def get_region_details(airport: airports.Airport) -> regions.Region:
"""
returns: (regions.Region)
iso_country: "NL"
name: "Netherlands"
region: "Europe"
sub_region: "Western Europe"
"""
r = regions.Regions()
return r.lookup(airport.iso_country)
# import the necessary packages
import numpy as np
import argparse
import cv2
import regions
# regions.Regions(xIntercept, width, length, yIntercept, rows, columns)
regions = regions.Regions(50, 400, 400, 50, 3, 3)
videoCapture = cv2.VideoCapture(0)
while True:
ret, image = videoCapture.read()
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
gray = cv2.blur(gray, (5, 5))
# detect circles in the image
circles = cv2.HoughCircles(gray, cv2.cv.CV_HOUGH_GRADIENT, 1.4, 30)
# ensure at least some circles were founds
if circles is not None:
# convert the (x, y) coordinates and radius of the circles to integers
circles = np.round(circles[0, :]).astype("int")
# loop over the (x, y) coordinates and radius of the circles
for (x, y, r) in circles:
# draw the circle in the output image, then draw a rectangle
# corresponding to the center of the circle
cv2.circle(image, (x, y), r, (0, 255, 0), 4)
cv2.rectangle(image, (x - 5, y - 5), (x + 5, y + 5), (0, 128, 255),
uniqueCoverdRegion_meta = list(set(coveredRegion_meta))
if len(uniqueCoverdRegion_meta) < minReadPairNum: continue
# filter by the ratio of valid read pairs
pairPos = F[17].split(';')
if float(pairPos.count("0")) / float(len(pairPos)) > 1 - minValidThres:
continue
# check for the covered region
coveredRegion_primary = F[9].split(';')
coveredRegion_pair = F[12].split(';')
coveredRegion_SA = F[15].split(';')
pairPos = F[17].split(';')
primaryPos = F[18].split(';')
region1 = regions.Regions()
region2 = regions.Regions()
for i in range(0, len(coveredRegion_primary)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region1.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region2.addMerge(reg)
for i in range(0, len(coveredRegion_SA)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_SA[i].split(','):
region2.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
# import the necessary packages
import numpy as np
import argparse
import cv2
import regions
#regions.Regions(xIntercept, width, length, yIntercept, rows, columns)
regions = regions.Regions(10,480,480,10,3,3)
videoCapture = cv2.VideoCapture(0)
while True:
ret, image = videoCapture.read()
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
gray = cv2.blur(gray,(5,5))
# detect circles in the image
circles = cv2.HoughCircles(gray, cv2.HOUGH_GRADIENT, 1.2, 75)
# ensure at least some circles were founds
if circles is not None:
# convert the (x, y) coordinates and radius of the circles to integers
circles = np.round(circles[0, :]).astype("int")
# loop over the (x, y) coordinates and radius of the circles
for (x, y, r) in circles:
# draw the circle in the output image, then draw a rectangle
# corresponding to the center of the circle
cv2.circle(image, (x, y), r, (0, 255, 0), 4)
cv2.rectangle(image, (x - 5, y - 5), (x + 5, y + 5), (0, 128, 255), -1)
def addImage(self, survey='poss1_red'):
self.w.set("frame new")
self.w.set('single')
self.w.set("dssstsci survey {0}".format(survey))
self.w.set("dssstsci size {0} {1} arcmin ".format(
self.size * self.inflate, self.size * self.inflate))
self.w.set("dssstsci coord {0} sexagesimal ".format(self.coordstring))
# add circles centered on the target position
r = regions.Regions("LDSS3C", units="fk5", path=finderdir)
imageepoch = float(
