def find_synteny_region(query, sbed, data, window, cutoff, colinear=False):
"""
Get all synteny blocks for a query, algorithm is single linkage
anchors are a window centered on query
Two categories of syntenic regions depending on what query is:
(Syntelog): syntenic region is denoted by the syntelog
(Gray gene): syntenic region is marked by the closest flanker
"""
regions = []
ysorted = sorted(data, key=lambda x: x[1])
g = Grouper()
a, b = tee(ysorted)
next(b, None)
for ia, ib in zip(a, b):
pos1, pos2 = ia[1], ib[1]
if pos2 - pos1 < window and sbed[pos1].seqid == sbed[pos2].seqid:
g.join(ia, ib)
for group in sorted(g):
(qflanker, syntelog), (far_flanker, far_syntelog), flanked = \
get_flanker(group, query)
# run a mini-dagchainer here, take the direction that gives us most anchors
if colinear:
y_indexed_group = [(y, i) for i, (x, y) in enumerate(group)]
lis = longest_increasing_subsequence(y_indexed_group)
lds = longest_decreasing_subsequence(y_indexed_group)
if len(lis) >= len(lds):
track = lis
orientation = "+"
else:
track = lds
orientation = "-"
group = [group[i] for (y, i) in track]
xpos, ypos = zip(*group)
score = min(len(set(xpos)), len(set(ypos)))
if qflanker == query:
gray = "S"
else:
gray = "G" if not flanked else "F"
score -= 1 # slight penalty for not finding syntelog
if score < cutoff:
continue
# y-boundary of the block
left, right = group[0][1], group[-1][1]
# this characterizes a syntenic region (left, right).
# syntelog is -1 if it's a gray gene
syn_region = (syntelog, far_syntelog, left, right, gray, orientation,
score)
regions.append(syn_region)
return sorted(regions, key=lambda x: -x[-1]) # decreasing synteny score
def find_synteny_region(query, sbed, data, window, cutoff, colinear=False):
"""
Get all synteny blocks for a query, algorithm is single linkage
anchors are a window centered on query
Two categories of syntenic regions depending on what query is:
(Syntelog): syntenic region is denoted by the syntelog
(Gray gene): syntenic region is marked by the closest flanker
"""
regions = []
ysorted = sorted(data, key=lambda x: x[1])
g = Grouper()
a, b = tee(ysorted)
next(b, None)
for ia, ib in izip(a, b):
pos1, pos2 = ia[1], ib[1]
if pos2 - pos1 < window and sbed[pos1].seqid == sbed[pos2].seqid:
g.join(ia, ib)
for group in sorted(g):
(qflanker, syntelog), (far_flanker, far_syntelog), flanked = \
get_flanker(group, query)
# run a mini-dagchainer here, take the direction that gives us most anchors
if colinear:
y_indexed_group = [(y, i) for i, (x, y) in enumerate(group)]
lis = longest_increasing_subsequence(y_indexed_group)
lds = longest_decreasing_subsequence(y_indexed_group)
if len(lis) >= len(lds):
track = lis
orientation = "+"
else:
track = lds
orientation = "-"
group = [group[i] for (y, i) in track]
xpos, ypos = zip(*group)
score = min(len(set(xpos)), len(set(ypos)))
if qflanker == query:
gray = "S"
else:
gray = "G" if not flanked else "F"
score -= 1 # slight penalty for not finding syntelog
if score < cutoff:
continue
# y-boundary of the block
left, right = group[0][1], group[-1][1]
# this characterizes a syntenic region (left, right).
# syntelog is -1 if it's a gray gene
syn_region = (syntelog, far_syntelog, left,
right, gray, orientation, score)
regions.append(syn_region)
return sorted(regions, key=lambda x: -x[-1]) # decreasing synteny score
def main(arg):
fp = open(arg)
N = int(fp.readline().strip())
a = [int(x) for x in fp.readline().split()]
assert N == len(a)
lis = longest_increasing_subsequence(a)
lds = longest_decreasing_subsequence(a)
print " ".join(str(x) for x in lis)
print " ".join(str(x) for x in lds)
def test_longest_decreasing_subsequence(input_array, expected):
from jcvi.algorithms.lis import longest_decreasing_subsequence
assert longest_decreasing_subsequence(input_array) == expected