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haploscanner.py
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haploscanner.py
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import numpy as np
import sys
import re
import itertools
import subprocess as sub
import matplotlib.pyplot as plt
allele_pattern = re.compile("L(\d+)\.A(\d+)")
def parse_haplos(filename):
possible_haplos_array = []
with open(filename,'r') as fp:
lines = fp.readlines()
for idx,line in enumerate(lines):
possible_haplos_array.append([])
haps_descr = line.strip().split(' ')
for item in haps_descr:
# assuming the input file is formatted ideally ...
res = allele_pattern.match(item)
locus,allele = map(int,res.groups())
# populate haplotypes array ...
possible_haplos_array[idx].append(allele)
return possible_haplos_array
def parse_pop(filename):
with open(filename,'r') as fp:
# first line ...
line = fp.readline()
loci, = re.match("LOCI (\d+)",line.strip()).groups()
loci = int(loci)
# loci lines ...
alleles = [0,]*loci
for locus in range(loci):
idx,num_al = re.match("L(\d+) (\d+)",fp.readline().strip()).groups()
alleles[int(idx)-1] = int(num_al)
# total number of alleles ...
tot_al = sum(alleles)
# allele frequencies ...
freq = []
for locus in range(loci):
freq.append([])
for allele in range(alleles[locus]):
freq[locus].append(0.0)
########################################
for allele in range(tot_al):
lidx,aidx,fin = re.match("L(\d+) A(\d+) (\d+\.\d+|AUTO)",fp.readline().strip()).groups()
lidx = int(lidx)-1
aidx = int(aidx)-1
freq[lidx][aidx] = float(fin) if fin != "AUTO" else round(1.0 - sum(freq[lidx]),3)
return freq
def check_pop(freq_arr):
for idx,locus_freqs in enumerate(freq_arr):
freq_norm = round(sum(locus_freqs),3)
if freq_norm != 1.0:
print "Troubles parsing population info: normalization failed @ locus %d"%(idx+1)
return False
return True
def generate_compliant_popinfo(freq_arr):
out_loci_string = ""
out_freq_string = ""
nloci = len(freq_arr)
out_loci_string += "LOCI %d\n"%nloci
for lid in range(nloci):
alleles_at_locus = len(freq_arr[lid])
out_loci_string += "L%d %d\n"%(lid+1,alleles_at_locus)
for aid in range(alleles_at_locus-1):
out_freq_string += "L%d A%d %.3f\n"%( lid+1, aid+1, round(freq_arr[lid][aid],3) )
out_freq_string += "L%d A%d AUTO\n"%( lid+1, alleles_at_locus )
return out_loci_string + out_freq_string
def parse_haplolimit_outfile(fname):
#
index_pattern = re.compile("H(\d+)")
haplo_pattern = re.compile("L(\d+)A(\d+)")
# skip 7 lines and then go on
with open(fname,'r') as fp:
skip_line_number = 7
for skip_line in range(skip_line_number):
fp.readline()
# start parsing the thing ...
haplo_out = []
for line in fp.readlines():
index,fmin,fmax,haplo = line.strip().split()
fmin,fmax = float(fmin),float(fmax)
index, = index_pattern.match(index).groups()
index = int(index)
haplo = haplo.strip(':').split(':')
haplo_parsed = [haplo_pattern.match(_hap).groups() for _hap in haplo]
recovered_haplo = [int(allele) if ((idx+1)==int(lid)) else None for idx,(lid,allele) in enumerate(haplo_parsed) ]
if None not in recovered_haplo:
entry = (index,fmin,fmax,recovered_haplo)
else:
print "could not parse the haplo output file ... exit!"
sys.exit(1)
# appending parsed info ...
haplo_out.append(entry)
return haplo_out
def parse_haplolimit_output(outlines):
#
index_pattern = re.compile("H(\d+)")
haplo_pattern = re.compile("L(\d+)A(\d+)")
# skip 7 lines and then go on
skip_line_number = 7
# start parsing the thing ...
haplo_out = []
for line in outlines[skip_line_number:]:
index,fmin,fmax,haplo = line.strip().split()
fmin,fmax = float(fmin),float(fmax)
index, = index_pattern.match(index).groups()
index = int(index)
haplo = haplo.strip(':').split(':')
haplo_parsed = [haplo_pattern.match(_hap).groups() for _hap in haplo]
recovered_haplo = [int(allele) if ((idx+1)==int(lid)) else None for idx,(lid,allele) in enumerate(haplo_parsed) ]
if None not in recovered_haplo:
entry = (index,fmin,fmax,recovered_haplo)
else:
print "could not parse the haplo output file ... exit!"