self.w.get('''fits header keyword "'DATE-OBS'" ''').split('-')[0])
old = self.star.atEpoch(imageepoch)
p = self.star.posstring
print p(old, imageepoch)
print p(self.star.current, self.star.epoch)
current = self.star.current
r.addLine(old.ra.degree,
old.dec.degree,
current.ra.degree,
current.dec.degree,
line='0 1',
color='red')
print old.ra.degree, old.dec.degree, current.ra.degree, current.dec.degree
r.addCircle(current.ra.degree,
current.dec.degree,
"{0}'".format(self.size / 2),
text="{0:.1f}' diameter".format(self.size),
font="bold {0:.0f}".format(np.round(14.0)))
r.addCircle(current.ra.degree, current.dec.degree,
"{0}'".format(2.0 / 60.0))
# add a compass
radius = self.size / 60 / 2
r.addCompass(current.ra.degree + 0.95 * radius,
current.dec.degree + 0.95 * radius,
"{0}'".format(self.size * self.inflate / 5))
r.addText(current.ra.degree,
current.dec.degree - 1.1 * radius,
self.name + ', ' + self.star.posstring(),
font='bold {0:.0f}'.format(np.round(16.0)),
color='red')
r.addText(current.ra.degree - 1.04 * radius,
current.dec.degree + 1.02 * radius,
'd(RA)={0:+3.0f}, d(Dec)={1:+3.0f} mas/yr'.format(
self.star.pmra, self.star.pmdec),
font='bold {0:.0f}'.format(np.round(12.0)),
color='red')
r.addText(current.ra.degree - 1.04 * radius,
current.dec.degree + 0.95 * radius,
'(image from {0})'.format(imageepoch),
font='bold {0:.0f}'.format(np.round(10.0)),
color='red')
# load regions into image
print(r)
r.write()
self.w.set("cmap invert yes")
self.w.set("colorbar no")
#self.w.set("rotate to {0}".format(int(np.round(90 -63 - self.star['rot'][0]))))
self.w.set("regions load {0}".format(r.filename))
def filterCoverRegion(inputFilePath, outputFilePath):
# min_read_pair_num = config.param_conf.getint("filter_condition", "min_read_pair_num")
# min_valid_read_pair_ratio = config.param_conf.getfloat("filter_condition", "min_valid_read_pair_ratio")
# min_cover_size = config.param_conf.getint("filter_condition", "min_cover_size")
# min_chimeric_size = config.param_conf.getint("filter_condition", "min_chimeric_size")
# anchor_size_thres = config.param_conf.getint("filter_condition", "anchor_size_thres")
min_read_pair_num = param_conf.min_read_pair_num
min_valid_read_pair_ratio = param_conf.min_valid_read_pair_ratio
min_cover_size = param_conf.min_cover_size
min_chimeric_size = param_conf.min_chimeric_size
anchor_size_thres = param_conf.anchor_size_thres
hIN = open(inputFilePath, 'r')
hOUT = open(outputFilePath, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
if F[0] == F[3] and abs(int(F[1]) - int(F[4])) < min_chimeric_size:
continue
coveredRegion_primary = F[9].split(';')
coveredRegion_pair = F[12].split(';')
coveredRegion_SA = F[15].split(';')
# check the number of unique read pairs
coveredRegion_meta = [
coveredRegion_primary[i] + ';' + coveredRegion_pair[i] + ';' +
coveredRegion_SA[i] for i in range(0, len(coveredRegion_primary))
]
uniqueCoverdRegion_meta = list(set(coveredRegion_meta))
if len(uniqueCoverdRegion_meta) < min_read_pair_num: continue
# check the maximum anchor size
coverRegionSize_primary = map(region_utils.getCoverSize,
coveredRegion_primary)
coverRegionSize_SA = map(region_utils.getCoverSize, coveredRegion_SA)
anchor_size = [
min(coverRegionSize_primary[i], coverRegionSize_SA[i])
for i in range(len(coverRegionSize_primary))
]
if max(anchor_size) < anchor_size_thres: continue
# filter by the ratio of valid read pairs
pairPos = F[17].split(';')
if float(pairPos.count("0")) / float(
len(pairPos)) > 1 - min_valid_read_pair_ratio:
continue
# check for the covered region
pairPos = F[17].split(';')
