def main(seq_a, seq_b, is_global, figure):
D = score_matrix(seq_a, seq_b, is_global=False)
path = backtrack(D, is_global)
f = format_matrix_tikz(D, path, seq_a, seq_b)
A, B = get_alignment(seq_a, seq_b, path)
block = tikz_matrix("block", body([A, B]), "below=of m")
start = tikz_matrix("seqs", body([seq_a, seq_b]), "above=of m")
figure.write(f + "\n" + block + "\n" + start)
# open("needlemanwunch.tex", "w").write(HEADER + f + "\n" + block + FOOTER)
" TODO: Add hlines and vlines to denote which letters are in the block "
def create_fm_figure(reference, query):
ref_mat = [list(reference), [str(i) for i in range(len(reference))]]
ref_fig = tikz_matrix("ref", body(ref_mat))
reference = reference + "$"
idxs, suffices = sort_suffices(reference)
bwt = [s[-1] for s in suffices]
occ = get_occurance_matrix(bwt)
counts = get_char_counts([s[0] for s in suffices]) + 1
matrix = matrix1(idxs, suffices, occ, counts).replace("#", "\$")
query_fig = tikz_matrix("query", body([query]), "below=of fm")
Figure("fma", "fm").write("\n".join((ref_fig, matrix, query_fig)))
def matrix1(idxs, suffices, occ, counts):
# counts = np.concatenate(([0], counts))
suffices = [row.replace("$", "#") for row in suffices]
occ = np.asanyarray(occ, dtype="int")
F = [
"$%s_%s$" %
(suffix[0], i - counts[lookup[suffix[0]]]) if suffix[0] != "#" else "#"
for i, suffix in enumerate(suffices)
]
L = [
"$%s_%s$" %
(suffix[-1], o[lookup[suffix[-1]]]) if suffix[-1] != "#" else "#"
for o, suffix in zip(occ, suffices)
]
elements = [[str(i), f, suffix[1:-1], l] + [str(o) for o in row]
for i, f, suffix, l, row in zip(idxs, F, suffices, L, occ)]
print(elements)
return tikz_matrix("fm", body(elements), "below=of ref")
rows = [
" & ".join([str(i)] + [f] + [suffix[1:-1]]) + [l]
for i, f, suffix, l in zip(idxs, F, suffices, L)
]
# rows = [str(i)+ "&".join(row[0], row[1:-1], row[-1]) for i, row in zip(idxs, suffices)]
# " & " + " & ".join(str(c) for c in row) for i, row in zip(idxs, suffices)]
occ_rows = ["&&" + "&".join(str(n) for n in row) + "\\\\" for row in occ]
rows = [row + occ_row for row, occ_row in zip(rows, occ_rows)]
rows = [
row + "\n \\hline" if i in counts else row
for i, row in enumerate(rows)
]
def generate_tikz(self, name, args=""):
self.name = name
prev_a_id = None
prev_b_id = None
del_a = False
del_b = False
for x, (c_a, c_b) in enumerate(zip(self._row_a, self._row_b)):
y = 0
if c_a != "-":
a_id = self.node(c_a, x, y)
y += 1
if prev_a_id is not None:
if del_a:
self.del_edge(prev_a_id, a_id)
else:
self.edge(prev_a_id, a_id)
prev_a_id = a_id
del_a = False
else:
del_a = True
if c_b != "-":
if c_a != c_b:
b_id = self.node(c_b, x, y)
else:
b_id = a_id
if prev_b_id is not None:
if del_b:
self.del_edge(prev_b_id, b_id)
else:
self.edge(prev_b_id, b_id)
prev_b_id = b_id
del_b = False
else:
del_b = True
return tikz_matrix(name, body(self._matrix), args) + "\n" + "\n".join(self.lines)
def format_matrix_tikz(D, path, seq_a, seq_b):
path_set = set(path)
lines = []
path_color = "red!25"
c_text = r"\textcolor{red}{%s}"
b_text = r"\textcolor{black!25}{%s}"
color = r"\cellcolor{blue!25}"
elements = [[
c_text % c if (i, j) in path_set else b_text % c
for j, c in enumerate(row)
] for i, row in enumerate(D)]
