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)