def main():
# Parse the command line
parser = OptionParser(usage = "usage: %prog [options] maf_file snp_file neutral_file window_size step_size")
parser.add_option("-o", "--outfile", help = "Specify file for output")
parser.add_option("-s", "--species", type = "string", default = "panTro2")
parser.add_option("-b", "--build", type = "string", default = "hg18")
(options, args) = parser.parse_args()
if len(args) != 5:
parser.error("Incorrect number of arguments")
else:
maf_filename = args[0]
snp_filename = args[1]
neutral_filename = args[2]
window_size = int(args[3])
step_size = int(args[4])
if options.outfile != None:
out_file = open(options.outfile, 'w')
#Generate snp and neutral bitsets
AR_snp_bitsets = binned_bitsets_from_file(open(snp_filename))
neutral_bitsets = binned_bitsets_from_file(open(neutral_filename))
# Generate divergence bitset from maf file
AR_div_bitsets = dict()
chr_lens = dict()
reader = bx.align.maf.Reader( open (maf_filename) )
for block in reader:
comp1 = block.get_component_by_src_start( options.build )
comp2 = block.get_component_by_src_start( options.species )
if comp1 is None or comp2 is None:
continue
# Chromosome, start, and stop of reference species alignment
chr = comp1.src.split( '.' )[1]
start = comp1.start
end = comp1.end
# Get or create bitset for this chromosome
if chr in AR_div_bitsets:
bitset = AR_div_bitsets[chr]
else:
bitset = AR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
chr_lens[chr] = comp1.get_src_size()
# Iterate over text and set diverged bit
pos = start
for ch1, ch2 in izip( comp1.text.upper(), comp2.text.upper() ):
if ch1 == '-': continue
if ch2 == '-':
pos += 1
continue
if ch1 != ch2 and not AR_snp_bitsets[chr][pos]:
bitset.set( pos )
pos += 1
# Debugging Code
# for chr in AR_div_bitsets:
# for pos in range(0, AR_div_bitsets[chr].size):
# if AR_div_bitsets[pos]:
# print >> sys.stderr, chr, pos, pos+1
# Copy div and snp bitsets
nonAR_snp_bitsets = dict()
for chr in AR_snp_bitsets:
nonAR_snp_bitsets[chr] = bx.bitset.BinnedBitSet()
nonAR_snp_bitsets[chr].ior(AR_snp_bitsets[chr])
nonAR_div_bitsets = dict()
for chr in AR_div_bitsets:
nonAR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
nonAR_div_bitsets[chr].ior(AR_div_bitsets[chr])
# Generates AR snps by intersecting with neutral intervals
for chr in AR_snp_bitsets:
AR_snp_bitsets[chr].iand(neutral_bitsets[chr])
# Generates AR divs by intersecting with neutral intervals
for chr in AR_div_bitsets:
AR_div_bitsets[chr].iand(neutral_bitsets[chr])
# Inverts the neutral intervals so now represents nonAR
for chr in neutral_bitsets:
neutral_bitsets[chr].invert()
# Generates nonAR snps by intersecting with masked neutral intervals
for chr in nonAR_snp_bitsets:
nonAR_snp_bitsets[chr].iand(neutral_bitsets[chr])
# Generates nonAR divs by intersecting with masked neutral intervals
for chr in nonAR_div_bitsets:
nonAR_div_bitsets[chr].iand(neutral_bitsets[chr])
for chr in AR_div_bitsets:
for window in range(0, chr_lens[chr] - window_size, step_size):
# neutral_size = neutral_bitsets[chr].count_range(window, window_size)
# if neutral_size < 9200: continue
AR_snp = AR_snp_bitsets[chr].count_range(window, window_size)
AR_div = AR_div_bitsets[chr].count_range(window, window_size)
nonAR_snp = nonAR_snp_bitsets[chr].count_range(window, window_size)
nonAR_div = nonAR_div_bitsets[chr].count_range(window, window_size)
if nonAR_snp >= 6 and nonAR_div >= 6 and AR_snp >= 6 and AR_div >= 6:
MK_pval = MK_chi_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)
else:
MK_pval = MK_fisher_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)
if options.outfile != None:
out_file.write("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f\n" % (chr, window, window+window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval))
else:
print "%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f" % (chr, window, window+window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval)
if options.outfile != None:
out_file.close()