sys.exit(1)
# appending parsed info ...
haplo_out.append(entry)
return haplo_out
# get intervals for parsed haplo out ...
# (5, 0.0, 0.014, [1, 1, 1, 5]),
def get_intervals(haplo_out):
to_ret = []
for entry in haplo_out:
_,fmin,fmax,_ = entry
to_ret.append(fmax-fmin)
return to_ret
def get_interval_ratios(int_numer,int_denom):
to_ret = []
# index = 0
for intn,intd in zip(int_numer,int_denom):
ratio = intn/intd if intd else 1.0
to_ret.append(ratio)
# index += 1
return to_ret
def prod(array):
prod_accum = 1.0
for item in array:
prod_accum *= item
return prod_accum
phaps = parse_haplos("./input/possibleHaps.txt")
# freqs = parse_pop("good_test.dat")
freqs = parse_pop("./input/lociInfo.txt")
check_pop(freqs)
pop_info_out = generate_compliant_popinfo(freqs)
phaps = np.asarray(phaps)
# print phaps
haps,loci = phaps.shape
#reconstruct alleles:
alleles = []
for locus in range(loci):
alleles.append( phaps[:,locus].max() )
children_at_locus = []
for locus in range(loci-1):
children_at_locus.append([])
for allele in range(alleles[locus]):
children_at_locus[locus].append([])
#################################
# groups_at_locus = [[]]*loci
# fill out those children of at different loci ...
for locus in range(loci-1):
for hap in range(haps):
children_at_locus[locus][ phaps[hap,locus]-1 ].append( phaps[hap,locus+1] )
# print children_at_locus[locus][ phaps[hap,locus]-1 ]
for hap in range(haps):
children_at_locus[locus][ phaps[hap,locus]-1 ] = tuple(sorted(set(children_at_locus[locus][ phaps[hap,locus]-1 ])))
children_at_locus[locus] = list(enumerate(children_at_locus[locus]))
# first key in a tuple ...
key = lambda tup: tup[1]
link = 1
links_freqs_str = ""
linked_la_str = ""
for locus in range(loci-1):
for shared_children,groups in itertools.groupby(sorted(children_at_locus[locus],key=key),key=key):
# print [parent[0]+1 for parent in groups],shared_children
# each of this things is a link!!!
parents = [parent[0]+1 for parent in groups] # @ locus
children = shared_children # @ locus+1
# let's calculate some frequencies ...
freq1 = round(sum([freqs[locus][ppp-1] for ppp in parents]),3)
freq2 = round(sum([freqs[locus+1][ccc-1] for ccc in children]),3)
# if (freq1 == freq2):
actual_freq = min(freq1,freq2)
links_freqs_str += "LINK%d %d %.3f\n" % (link,len(parents)+len(children),actual_freq)
# else:
# print "ACHTUNG ACHTUNG ACHTUNG!!!!!!!!! %.2f != %.2f"%(freq1,freq2)
for ppp in parents:
linked_la_str += "LINK%d L%d A%d\n"%(link,locus+1,ppp)
for ccc in children:
linked_la_str += "LINK%d L%d A%d\n"%(link,locus+2,ccc)
link += 1
# let's get the intervals first - without ever restricting any haplotypes ...
linkages = link-1
link_info_out = "LINKAGE %d\n"%linkages + links_freqs_str + linked_la_str
filename = "input_test_ASIS.dat"
with open(filename,'w') as fp:
fp.write( pop_info_out + link_info_out )
#
# after the file is written, we can go ahead and launch haplotest program!!!
output_lines = sub.check_output("./bin/testhaplo %s"%filename,shell=True).strip().split('\n')
parsed_out_initial = parse_haplolimit_output(output_lines)
intervals_initial = get_intervals(parsed_out_initial)
# let's get bare haplotypes ...
haplotypes_only_initial = [_[3] for _ in parsed_out_initial]
# transform phaps back to python lists (silly but ...)
phaps_list = [list(_) for _ in phaps]
def index_possible_haps(pos_haps,haps_initial):
indices = []
for the_hap in pos_haps:
the_hap_index = haplotypes_only_initial.index(the_hap)
indices.append(the_hap_index)
