def test_others():
filename = sequana_data("test_fasta.fasta")
ff = FastA(filename)
assert len(ff) == 16
assert len(ff.comments) == 16
assert len(ff.names) == 16
assert len(ff.sequences) == 16
assert is_fasta(filename) == True
ff.get_lengths_as_dict()
with TempFile(suffix='.fasta') as fh:
ff.select_random_reads(4, output_filename=fh.name)
ff.select_random_reads([1, 2, 3], output_filename=fh.name)
ff.select_random_reads({1, 2, 3}, output_filename=fh.name)
assert ff.get_stats()['N'] == 16
assert ff.get_stats()['mean_length'] > 454
with TempFile(suffix='.fasta') as fh:
ff.reverse_and_save(fh.name)
ff.to_fasta(fh.name)
ff.to_igv_chrom_size(fh.name)
def test_fasta_filtering():
filename = sequana_data("test_fasta_filtering.fa")
ff = FastA(filename)
with TempFile(suffix='.fasta') as fh:
ff.to_fasta(fh.name)
ff.save_ctg_to_fasta("A", fh.name)
with TempFile(suffix='.fasta') as fh:
ff.filter(fh.name, names_to_exclude=["A", "B"])
reader = FastA(fh.name)
assert set(reader.names) == set(["C", "D"])
ff = FastA(filename)
with TempFile(suffix='.fasta') as fh:
ff.filter(fh.name, names_to_keep=[
"A",
])
reader = FastA(fh.name)
assert set(reader.names) == set(['A'])