primaryPos = F[18].split(';')
region1 = regions.Regions()
region2 = regions.Regions()
for i in range(0, len(coveredRegion_primary)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region1.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region2.addMerge(reg)
for i in range(0, len(coveredRegion_SA)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_SA[i].split(','):
region2.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
for reg in coveredRegion_SA[i].split(','):
region1.addMerge(reg)
for i in range(0, len(coveredRegion_pair)):
if (primaryPos[i] == "1"
and pairPos[i] == "1") or (primaryPos[i] == "2"
and pairPos[i] == "2"):
for reg in coveredRegion_pair[i].split(','):
region1.addMerge(reg)
elif (primaryPos[i] == "1"
and pairPos[i] == "2") or (primaryPos[i] == "2"
and pairPos[i] == "1"):
for reg in coveredRegion_pair[i].split(','):
region2.addMerge(reg)
region1.reduceMerge()
region2.reduceMerge()
if region1.regionSize() < min_cover_size or region2.regionSize(
) < min_cover_size:
continue
print >> hOUT, '\t'.join(F)
hIN.close()
hOUT.close()
def extractSplicingPattern(inputFilePath, outputFilePath):
# reference_genome = config.param_conf.get("alignment", "reference_genome")
reference_genome = param_conf.reference_genome
hIN = open(inputFilePath, 'r')
hOUT = open(outputFilePath, 'w')
for line in hIN:
F = line.rstrip('\n').split('\t')
# check for the covered region
coveredRegion_primary = F[9].split(';')
coveredRegion_pair = F[12].split(';')
coveredRegion_SA = F[15].split(';')
pairPos = F[17].split(';')
primaryPos = F[18].split(';')
####################
splice2count1 = {}
splice2count2 = {}
# get the splicing position for the primary reads
for i in range(0, len(coveredRegion_primary)):
regs = coveredRegion_primary[i].split(',')
if len(regs) == 1: continue
chr_reg = ""
start_reg = []
end_reg = []
for reg in regs:
mReg = regRe.match(reg)
chr_reg = mReg.group(1)
start_reg.append(int(mReg.group(2)))
end_reg.append(int(mReg.group(3)))
start_reg.sort()
end_reg.sort()
for j in range(0, len(start_reg) - 1):
regKey = (chr_reg, int(end_reg[j]), int(start_reg[j + 1]))
if primaryPos[i] == "1" and pairPos != "0":
splice2count1[regKey] = (splice2count1[regKey] + 1
if regKey in splice2count1 else 1)
elif primaryPos[i] == "2" and pairPos != "0":
splice2count2[regKey] = (splice2count2[regKey] + 1
if regKey in splice2count2 else 1)
# get the splicing position for the supplementary reads
for i in range(0, len(coveredRegion_SA)):
regs = coveredRegion_SA[i].split(',')
if len(regs) == 1: continue
chr_reg = ""
start_reg = []
end_reg = []
for reg in regs:
mReg = regRe.match(reg)
chr_reg = mReg.group(1)
start_reg.append(int(mReg.group(2)))
end_reg.append(int(mReg.group(3)))
start_reg.sort()
end_reg.sort()
for j in range(0, len(start_reg) - 1):
regKey = (chr_reg, int(end_reg[j]), int(start_reg[j + 1]))
if primaryPos[i] == "1" and pairPos != "0":
splice2count2[regKey] = (splice2count2[regKey] + 1
if regKey in splice2count2 else 1)
elif primaryPos[i] == "2" and pairPos != "0":
splice2count1[regKey] = (splice2count1[regKey] + 1
if regKey in splice2count1 else 1)
# get the splicing position for the pair reads
for i in range(0, len(coveredRegion_pair)):
regs = coveredRegion_pair[i].split(',')
if len(regs) == 1: continue
chr_reg = ""
start_reg = []
end_reg = []
for reg in regs:
mReg = regRe.match(reg)
chr_reg = mReg.group(1)
start_reg.append(int(mReg.group(2)))
end_reg.append(int(mReg.group(3)))
start_reg.sort()
end_reg.sort()