return indices
# now get the indices of those haplotypes ...
phaps_indices = enumerate(index_possible_haps(phaps_list,haplotypes_only_initial))
# once ready, sort em by the fmax!
indices_sorted_by_fmax = list(sorted(
[ (_pos,_glob, parsed_out_initial[_glob][2]) for _pos,_glob in phaps_indices],
key=lambda x: x[2],
reverse=True ))
# extracting re-sorted data here ...
phaps_list = [ phaps_list[idx] for idx,_,_ in indices_sorted_by_fmax ]
phaps_indices = [ idx for _,idx,_ in indices_sorted_by_fmax ]
# let's draw stuff ...
fig,ax = plt.subplots(figsize=(10,4))
fmin_arr_init = []
fmax_arr_init = []
for phap_idx in range(21):
# get its global index ...
global_haplo_index = phaps_indices[phap_idx]
# get interval initial of this guy ...
_,fmin,fmax,_ = parsed_out_initial[global_haplo_index]
# ...
fmin_arr_init.append(fmin)
fmax_arr_init.append(fmax)
#
def plot_haplo_range(ax,fmin_arr,fmax_arr,fillcolor='red'):
# def nonlinear(x):
# return np.sqrt(x)*np.sqrt(1.0-x)
# transform = np.vectorize(lambda x: np.power(x,0.75)*np.power((1.0-x),0.75))
transform = np.vectorize(lambda x: x)
#
xxx = range(1,22)
#
ax.plot(xxx,transform(fmin_arr),color='blue',linestyle='-',marker='_',mec='black',mew=2.0,ms=10)
ax.plot(xxx,transform(fmax_arr),color='red',linestyle='-',marker='_',mec='black',mew=2.0,ms=10)
#
ax.fill_between(xxx, transform(fmax_arr), transform(fmin_arr), facecolor=fillcolor, alpha=0.5)
#
ax.set_xlim(0,22)
