from optparse import OptionParser
parser = OptionParser(description=description)
parser.add_option("-b","--ibdfile",dest="ibdfile",help="name of file to read ibd from (or '-' for stdin)",default="-")
parser.add_option("-o","--outfile",dest="outfile",help="name of file to output merged ibd from (or '-' for stdout)",default="-")
parser.add_option("-g","--gaplen",dest="gaplen",help="merge blocks separated by a block no longer than this long (in MORGANS)", default=0.0)
parser.add_option("-c","--chromfile",dest="chromfile",help="file to parse chromosome lengths from (e.g. logfile for that run)", default=None)
(options,args) = parser.parse_args()
# size of maximum gap to merge
gapthresh = float(options.gaplen)
# find chromosome lengths
try:
if options.chromfile is None:
chromfile = coal.fileopt( re.sub("\.fibd\.gz$",".log",options.ibdfile), "r")
else:
chromfile = coal.fileopt(options.chromfile,"r")
except:
raise ValueError("Invalid chromfile specification.")
for line in chromfile:
if line.startswith("chromosome ending positions:"):
chrends = eval( line[28:].strip() )
break
try:
chrstartends = zip( [0.0]+chrends[:-1], chrends )
except NameError:
raise ValueError("Can't find 'chromosome ending positions:' in chromfile.")
dest="minlen",
help=
"minimum length of IBD block to record IN MORGANS (default value 0.005M = 0.5cM)",
default=None)
parser.add_option(
"-g",
"--gaplen",
dest="gaplen",
help=
"gap length, IN MORGANS: blocks closer together than this will be recorded even if shorter than minlen (default value 0.5M = 50cM)",
default=None)
(options, args) = parser.parse_args()
# read in parameters etc
if options.infile is not None:
infile = coal.fileopt(options.infile, "r")
inparams = infile.read()
exec(inparams)
# command line options supercede statements in infile
ibdfile = coal.fileopt(options.ibdfile, "w")
# coalfile = coal.fileopt(options.coalfile, "w")
logfile = coal.fileopt(options.logfile, "w")
ngens = int(options.ngens)
if options.nesize is not None:
ancnefn = lambda t: {}.fromkeys(pop.keys(), int(options.nesize))
else:
try:
if type(ancnefn) == type({}):
ancnefn = lambda t: ancnefn
import coalpedigree as cp
parser = OptionParser(description=description)
parser.add_option("-b","--ibdfile",dest="ibdfile",help="name of file to read ibd from (or '-' for stdout)",default="-")
parser.add_option("-o","--outfile",dest="outfile",help="name of output ibd file (or '-' for stdin)")
parser.add_option("-l","--logfile",dest="logfile",help="name of log file (or '-' for stdout)",default="-")
parser.add_option("-n","--minminlen",dest="minminlen",help="totally ignore any blocks shorter than this length", default=0.0)
parser.add_option("-g","--gaplen",dest="gaplen",help="merge blocks separated by a block no longer than this long", default=0.0)
parser.add_option("-m","--minlen",dest="minlen",help="only keep any blocks (including merged ones) at least this long", default=0.0)
(options,args) = parser.parse_args()
minminlen = float(options.minminlen)
gaplen = float(options.gaplen)
minlen = float(options.minlen)
ibdfile = cp.fileopt(options.ibdfile, "r")
outfile = cp.fileopt(options.outfile, "w")
logfile = cp.fileopt(options.logfile, "w")
results = {}
# results is a dict indexed by pairs of ids
# with entries a list of [start,end,nsegs]
logfile.write("winnow.py: "+options.ibdfile+"\n")
logfile.write("writing to " + options.outfile + "\n")
logfile.write("totally ignoring blocks below: " + str(minminlen) + "\n")
logfile.write("merging closer than gaplen: " + str(gaplen) + "\n")
logfile.write("outputting merged blocks longer than: " + str(minlen) + "\n")
nin = 0
nskip = 0
# parser.add_option("-c","--coalfile",dest="coalfile",help="name of file to write final coalescent info to (or '-' for stdout)",default="-")
parser.add_option("-b","--ibdfile",dest="ibdfile",help="name of file to write final ibd blocks to (or '-' for stdout)",default="-")
parser.add_option("-l","--logfile",dest="logfile",help="name of log file (or '-' for stdout)",default="-")
parser.add_option("-i","--infile",dest="infile",help="name of input file to get parameters from (or '-' for stdin)")
parser.add_option("-t","--ngens",dest="ngens",help="total number of generations to simulate",default="10")
parser.add_option("-n","--nesize",dest="nesize",help="effective population size")
parser.add_option("-m","--migprob",dest="migprob",help="migration probability")
parser.add_option("-s","--samplesizes",dest="sampsizes",help="sample sizes")
parser.add_option("-e","--minlen",dest="minlen",help="minimum length of IBD block to record IN MORGANS (default value 0.005M = 0.5cM)",default=None)
parser.add_option("-g","--gaplen",dest="gaplen",help="gap length, IN MORGANS: blocks closer together than this will be recorded even if shorter than minlen (default value 0.5M = 50cM)",default=None)
(options,args) = parser.parse_args()
# read in parameters etc
if options.infile is not None:
infile = coal.fileopt(options.infile,"r")
inparams = infile.read()
exec(inparams)
# command line options supercede statements in infile
ibdfile = coal.fileopt(options.ibdfile, "w")
# coalfile = coal.fileopt(options.coalfile, "w")
logfile = coal.fileopt(options.logfile, "w")
ngens = int(options.ngens)
if options.nesize is not None:
ancnefn = lambda t: {}.fromkeys(pop.keys(),int(options.nesize))
else:
try:
if type(ancnefn) == type({}):
ancnefn = lambda t: ancnefn
dest="gaplen",
help="merge blocks separated by a block no longer than this long",
default=0.0)
parser.add_option(
"-m",
"--minlen",
dest="minlen",
help="only keep any blocks (including merged ones) at least this long",
default=0.0)
(options, args) = parser.parse_args()
minminlen = float(options.minminlen)
gaplen = float(options.gaplen)
minlen = float(options.minlen)
ibdfile = cp.fileopt(options.ibdfile, "r")
outfile = cp.fileopt(options.outfile, "w")
logfile = cp.fileopt(options.logfile, "w")
results = {}
# results is a dict indexed by pairs of ids
# with entries a list of [start,end,nsegs]
logfile.write("winnow.py: " + options.ibdfile + "\n")
logfile.write("writing to " + options.outfile + "\n")
logfile.write("totally ignoring blocks below: " + str(minminlen) + "\n")
logfile.write("merging closer than gaplen: " + str(gaplen) + "\n")
logfile.write("outputting merged blocks longer than: " + str(minlen) + "\n")
nin = 0
nskip = 0
default=0.0)
parser.add_option(
"-c",
"--chromfile",
dest="chromfile",
help="file to parse chromosome lengths from (e.g. logfile for that run)",
default=None)
(options, args) = parser.parse_args()
# size of maximum gap to merge
gapthresh = float(options.gaplen)
# find chromosome lengths
try:
if options.chromfile is None:
chromfile = coal.fileopt(
re.sub("\.fibd\.gz$", ".log", options.ibdfile), "r")
else:
chromfile = coal.fileopt(options.chromfile, "r")
except:
raise ValueError("Invalid chromfile specification.")
for line in chromfile:
if line.startswith("chromosome ending positions:"):
chrends = eval(line[28:].strip())
break
try:
chrstartends = zip([0.0] + chrends[:-1], chrends)
except NameError:
raise ValueError("Can't find 'chromosome ending positions:' in chromfile.")
results = {}