def test_align():
istring, jstring, submatr = submat.read('pam200')
ali = aligner.Aligner.from_submatr(istring, jstring, submatr)
path = locate_tests('data/rmlA.2x.fa')
iseq, jseq = fasta.read(path, castfunc=lambda x: [s.seq for s in x])
with Timer('align'):
for i in range(repeat):
matrx, istring, jstring = ali.align(iseq, jseq, backtrack=True)
mstring = aligner.gen_match_string(istring, jstring)
for items in molbiox.frame.streaming.chunkwise(60, istring, mstring, jstring):
bunch = six.b('\n').join(items).decode('ascii')
print(bunch, end='\n\n', file=sys.stderr)
def test():
path = locate_tests('data/lwcsample.tsv')
elements = molbiox.io.arrows.read_lwcfile(path, 16, castfunc=list)
arr = ([elem['head'], elem['tail'], 1000] for elem in elements)
results = ArrowCalc().calc(arr) / 20
polygons = arrows.format_points(results)
for elem, pg in zip(elements, polygons):
elem['polygon'] = pg
elem['text_x'] = (elem['head'] + elem['tail']) / 2. / 20
elem['text_y'] = 920 / 20
# print(elem, file=sys.stderr)
res = arrows.render_svg(elements=elements)
print(res)
