for t in xrange(ngens):
logfile.write(" t=" + str(t) + "\n")
if t % 10 == 0:
logfile.write(" census (num segments, num indivs): " +
str(coal.census(pop, sampsizes=sampsizes)) + "\n")
logfile.flush()
coal.parents(pop, ancne=ancnefn(t), migprobs=migprobs(t), t=t)
if _exitnow:
# there's been a ctrl-c; stop now.
break
logfile.write(" census (num indivs, num segments): " +
str(coal.census(pop, sampsizes=sampsizes)) + "\n")
logfile.write("Done with simulation at " +
time.strftime("%d %h %Y %H:%M:%S", time.localtime()) +
"; now writing out IBD info.\n")
coal.writeibd(pop, minlen=minlen, gaplen=gaplen, outfile=ibdfile)
# writecoal(ibdict,outfile=coalfile)
# pdb.set_trace()
logfile.write("\n")
logfile.write("Closing ibd file...\n")
ibdfile.close()
logfile.write("All done at " +
time.strftime("%d %h %Y %H:%M:%S", time.localtime()) + "\n")
# coalfile.close()
logfile.close()
logfile.write("chromosome ending positions: " + str(list(coal.chrpos)+[coal.chrlen]) + "\n")
logfile.write("\n")
logfile.write("Beginning ------------\n")
# here is where the action happens
for t in xrange(ngens):
logfile.write(" t="+str(t)+"\n")
if t%10==0:
logfile.write(" census (num segments, num indivs): " + str(coal.census(pop,sampsizes=sampsizes))+ "\n")
logfile.flush()
coal.parents(pop,ancne=ancnefn(t),migprobs=migprobs(t),t=t)
if _exitnow:
# there's been a ctrl-c; stop now.
break
logfile.write(" census (num indivs, num segments): " + str(coal.census(pop,sampsizes=sampsizes))+ "\n")
logfile.write("Done with simulation at " + time.strftime("%d %h %Y %H:%M:%S", time.localtime()) + "; now writing out IBD info.\n" )
coal.writeibd(pop,minlen=minlen,gaplen=gaplen,outfile=ibdfile)
# writecoal(ibdict,outfile=coalfile)
# pdb.set_trace()
logfile.write("\n")
logfile.write("Closing ibd file...\n")
ibdfile.close()
logfile.write("All done at " + time.strftime("%d %h %Y %H:%M:%S", time.localtime()) + "\n" )
# coalfile.close()
logfile.close()
return dict(a=max(10,100-5*t),b=10)
coal.chrlens = ( 2.0, 1.0 )
coal.chrpos = tuple( [ sum( coal.chrlens[0:k] ) for k in range(1,len(coal.chrlens)) ] ) # cumulative sum: position if lined up end-to-end
coal.chrlen = sum(coal.chrlens) # the last one (total length)
start = time.time()
pop = coal.initpop(sampsizes)
ibdict = {}
poplist = []
for t in xrange(20):
print " ----", t
coal.parents(pop,t=t,ibdict=ibdict,migprobs=migprobs,ancne=ancnefn(t))
coal.sanity(pop,sampsizes=sampsizes,ancne=ancnefn(t),print_details=True)
coal.writeibd(pop,minlen=0.0,gaplen=0.0,filename="test-fibd-"+("%(t)02d" % {'t':t})+".gz")
poplist.append( copy.deepcopy(pop) )
print time.time()-start
# run this to look at the above.
rscript <- '''
source("~/projects/genome/ibd-blocks-fns.R")
fnames <- list.files(".","test-fibd-[0-9]*.gz")
.chrlens <- c(2,1)
.chrstarts <- c(0,2,3)
ibd <- lapply( fnames, read.table, header=TRUE )
for (k in seq_along(ibd)) {
ibd[[k]]$chrom <- findInterval( ibd[[k]]$start, .chrstarts, rightmost.closed=TRUE )
tmp <- length(.chrstarts) - findInterval( -ibd[[k]]$end, rev(-.chrstarts), rightmost.closed=TRUE )
sum(coal.chrlens[0:k]) for k in range(1, len(coal.chrlens))
]) # cumulative sum: position if lined up end-to-end
coal.chrlen = sum(coal.chrlens) # the last one (total length)
start = time.time()
pop = coal.initpop(sampsizes)
ibdict = {}
poplist = []
for t in xrange(20):
print " ----", t
coal.parents(pop, t=t, ibdict=ibdict, migprobs=migprobs, ancne=ancnefn(t))
coal.sanity(pop, sampsizes=sampsizes, ancne=ancnefn(t), print_details=True)
coal.writeibd(pop,
minlen=0.0,
gaplen=0.0,
filename="test-fibd-" + ("%(t)02d" % {
't': t
}) + ".gz")
poplist.append(copy.deepcopy(pop))
print time.time() - start
# run this to look at the above.
rscript < - '''
source("~/projects/genome/ibd-blocks-fns.R")
fnames <- list.files(".","test-fibd-[0-9]*.gz")
.chrlens <- c(2,1)
.chrstarts <- c(0,2,3)
ibd <- lapply( fnames, read.table, header=TRUE )
for (k in seq_along(ibd)) {