def test_fastq_unzipped():
for thisdata in [data, datagz]:
# isntanciation
f = fastq.FastQ(thisdata)
assert f.data_format == "Illumina_1.8+"
# count lines
# rune it twice because we want to make sure re-running count_lines
# (decompression with zlib) works when run again.
assert f.count_lines() == 1000
assert f.count_lines() == 1000
assert f.count_reads() == 250
assert f.count_reads() == 250
# extract head of the file into an unzipped file
ft = TempFile()
f.extract_head(100, ft.name)
fcheck = fastq.FastQ(ft.name)
assert fcheck.count_lines() == 100
ft.delete()
# extract head of the file and zip output
ft = TempFile(suffix=".gz")
f.extract_head(100, ft.name)
fcheck = fastq.FastQ(ft.name)
assert fcheck.count_lines() == 100
ft.delete()
with FastQ(thisdata) as ff:
assert len(ff) == 250
with TempFile() as fh:
selection = f.select_random_reads(10, fh.name)
f.select_random_reads(selection, fh.name)
def test_split():
# general tests
f = fastq.FastQ(data)
try:
f.split_lines(250) # not a multiple of 4
assert False
except:
assert True
#
outputs = f.split_lines(500)
assert len(outputs) == 2
remove_files(outputs)
outputs = f.split_lines(256)
assert len(outputs) == 4
remove_files(outputs)
# Now tests the zip/unzip cases
f = fastq.FastQ(data)
outputs = f.split_lines(500, gzip=False)
remove_files(outputs)
outputs = f.split_lines(500, gzip=True)
remove_files(outputs)
f = fastq.FastQ(datagz)
outputs = f.split_lines(500, gzip=False)
remove_files(outputs)
outputs = f.split_lines(500, gzip=True)
remove_files(outputs)
f.split_lines(1000000) is None # too many
def test_basic():
f = fastq.FastQ(data)
assert f.stats() == {
'N': 250,
'mean_read_length': 101.0,
'sum_read_length': 25250
}
def test_others():
# kmer
f = fastq.FastQ(data)
f.to_kmer_content()
#krona
with TempFile() as fh:
f.to_krona(5, fh.name)
assert f == f
f1 = fastq.FastQ(data)
f2 = fastq.FastQ(sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz"))
assert f1 != f2
f1 = fastq.FastQ(data)
f2 = fastq.FastQ(data)
assert f1 == f2
def test_basic():
assert is_fastq(data) == True
f = fastq.FastQ(data)
assert f.stats() == {
'N': 250,
'mean_read_length': 101.0,
'sum_read_length': 25250
}
f.get_lengths()
ft = TempFile()
f.to_fasta(ft.name)
def test_identifiers():
f = fastq.FastQ(data)
identifier = fastq.Identifier(f.next()["identifier"])
assert identifier.version == 'Illumina_1.8+'
identifier = fastq.Identifier(f.next()["identifier"], "Illumina_1.8+")
assert identifier.version == 'Illumina_1.8+'
identifier = fastq.Identifier("@prefix:1_13_573/1")
assert identifier.version == "unknown"
identifier = fastq.Identifier("@SEQ:1:1101:9010:3891#0/1")
identifier = fastq.Identifier("@SEQ:1:1101:9010:3891#0/1",
version="Illumina_1.4+")
print(identifier)
identifier.__repr__()
def test_filter():
f = fastq.FastQ(data)
# keeps all
with TempFile() as fh:
f.filter(min_bp=80,
max_bp=120,
output_filename=fh.name,
progressbar=False)
assert len(f) == 250
ff = FastQ(fh.name)
assert len(ff) == 250
# keeps nothing
with TempFile() as fh:
f.filter(min_bp=80, max_bp=90, output_filename=fh.name)
assert len(f) == 250
ff = FastQ(fh.name)
assert len(ff) == 0
def test_select_reads():
f = fastq.FastQ(data)
ft = TempFile()
f.select_reads(["HISEQ:426:C5T65ACXX:5:2302:4953:2090"],
output_filename=ft.name)