for j in range(0, len(start_reg) - 1):
regKey = (chr_reg, int(end_reg[j]), int(start_reg[j + 1]))
if (primaryPos[i] == "1"
and pairPos[i] == "1") or (primaryPos[i] == "2"
and pairPos[i] == "2"):
splice2count1[regKey] = (splice2count1[regKey] + 1
if regKey in splice2count1 else 1)
elif (primaryPos[i] == "1"
and pairPos[i] == "2") or (primaryPos[i] == "2"
and pairPos[i] == "1"):
splice2count2[regKey] = (splice2count2[regKey] + 1
if regKey in splice2count2 else 1)
####################
####################
splice2count1_ref = {}
splice2count2_ref = {}
for key in splice2count1:
splice2count1_ref[key] = 0
for key in splice2count2:
splice2count2_ref[key] = 0
# check about each splicing position for the primary reads
for i in range(0, len(coveredRegion_primary)):
for reg in coveredRegion_primary[i].split(','):
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if primaryPos[i] == "1" and pairPos != "0":
for key in splice2count1:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
if primaryPos[i] == "2" and pairPos != "0":
for key in splice2count2:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
# check about each splicing position for the supplementary reads
for i in range(0, len(coveredRegion_SA)):
for reg in coveredRegion_SA[i].split(','):
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if primaryPos[i] == "1" and pairPos != "0":
for key in splice2count2:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
if primaryPos[i] == "2" and pairPos != "0":
for key in splice2count1:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
# check about each splicing position for the pair reads
for i in range(0, len(coveredRegion_pair)):
for reg in coveredRegion_pair[i].split(','):
if reg == "*": continue
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if (primaryPos[i] == "1"
and pairPos[i] == "1") or (primaryPos[i] == "2"
and pairPos[i] == "2"):
for key in splice2count1:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count1_ref[key] = splice2count1_ref[key] + 1
if (primaryPos[i] == "1"
and pairPos[i] == "2") or (primaryPos[i] == "2"
and pairPos[i] == "1"):
for key in splice2count2:
chr_key, start_key, end_key = key[0], key[1], key[2]
# if the given region cover arround the spliced sites
if F[2] == "+" and start_reg <= end_key - 5 and end_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
if F[2] == "-" and start_reg <= start_key - 5 and start_key + 5 <= end_reg:
splice2count2_ref[key] = splice2count2_ref[key] + 1
####################
####################
# check whether we should adopt each splice junction
spliceJunction1 = []
spliceJunction2 = []
for key in splice2count1:
if splice2count1[key] > splice2count1_ref[key]:
spliceJunction1.append(key)
for key in splice2count2:
if splice2count2[key] > splice2count2_ref[key]:
spliceJunction2.append(key)
####################
####################
region1 = regions.Regions()
region2 = regions.Regions()
for i in range(0, len(coveredRegion_primary)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region1.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
for reg in coveredRegion_primary[i].split(','):
region2.addMerge(reg)
for i in range(0, len(coveredRegion_SA)):
if primaryPos[i] == "1" and pairPos != "0":
for reg in coveredRegion_SA[i].split(','):
region2.addMerge(reg)
elif primaryPos[i] == "2" and pairPos != "0":
for reg in coveredRegion_SA[i].split(','):
region1.addMerge(reg)
for i in range(0, len(coveredRegion_pair)):
if (primaryPos[i] == "1"
and pairPos[i] == "1") or (primaryPos[i] == "2"
and pairPos[i] == "2"):