def main():
# Parse the command line
parser = OptionParser(usage = "usage: %prog [options] maf_file snp_file neutral_file window_size step_size")
parser.add_option("-o", "--outfile", help = "Specify file for output")
parser.add_option("-s", "--species", type = "string", default = "panTro2")
parser.add_option("-b", "--build", type = "string", default = "hg18")
(options, args) = parser.parse_args()
if len(args) != 5:
parser.error("Incorrect number of arguments")
else:
maf_filename = args[0]
snp_filename = args[1]
neutral_filename = args[2]
window_size = int(args[3])
step_size = int(args[4])
if options.outfile != None:
out_file = open(options.outfile, 'w')
#Generate snp and neutral bitsets
AR_snp_bitsets = binned_bitsets_from_file(open(snp_filename))
neutral_bitsets = binned_bitsets_from_file(open(neutral_filename))
# Generate divergence bitset from maf file
AR_div_bitsets = dict()
chr_lens = dict()
reader = bx.align.maf.Reader( open (maf_filename) )
for block in reader:
comp1 = block.get_component_by_src_start( options.build )
comp2 = block.get_component_by_src_start( options.species )
if comp1 is None or comp2 is None:
continue
# Chromosome, start, and stop of reference species alignment
chr = comp1.src.split( '.' )[1]
start = comp1.start
end = comp1.end
# Get or create bitset for this chromosome
if chr in AR_div_bitsets:
bitset = AR_div_bitsets[chr]
else:
bitset = AR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
chr_lens[chr] = comp1.get_src_size()
# Iterate over text and set diverged bit
pos = start
for ch1, ch2 in izip( comp1.text.upper(), comp2.text.upper() ):
if ch1 == '-': continue
if ch2 == '-':
pos += 1
continue
if ch1 != ch2 and not AR_snp_bitsets[chr][pos]:
bitset.set( pos )
pos += 1
# Debugging Code
# for chr in AR_div_bitsets:
# for pos in range(0, AR_div_bitsets[chr].size):
# if AR_div_bitsets[pos]:
# print >> sys.stderr, chr, pos, pos+1
# Copy div and snp bitsets
nonAR_snp_bitsets = dict()
for chr in AR_snp_bitsets:
nonAR_snp_bitsets[chr] = bx.bitset.BinnedBitSet()
nonAR_snp_bitsets[chr].ior(AR_snp_bitsets[chr])
nonAR_div_bitsets = dict()
for chr in AR_div_bitsets:
nonAR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
nonAR_div_bitsets[chr].ior(AR_div_bitsets[chr])
# Generates AR snps by intersecting with neutral intervals
for chr in AR_snp_bitsets:
AR_snp_bitsets[chr].iand(neutral_bitsets[chr])
# Generates AR divs by intersecting with neutral intervals
for chr in AR_div_bitsets:
AR_div_bitsets[chr].iand(neutral_bitsets[chr])
# Inverts the neutral intervals so now represents nonAR
for chr in neutral_bitsets:
neutral_bitsets[chr].invert()
# Generates nonAR snps by intersecting with masked neutral intervals
for chr in nonAR_snp_bitsets:
nonAR_snp_bitsets[chr].iand(neutral_bitsets[chr])
# Generates nonAR divs by intersecting with masked neutral intervals
for chr in nonAR_div_bitsets:
nonAR_div_bitsets[chr].iand(neutral_bitsets[chr])
for chr in AR_div_bitsets:
for window in range(0, chr_lens[chr] - window_size, step_size):
# neutral_size = neutral_bitsets[chr].count_range(window, window_size)
# if neutral_size < 9200: continue
AR_snp = AR_snp_bitsets[chr].count_range(window, window_size)
AR_div = AR_div_bitsets[chr].count_range(window, window_size)
nonAR_snp = nonAR_snp_bitsets[chr].count_range(window, window_size)
nonAR_div = nonAR_div_bitsets[chr].count_range(window, window_size)
if nonAR_snp >= 6 and nonAR_div >= 6 and AR_snp >= 6 and AR_div >= 6:
MK_pval = MK_chi_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)
else:
MK_pval = MK_fisher_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)
if options.outfile != None:
out_file.write("%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f\n" % (chr, window, window+window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval))
else:
print "%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f" % (chr, window, window+window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval)
if options.outfile != None:
out_file.close()