m = tikz_matrix("m", body(elements))
seq_template = r"\path[-stealth] (m-%s-1) edge [draw=none] node [left=0.5em] {%s} (m-%s-1);"
seq_template_b = r"\path[-stealth] (m-%s-%s) edge [draw=none] node [above=0.5em] {%s} (m-%s-%s);"
seq_a_text = "\n".join(seq_template % (i + 1, c, i + 2)
for i, c in enumerate(seq_a))
seq_b_text = "\n".join(seq_template_b % (1, i + 1, c, 1, i + 2)
for i, c in enumerate(seq_b))
edge_template = r"\path[-stealth] (m-%s-%s) edge[color=red] (m-%s-%s);"
edges = "\n".join([
edge_template % (i + 1, j + 1, k + 1, l + 1)
for (i, j), (k, l) in zip(path[:-1], path[1:])
])
return "\n".join((m, seq_a_text, seq_b_text, edges))
def to_tikz(self, horizontal=True):
lines = []
labels = [self._labels] if horizontal else [[c] for c in self._labels]
lines.append(tikz_matrix("m", body(labels)))
lines.extend(
self.get_edge(i, j, horizontal)
for i, js in self._edges.iteritems() for j in js)
return "\n".join(lines)
def to_file(self, filename):
f = open(filename, "w")
f.write(self.header + "\n")
# f.write(self._row_a + "\n")
f.write(tikz_matrix("seq", body(self._matrix))+"\n")
for line in self.lines:
f.write(line+"\n")
f.write(self.footer)
f.close()
subprocess.call(["pdflatex", filename])
def create_figure(seq, interval_dict, query):
seq_fig = tikz_matrix("seq", body([seq, "".join(rev_c[c] for c in seq)]))
query_fig = tikz_matrix("q", body([query]), "below=of seq")
rec_1 = r"\node[color=%s, draw, dashed, rounded corners, fit=(seq-1-%s) (seq-1-%s)] {};"
rec_2 = r"\node[color=%s, draw, dashed, rounded corners, fit=(seq-2-%s) (seq-2-%s)] {};"
rec_q = r"\node[color=%s, draw, dashed, rounded corners, fit=(q-1-%s) (q-1-%s)] {};"
lines = []
N = len(seq)
i = 0
for (s, e), (intervals, reverse_intervals) in interval_dict.iteritems():
lines.append(rec_q % (colors[i], s + 1, e))
for (start, end) in intervals:
lines.append(rec_1 % (colors[i], start + 1, end))
for start, end in reverse_intervals:
lines.append(rec_2 % (colors[i], N - end + 1, N - start))
i += 1
content = seq_fig + "\n" + query_fig + "\n" + "\n".join(lines)
content = content.replace("$", r"\$")
return content
path = backtrack_g(m, seq_graph, seq_graph2)
print path
figure = Figure("seqgraph_a", "seqalign_figs")
c_text = r"\textcolor{red}{%s}"
b_text = r"\textcolor{black!25}{%s}"
m = [[
c_text % c if (i, j) in path else b_text % c for j, c in enumerate(row)
] for i, row in enumerate(m)]
elems = [list("." + labels)] + [[c] + row for c, row in zip(labels2, m)]
edges2 = seq_graph2.get_tikz_edges()
edges = seq_graph.get_tikz_edges(False)
path_edge_template = r"\path[-stealth] (m-%s-%s) edge[color=red] (m-%s-%s);"
path_edges = "\n".join([
path_edge_template % (i + 2, j + 2, k + 2, l + 2)
for (i, j), (k, l) in zip(path[:-1], path[1:])
])
A, B = get_alignment(seq_graph._labels, seq_graph2._labels, path)
alignment_matrix = tikz_matrix("am", body([A, B]), "below=of m")
init = align2.generate_tikz("ga", "")
init2 = align1.generate_tikz("gb", "below=of ga,")
content = "\n".join([
init, init2,
tikz_matrix("m", body(elems), "below=of gb,"), edges, edges2,
path_edges, alignment_matrix
])
content = content.replace("#", r"\#")
figure.write(content)
# figure.write(seq_graph.to_tikz(False))
# print(edges)