def test_alignment_conversion():
path = os.path.join(data_dir("sequence"), "alignment.fasta")
file = fasta.FastaFile.read(path)
alignment = fasta.get_alignment(file)
assert str(alignment) == ("ADTRCGTARDCGTR-DRTCGRAGD\n"
"ADTRCGT---CGTRADRTCGRAGD\n"
"ADTRCGTARDCGTRADR--GRAGD")
file2 = fasta.FastaFile()
fasta.set_alignment(file2, alignment, seq_names=["seq1", "seq2", "seq3"])
alignment2 = fasta.get_alignment(file2)
assert str(alignment) == str(alignment2)
def show_example(ax, colors):
fasta_file = fasta.FastaFile.read(EXAMPLE_FILE_NAME)
alignment = fasta.get_alignment(fasta_file)
alignment = alignment[:60]
graphics.plot_alignment_type_based(ax,
alignment,
spacing=2.0,
symbols_per_line=len(alignment),
color_scheme=colors)