def foo(queue):
import rpy2.rinterface as rinterface
rinterface.endr(1)
try:
tmp = ri.SexpVector([1, 2], ri.INTSXP)
res = (False, None)
except RuntimeError, re:
res = (True, re)
def foo(queue):
import rpy2.rinterface as rinterface
rinterface.endr(1)
try:
tmp = ri.SexpVector([1,2], ri.INTSXP)
res = (False, None)
except RuntimeError, re:
res = (True, re)
def foo(queue):
import rpy2.rinterface as rinterface
rdate = rinterface.baseenv['date']
rinterface.endr(1)
try:
tmp = rdate()
res = (False, None)
except RuntimeError, re:
res = (True, re)
def foo(queue):
import rpy2.rinterface as rinterface
rdate = rinterface.baseenv['date']
rinterface.endr(1)
try:
tmp = rdate()
res = (False, None)
except RuntimeError, re:
res = (True, re)
def _call_with_ended_r(queue):
import rpy2.rinterface_cffi as rinterface
rinterface.initr()
rdate = rinterface.baseenv['date']
rinterface.endr(0)
try:
rdate()
res = (False, None)
except RuntimeError as re:
res = (True, re)
except Exception as e:
res = (False, e)
queue.put(res)
def foo(queue):
import rpy2.rinterface as rinterface
rdate = rinterface.baseenv["date"]
rinterface.endr(1)
try:
tmp = rdate()
res = (False, None)
except RuntimeError as re:
res = (True, re)
except Exception as e:
res = (False, e)
queue.put(res)
def testNewWithoutInit(self):
self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble
ri.endr(1)
self.assertRaises(RuntimeError, ri.SexpVector, [1,2], ri.INTSXP)
#FIXME: trouble... does not initialize R when failing the test
ri.initr()
def end_R():
rinterface.endr()
def closeEvent(self, event = None):
try:
ri.endr()
except:
pass
def end_R():
rinterface.endr()
def testCallErrorWhenEndedR(self):
self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble
t = rinterface.baseNameSpaceEnv['date']
rinterface.endr(1)
self.assertRaises(RuntimeError, t)
rinterface.initr()
def closeEvent(self, event=None):
try:
ri.endr()
except:
pass
def convert_file(self, f, exc_handler=None, buffsize=10000):
SeqArray = importr("SeqArray")
file = SeqArray.seqOpen(os.path.realpath(f.name))
sample = SeqArray.seqGetData(file, "sample.id")
robjects.r('sampleID = {sample}'.format(sample=sample.r_repr()))
numOfVariants = SeqArray.seqSummary(file, varname="variant.id")[0]
robjects.r('''
output <- function(data) {
lines <- matrix(, nrow = 0, ncol = 6)
chrom = data[[1]]
pos = data[[2]]
alleles <- c(strsplit(data[[3]][1], ",")[[1]], ".")
genotype = data[[4]]
internalWrite <- function(alt, hom_het, id) {
lines <<- rbind(lines, c(chrom, pos, alleles[1], alt, hom_het, id))
}
genotype[is.na(genotype)] = length(alleles) - 1
for (col in 1:ncol(genotype)) {
num1 = genotype[1, col] + 1
num2 = genotype[2, col] + 1
id = sampleID[col]
if (num1 == 1 & num2 == 1) {
#nothing to print
}
else if (num1 != 1 & num2 == 1) {
internalWrite(alleles[num1], "het", id)
}
else if (num1 == 1 & num2 != 1) {
internalWrite(alleles[num2], "het", id)
}
else if (num1 == num2) {
internalWrite(alleles[num1], "hom", id)
}
else {
internalWrite(alleles[num1], "het", id)
internalWrite(alleles[num2], "het", id)
}
}
return(lines)
}
''')
output = robjects.globalenv['output']
@ri.rternalize
def printWithStops(data):
result = []
lines = output(data)
rows = len(lines) // 6
for line in range(rows):
result.append(" ".join([
lines[line], lines[line + rows], lines[line + (2 * rows)],
lines[line + (3 * rows)], lines[line + (4 * rows)],
lines[line + (5 * rows)]
]))
return StrVector(result)
#returns pairs (a,b) such that the first a is equal to i, the last b is equal to n+1. If we look at all a's inclusively and all b's
#exclusively then this generates intervals that partition the set of numbers from 1 to n (inclusively) such that all intervals
#contain a buff amount of numbers except for possibly the last interval
def inclusiveRanges(i, n, buff):
while i <= n:
if i + buff > n + 1:
buff -= i + buff - n - 1
yield [i, i + buff]
i += buff
for start, end in inclusiveRanges(1, numOfVariants, buffsize):
try:
robjects.r('array = c({previous}:{next})'.format(
previous=start, next=end - 1))
SeqArray.seqSetFilter(file,
variant_sel=robjects.globalenv['array'],
verbose=False)
result = SeqArray.seqApply(
file,
StrVector(["chromosome", "position", "allele",
"genotype"]),
FUN=printWithStops,
margin="by.variant",
as_is="list")
for variant in result:
for charLine in variant:
try:
line = charLine.split()
if line[3] == '.':
continue
result = [{
'chrom': line[0],
'pos': line[1],
'ref_base': line[2],
'alt_base': line[3],
'tags': None,
'sample_id': line[5],
'zygosity': line[4]
}]
yield 0, line, result
except Exception as e:
if exc_handler:
exc_handler(0, "", e)
continue
else:
raise e
except Exception as e:
if exc_handler:
exc_handler(0, "", e)
continue
else:
raise e
#closes the embedded R subprocess and deletes rpy2 objects
ri.endr(0)
del file, output, printWithStops, sample, variant
#references for r interface usage from here:
#http://rpy.sourceforge.net/rpy2/doc-2.2/html/rinterface.html
#initialize the embedded r
ri.initr()
r=ro.r
#generate some random data
mu, sigma = 0, 0.1 # mean and standard deviation
s = np.random.normal(mu, sigma, 1000)
#plot the random data using matplotlib (for comparison to the shiny app)
count, bins, ignored = plt.hist(s, 30, normed=True)
plt.plot(bins, 1/(sigma * np.sqrt(2 * np.pi)) * np.exp( - (bins - mu)**2 / (2 * sigma**2) ), linewidth=2, color='r')
plt.show(block=False)
#pass the series to R
ro.globalenv["dataseries"] = ro.FloatVector(s)
#call teh shiny app, and return when the user presses a button
#gist on how to exit cleanly: https://gist.github.com/trestletech/5948876
ro.r('''
library(shiny)
runApp()
quit()
''' )
#end the embedded interface
ri.endr(0)
