# open("fm.tex", "w").write(table)
# subprocess.call(["pdflatex", "fm.tex"])
# print(counts)
fm = FMIndex(counts, occ, np.array(idxs))
query = "TACTGATG"
# query = "ACCGTTAGAGTCAG"
smems = {
smem
for i in range(len(query)) for smem in fm.find_smem(query, i)
}
mems = fm.find_mems(query)
sa = SuffixArray(idxs)
print(smems)
matches = {(t[0], t[1]): sa.get_intervals(t[2], t[1] - t[0])
for t in smems}
print(matches)
print(mems)
fig = Figure("memfig", "memfigs")
fig.write(create_figure(orig_seq, matches, query))
#
# print fm.find_seq("ACGT")
# print fm.find_seq("CG")
# for s in suffices:
# print s
"""
ATTGAC
ATTCAC
"""
rev_c = {"A": "T", "C": "G", "G": "C", "T": "A", "$": "$"}
colors = ["red", "green", "blue", "yellow"]
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
if __name__ == "__main__":
fig = Figure("memfig", "memfigs")
fig.write(create_figure("ATTCT", {1: ([(0, 3), (2, 5)], [(1, 3)])}))
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)
