def test_demultiplex():
multiout = os.path.join(os.path.dirname(__file__), 'data', 'tmp-demulti.{name}.fasta')
params = ['-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o', multiout, datapath('twoadapters.fasta')]
assert cutadapt.main(params) is None
assert files_equal(cutpath('twoadapters.first.fasta'), multiout.format(name='first'))
assert files_equal(cutpath('twoadapters.second.fasta'), multiout.format(name='second'))
assert files_equal(cutpath('twoadapters.unknown.fasta'), multiout.format(name='unknown'))
os.remove(multiout.format(name='first'))
os.remove(multiout.format(name='second'))
os.remove(multiout.format(name='unknown'))
def test_info_file():
with temporary_path("infotmp.txt") as infotmp:
run([
"--info-file", infotmp, '-a',
'adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT'
], "illumina.fastq", "illumina.fastq.gz")
assert files_equal(cutpath('illumina.info.txt'), infotmp)
def test_paired_end_legacy():
'''--paired-output, no -A/-B/-G'''
with temporary_path("paired-tmp.fastq") as pairedtmp:
# the -m 14 filters out one read, which should then also be filtered out in the second output file
run(['-a', 'TTAGACATAT', '-m', '14', '--paired-output', pairedtmp],
'paired.m14.1.fastq', 'paired.1.fastq', 'paired.2.fastq')
assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_too_short_no_primer():
'''--too-short-output and --trim-primer'''
run(
"-c -m 5 -a 330201030313112312 --trim-primer --too-short-output tooshort.tmp.fa",
"minlen.noprimer.fa", "lengths.fa")
assert files_equal(datapath('tooshort.noprimer.fa'), "tooshort.tmp.fa")
os.remove('tooshort.tmp.fa')
def test_untrimmed_paired_output():
with temporary_path("tmp-paired.1.fastq") as tmp1:
with temporary_path("tmp-paired.2.fastq") as tmp2:
with temporary_path("tmp-untrimmed.1.fastq") as untrimmed1:
with temporary_path("tmp-untrimmed.2.fastq") as untrimmed2:
params = [
'-a', 'TTAGACATAT',
'-o', tmp1, '-p', tmp2,
'--untrimmed-output', untrimmed1,
'--untrimmed-paired-output', untrimmed2,
datapath('paired.1.fastq'), datapath('paired.2.fastq')
]
assert cutadapt.main(params) is None
assert files_equal(cutpath('paired-untrimmed.1.fastq'), untrimmed1)
assert files_equal(cutpath('paired-untrimmed.2.fastq'), untrimmed2)
assert files_equal(cutpath('paired-trimmed.1.fastq'), tmp1)
assert files_equal(cutpath('paired-trimmed.2.fastq'), tmp2)
def test_demultiplex():
multiout = os.path.join(os.path.dirname(__file__), 'data',
'tmp-demulti.{name}.fasta')
params = [
'-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o',
multiout,
datapath('twoadapters.fasta')
]
assert cutadapt.main(params) is None
assert files_equal(cutpath('twoadapters.first.fasta'),
multiout.format(name='first'))
assert files_equal(cutpath('twoadapters.second.fasta'),
multiout.format(name='second'))
assert files_equal(cutpath('twoadapters.unknown.fasta'),
multiout.format(name='unknown'))
os.remove(multiout.format(name='first'))
os.remove(multiout.format(name='second'))
os.remove(multiout.format(name='unknown'))
def test_untrimmed_paired_output():
with temporary_path("tmp-paired.1.fastq") as tmp1:
with temporary_path("tmp-paired.2.fastq") as tmp2:
with temporary_path("tmp-untrimmed.1.fastq") as untrimmed1:
with temporary_path("tmp-untrimmed.2.fastq") as untrimmed2:
params = [
'-a', 'TTAGACATAT', '-o', tmp1, '-p', tmp2,
'--untrimmed-output', untrimmed1,
'--untrimmed-paired-output', untrimmed2,
datapath('paired.1.fastq'),
datapath('paired.2.fastq')
]
assert cutadapt.main(params) is None
assert files_equal(cutpath('paired-untrimmed.1.fastq'),
untrimmed1)
assert files_equal(cutpath('paired-untrimmed.2.fastq'),
untrimmed2)
assert files_equal(cutpath('paired-trimmed.1.fastq'), tmp1)
assert files_equal(cutpath('paired-trimmed.2.fastq'), tmp2)
