def make_rectangles_from_genome(options):
k = options.k
ingraph = Graph()
_, genome = fastaparser.read_fasta(options.genome).next()
ingraph.make_graph(genome, int(k))
edges_before_loop_DG = ingraph.find_loops(10, 1000)
ingraph.save(os.path.join(options.out_dir,"graph"))
rs = RectangleSet(ingraph, int(options.d))
rs.filter_without_prd()
f_left = open(os.path.join(options.out_dir, "paired_genom_contigs_1.fasta"),"w") # TODO: what is it?
f_right = open(os.path.join(options.out_dir, "paired_genom_contigs_2.fasta"),"w") # TODO: what is it?
contigs_id = 0
for key, rect in rs.rectangles.items():
for key, diag in rect.diagonals.items():
e1 = rect.e1.seq
e2 = rect.e2.seq
f_left.write(">" + str(contigs_id) + "/1\n")
f_left.write(e1[diag.offseta:diag.offsetc])
f_left.write("\n")
f_right.write(">"+str(contigs_id) + "/2\n")
f_right.write(e2[diag.offsetb:diag.offsetd])
f_right.write("\n")
contigs_id += 1
bgraph = rs.bgraph_from_genome()
bgraph.condense()
outgraph = bgraph.project(options.out_dir, False)
outgraph.fasta(open(os.path.join(options.out_dir, 'rectangles.fasta'), 'w'))