for reg in coveredRegion_pair[i].split(','):
region1.addMerge(reg)
elif (primaryPos[i] == "1"
and pairPos[i] == "2") or (primaryPos[i] == "2"
and pairPos[i] == "1"):
for reg in coveredRegion_pair[i].split(','):
region2.addMerge(reg)
region1.reduceMerge()
region2.reduceMerge()
####################
####################
contig1 = []
contig2 = []
tempPos = int(F[1])
if F[2] == "+":
for key in sorted(spliceJunction1,
key=lambda x: x[2],
reverse=True):
if tempPos < key[2]: continue
minStart = float("inf")
for reg in region1.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if tempPos <= end_reg and start_reg < minStart:
minStart = start_reg
if minStart != float("inf"):
contig1.append((chr_reg, max(key[2], minStart), tempPos))
if minStart > key[2]: break
tempPos = key[1]
minStart = float("inf")
for reg in region1.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if tempPos <= end_reg and start_reg < minStart:
minStart = start_reg
if minStart != float("inf"):
contig1.append((chr_reg, minStart, tempPos))
if F[2] == "-":
for key in sorted(spliceJunction1, key=lambda x: x[1]):
if tempPos > key[1]: continue
maxEnd = -float("inf")
for reg in region1.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if start_reg <= tempPos and end_reg > maxEnd:
maxEnd = end_reg
if maxEnd != -float("inf"):
contig1.append((chr_reg, tempPos, min(key[1], maxEnd)))
if maxEnd < key[1]: break
tempPos = key[2]
maxEnd = -float("inf")
for reg in region1.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if start_reg <= tempPos and end_reg > maxEnd:
maxEnd = end_reg
if maxEnd != -float("inf"):
contig1.append((chr_reg, tempPos, maxEnd))
tempPos = int(F[4])
if F[5] == "+":
for key in sorted(spliceJunction2,
key=lambda x: x[2],
reverse=True):
if tempPos < key[2]: continue
minStart = float("inf")
for reg in region2.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if tempPos <= end_reg and start_reg < minStart:
minStart = start_reg
if minStart != float("inf"):
contig2.append((chr_reg, max(key[2], minStart), tempPos))
if minStart > key[2]: break
tempPos = key[1]
minStart = float("inf")
for reg in region2.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if tempPos <= end_reg and start_reg < minStart:
minStart = start_reg
if minStart != float("inf"):
contig2.append((chr_reg, minStart, tempPos))
if F[5] == "-":
for key in sorted(spliceJunction2, key=lambda x: x[1]):
if tempPos > key[1]: continue
maxEnd = -float("inf")
for reg in region2.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if start_reg <= tempPos and end_reg > maxEnd:
maxEnd = end_reg
if maxEnd != -float("inf"):
contig2.append((chr_reg, tempPos, min(key[1], maxEnd)))
if maxEnd < key[1]: break
tempPos = key[2]
maxEnd = -float("inf")
for reg in region2.regionVec:
mReg = regRe.match(reg)
chr_reg, start_reg, end_reg = mReg.group(1), int(
mReg.group(2)), int(mReg.group(3))
if start_reg <= tempPos and end_reg > maxEnd:
maxEnd = end_reg
if maxEnd != -float("inf"):
contig2.append((chr_reg, tempPos, maxEnd))
####################
contigSeq1 = ""
contigSeq2 = ""
inSeq = ';'.join(list(set(F[6].split(';'))))
contigSeq1 = seq_utils.getSeq(reference_genome, contig1)
contigSeq2 = seq_utils.getSeq(reference_genome, contig2)
if F[2] == "+": contigSeq1 = seq_utils.reverseComplement(contigSeq1)
if F[5] == "+": contigSeq2 = seq_utils.reverseComplement(contigSeq2)
print >> hOUT, '\t'.join([
'\t'.join(F[0:6]),
str(inSeq),
str(len(F[8].split(';'))),
str(contig1),
str(contig2), contigSeq1, contigSeq2
])
hIN.close()
hOUT.close()