def test_too_long():
'''--too-long-output'''
run("-c -M 5 --too-long-output toolong.tmp.fa -a 330201030313112312", "maxlen.fa", "lengths.fa")
assert files_equal(datapath('toolong.fa'), "toolong.tmp.fa")
os.remove('toolong.tmp.fa')
def test_explicit_format_with_paired():
with temporary_path("paired-tmp.fastq") as pairedtmp:
run([
'--format=fastq', '-a', 'TTAGACATAT', '-m', '14', '-p', pairedtmp
], 'paired.m14.1.fastq', 'paired.1.txt', 'paired.2.txt')
assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_restfront():
with temporary_path("rest.txt") as path:
run(['-g', 'ADAPTER', '-N', '-r', path], "restfront.fa", "rest.fa")
assert files_equal(datapath('restfront.txt'), path)
def test_untrimmed_output():
with temporary_path('untrimmed.tmp.fastq') as tmp:
run(['-a', 'TTAGACATATCTCCGTCG', '--untrimmed-output', tmp],
'small.trimmed.fastq', 'small.fastq')
assert files_equal(cutpath('small.untrimmed.fastq'), tmp)
def test_rest():
'''-r/--rest-file'''
with temporary_path('rest.tmp') as rest_tmp:
run(['-b', 'ADAPTER', '-N', '-r', rest_tmp], "rest.fa", "rest.fa")
assert files_equal(datapath('rest.txt'), rest_tmp)
def test_paired_end_legacy():
'''--paired-output, no -A/-B/-G'''
with temporary_path("paired-tmp.fastq") as pairedtmp:
# the -m 14 filters out one read, which should then also be filtered out in the second output file
run(['-a', 'TTAGACATAT', '-m', '14', '--paired-output', pairedtmp], 'paired.m14.1.fastq', 'paired.1.fastq', 'paired.2.fastq')
assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_rest():
'''-r/--rest-file'''
with temporary_path('rest.tmp') as rest_tmp:
run(['-b', 'ADAPTER', '-N', '-r', rest_tmp], "rest.fa", "rest.fa")
assert files_equal(datapath('rest.txt'), rest_tmp)
def test_untrimmed_output():
with temporary_path('untrimmed.tmp.fastq') as tmp:
run(['-a', 'TTAGACATATCTCCGTCG', '--untrimmed-output', tmp], 'small.trimmed.fastq', 'small.fastq')
assert files_equal(cutpath('small.untrimmed.fastq'), tmp)
def test_too_short():
'''--too-short-output'''
run("-c -m 5 -a 330201030313112312 --too-short-output tooshort.tmp.fa",
"minlen.fa", "lengths.fa")
assert files_equal(datapath('tooshort.fa'), "tooshort.tmp.fa")
os.remove('tooshort.tmp.fa')
def test_too_short_no_primer():
'''--too-short-output and --trim-primer'''
run("-c -m 5 -a 330201030313112312 --trim-primer --too-short-output tooshort.tmp.fa", "minlen.noprimer.fa", "lengths.fa")
assert files_equal(datapath('tooshort.noprimer.fa'), "tooshort.tmp.fa")
os.remove('tooshort.tmp.fa')
def test_too_short():
'''--too-short-output'''
run("-c -m 5 -a 330201030313112312 --too-short-output tooshort.tmp.fa", "minlen.fa", "lengths.fa")
assert files_equal(datapath('tooshort.fa'), "tooshort.tmp.fa")
os.remove('tooshort.tmp.fa')
def test_restfront():
with temporary_path("rest.txt") as path:
run(['-g', 'ADAPTER', '-N', '-r', path], "restfront.fa", "rest.fa")
assert files_equal(datapath('restfront.txt'), path)
def test_explicit_format_with_paired():
with temporary_path("paired-tmp.fastq") as pairedtmp:
run(['--format=fastq', '-a', 'TTAGACATAT', '-m', '14', '-p', pairedtmp], 'paired.m14.1.fastq', 'paired.1.txt', 'paired.2.txt')
assert files_equal(cutpath('paired.m14.2.fastq'), pairedtmp)
def test_too_long():
'''--too-long-output'''
run("-c -M 5 --too-long-output toolong.tmp.fa -a 330201030313112312",
"maxlen.fa", "lengths.fa")
assert files_equal(datapath('toolong.fa'), "toolong.tmp.fa")
os.remove('toolong.tmp.fa')
def test_info_file():
with temporary_path("infotmp.txt") as infotmp:
run(["--info-file", infotmp, '-a', 'adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT'], "illumina.fastq", "illumina.fastq.gz")
assert files_equal(cutpath('illumina.info.txt'), infotmp)
