs, cleaned_seqs):
assert read.sequence == raw_seq
assert read.cleaned_seq == clean_seq
def test_interleave_reads_1_fq():
# test input files
infile1 = utils.get_test_data('paired.fq.1')
infile2 = utils.get_test_data('paired.fq.2')
# correct output
ex_outfile = utils.get_test_data('paired.fq')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
r = open(ex_outfile).read()
q = open(outfile).read()
assert r == q, (r, q)
def test_interleave_reads_1_fq():
# test input files
infile1 = utils.get_test_data('paired.fq.1')
infile2 = utils.get_test_data('paired.fq.2')
# correct output
ex_outfile = utils.get_test_data('paired.fq')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
r = open(ex_outfile).read()
q = open(outfile).read()
assert r == q, (r, q)
def test_interleave_read_badleft_badright():
# create input files
infile1 = utils.get_test_data('paired-broken.fq.badleft')
infile2 = utils.get_test_data('paired-broken.fq.badright')
# correct output
ex_outfile = utils.get_test_data('paired-broken.fq.paired_bad')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
n = 0
for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_interleave_read_seq1_fq():
# create input files
infile1 = utils.get_test_data('paired-slash1.fq.1')
infile2 = utils.get_test_data('paired-slash1.fq.2')
# correct output
ex_outfile = utils.get_test_data('paired-slash1.fq')
# actual output file
outfile = utils.get_temp_filename('out.fq')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
n = 0
for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_interleave_reads_2_fa():
# test input files
infile1 = utils.get_test_data('paired.fa.1')
infile2 = utils.get_test_data('paired.fa.2')
# correct output
ex_outfile = utils.get_test_data('paired.fa')
# actual output file
outfile = utils.get_temp_filename('out.fa')
script = 'interleave-reads.py'
args = [infile1, infile2, '-o', outfile]
utils.runscript(script, args)
n = 0
for r, q in zip(screed.open(ex_outfile), screed.open(outfile)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_extract_paired_reads_unpaired():
# test input file
infile = utils.get_test_data('random-20-a.fa')
# actual output files...
outfile1 = utils.get_temp_filename('unpaired.pe.fa')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('unpaired.se.fa', in_dir)
script = 'extract-paired-reads.py'
args = [infile]
(_, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert 'no paired reads!? check file formats...' in err, err
def test_extract_paired_reads_unpaired():
# test input file
infile = utils.get_test_data('random-20-a.fa')
# actual output files...
outfile1 = utils.get_temp_filename('unpaired.pe.fa')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('unpaired.se.fa', in_dir)
script = 'extract-paired-reads.py'
args = [infile]
(_, _, err) = utils.runscript(script, args, in_dir, fail_ok=True)
assert 'no paired reads!? check file formats...' in err, err
def test_extract_paired_reads_2_fq():
# test input file
infile = utils.get_test_data('paired-mixed.fq')
ex_outfile1 = utils.get_test_data('paired-mixed.fq.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fq.se')
# actual output files...
outfile1 = utils.get_temp_filename('paired-mixed.fq.pe')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fq.se', in_dir)
script = 'extract-paired-reads.py'
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1),
screed.open(outfile1)):
n += 1
assert r.name == q.name, (r.name, q.name, n)
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2),
screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.quality == q.quality
assert n > 0
def test_read_bundler_empty_file():
infile = utils.get_test_data('empty-file')
with pytest.raises(OSError):
records = [r for r in khmer.ReadParser(infile)]
def test_read_bundler_single_read():
infile = utils.get_test_data('single-read.fq')
records = [r for r in khmer.ReadParser(infile)]
bundle = khmer.utils.ReadBundle(*records)
assert bundle.num_reads == 1
assert bundle.reads[0].sequence == bundle.reads[0].cleaned_seq
def test_read_bundler_single_read():
infile = utils.get_test_data('single-read.fq')
records = [r for r in khmer.ReadParser(infile)]
bundle = khmer.utils.ReadBundle(*records)
assert bundle.num_reads == 1
assert bundle.reads[0].sequence == bundle.reads[0].cleaned_seq
def test_read_bundler_empty_file():
infile = utils.get_test_data('empty-file')
with pytest.raises(OSError):
records = [r for r in khmer.ReadParser(infile)]