# ax.set_ylim(0,1.0)
# plt.show()
# # uncomment for massive plotting ...
# # plot_haplo_range(ax,fmin_arr_init,fmax_arr_init,fillcolor='gray')
# # scan haplotype number XXX :
# scan_hap_idx = 13
# #
# #
# print "haplotype N %d looking like "%(scan_hap_idx+1)
# print phaps_list[scan_hap_idx]
# # get its global index ...
# global_haplo_index = phaps_indices[scan_hap_idx]
# # get interval initial of this guy ...
# num = 12
# _,fmin,fmax,_ = parsed_out_initial[global_haplo_index]
# #
# print "freq_range: ",fmin,fmax
# #
# scan_hap_freq = [ round(_,3) for _ in np.linspace(fmin,fmax,num) ]
# #
# #
# # scan_hap_freq = [0.272,0.28,0.29,0.3,0.31,0.32,0.33,0.34,0.35,0.36,0.37,0.38,0.381]
# # # get its global index ...
# # global_haplo_index = phaps_indices[scan_hap_idx]
# #
# #
# for hap_fixed_freq in scan_hap_freq:
# # add 1 more link to fixate that haplotype ...
# linkages = link
# links_freqs_str_ADD = "LINK%d %d %.3f\n" % ( linkages, loci, hap_fixed_freq )
# linked_la_str_ADD = ""
# for lid in range(loci):
# linked_la_str_ADD += "LINK%d L%d A%d\n"%( linkages, lid+1, phaps_list[scan_hap_idx][lid])
# link_info_out = "LINKAGE %d\n"%linkages + (links_freqs_str+links_freqs_str_ADD) + (linked_la_str+linked_la_str_ADD)
# # pop_info_out
# # output file ...
# filename = "input_test_%d_%.3f.dat"%(scan_hap_idx+1,hap_fixed_freq)
# with open(filename,'w') as fp:
# fp.write( pop_info_out + link_info_out )
# #
# # after the file is wsritten, we can go ahead and launch haplotest program!!!
# output_lines = sub.check_output("./bin/testhaplo %s"%filename,shell=True).strip().split('\n')
# parsed_out = parse_haplolimit_output(output_lines)
# intervals = get_intervals(parsed_out)
# ratios = get_interval_ratios(intervals,intervals_initial)
# # calculate ratios excluding that haplotype (it if fixed and always result in a zero result!) ...
# ratios_product = prod(ratios[:global_haplo_index]+ratios[(global_haplo_index+1):])
# # print hap_fixed_freq,ratios_product
# #
# #
# fmin_arr_constr = []
# fmax_arr_constr = []
# for phap_idx in range(21):
# # get its global index ...
# global_haplo_index = phaps_indices[phap_idx]
# # get interval initial of this guy ...
# _,fmin,fmax,_ = parsed_out[global_haplo_index]
# # ...
# fmin_arr_constr.append(fmin)
# fmax_arr_constr.append(fmax)
# #
# #
# # uncomment if plotting is needed ...
# ax.cla()
# plot_haplo_range(ax,fmin_arr_init,fmax_arr_init,fillcolor='gray')
# plot_haplo_range(ax,fmin_arr_constr,fmax_arr_constr,fillcolor='red')
# plt.savefig("scan_h%d_f%.3f.png"%((scan_hap_idx+1),hap_fixed_freq),dpi=150)
# plt.show()
# plt.savefig("scan_h%d_f%.3f.pdf"%((scan_hap_idx+1),scan_hap_freq[0]))
# scan haplotype number XXX :
for scan_hap_idx in range(21):
print "haplotype N %d looking like "%(scan_hap_idx+1)
print phaps_list[scan_hap_idx]
print
# scan_hap_freq = [0.272,0.28,0.29,0.3,0.31,0.32,0.33,0.34,0.35,0.36,0.37,0.38,0.381]
# get its global index ...
global_haplo_index = phaps_indices[scan_hap_idx]
# get interval initial of this guy ...
num = 12
_,fmin,fmax,_ = parsed_out_initial[global_haplo_index]
scan_hap_freq = [ round(_,3) for _ in np.linspace(fmin,fmax,num) ]
#
#
distro = []
#
#
for hap_fixed_freq in scan_hap_freq:
# add 1 more link to fixate that haplotype ...
linkages = link
links_freqs_str_ADD = "LINK%d %d %.3f\n" % ( linkages, loci, hap_fixed_freq )
linked_la_str_ADD = ""
for lid in range(loci):
linked_la_str_ADD += "LINK%d L%d A%d\n"%( linkages, lid+1, phaps_list[scan_hap_idx][lid])
link_info_out = "LINKAGE %d\n"%linkages + (links_freqs_str+links_freqs_str_ADD) + (linked_la_str+linked_la_str_ADD)
# pop_info_out
# output file ...
filename = "input_test_%d_%.3f.dat"%(scan_hap_idx+1,hap_fixed_freq)
with open(filename,'w') as fp:
fp.write( pop_info_out + link_info_out )
#
# after the file is written, we can go ahead and launch haplotest program!!!
output_lines = sub.check_output("./bin/testhaplo %s"%filename,shell=True).strip().split('\n')
parsed_out = parse_haplolimit_output(output_lines)
intervals = get_intervals(parsed_out)
ratios = get_interval_ratios(intervals,intervals_initial)
# calculate ratios excluding that haplotype (it if fixed and always result in a zero result!) ...
# #
# # using all ~200-300 "nonzero" haplotypes (including "prohibitet ones")
# ratios_product = prod(ratios[:global_haplo_index]+ratios[(global_haplo_index+1):])
# #
# # alternative - using just 21 possible haps excluding the one that is fixed ...
prod_hhh = 1.0
for hidx in phaps_indices:
if hidx != global_haplo_index:
prod_hhh *= ratios[hidx]
#
ratios_product = prod_hhh
#
#
# print hap_fixed_freq,ratios_product
#
#
distro.append((hap_fixed_freq,ratios_product))
#
# now plot violin-like plot ...
xarr = [x for x,_ in distro]
max_ratio = max([y for _,y in distro])
if max_ratio == 0.0:
yup = [ (21-scan_hap_idx)+0.3 for yy in [y for _,y in distro]]
ydown = [ (21-scan_hap_idx)-0.3 for yy in [y for _,y in distro]]
else:
yup = [ (21-scan_hap_idx)+0.4*yy/max_ratio for yy in [y for _,y in distro]]
ydown = [ (21-scan_hap_idx)-0.4*yy/max_ratio for yy in [y for _,y in distro]]
# ax.plot(xarr,y)
ax.fill_between(xarr, yup, ydown, facecolor="blue", alpha=0.75)
ax.set_ylim(0,22)
plt.show()
# # print "LINKAGE %d"%(link-1)
# # print links_freqs_str + linked_la_str
# # print linked_la_str
# # link_info_out = "LINKAGE %d\n"%(link-1) + links_freqs_str + linked_la_str