split_line = line.strip().split()
if found_name_line:
if len(split_line) != num_ind + 1: raise Exception
locus = split_line[0]
genotypes = split_line[1:num_ind + 1]
genotypes_of_locus[locus] = genotypes
else:
if len(line.strip().split()) == num_ind + 1:
individuals = line.strip().split()[1:num_ind + 1]
found_name_line = True
return(genotypes_of_locus)
ini_map, num_loci_on_lg = parse_map_file("Y:\WORK\WAPLES\Stacks_mapping\Chum_data\mst\chum_08_iter0_mstmap.map", 'mst')
genotypes_of_locus = parse_mst_map_infile("Y:\WORK\WAPLES\Stacks_mapping\Chum_data\mst\chum_08_iter0_mstmap.txt", 140)
int_arr = convert_genotypes_to_int_array(genotypes_of_locus, ini_map)
to_be_removed = 0
start_index = 0
end_index = 0
# What do we do if missing genotypes sit next to potential double crossovers?
with open ('Y:\WORK\WAPLES\Stacks_mapping\pest_out.tsv', 'w') as OUTFILE:
start_index = 0
end_index = 0
OUTFILE.write(("{}\t"*13+"\n").format("LG", "length", "end_index", "start_index", "current_LG.shape", "ind_count", "ind_genotypes", "nonzero_genotypes", "count_non_zero", "crossovers", "dbl_crossovers", "flag", "corrected_crossovers"))
for LG, length in num_loci_on_lg.items():
end_index += length
chum_fams.write_Rqtl('CMUW10X_0008', 'Z:/HOME/Waples/Stacks_mapping/Chum_data/psv/chum_08_switched_3_Rqtl.txt', switched_mappable_3[0], switched_mappable_3[1])
chum_fams.write_mstmap('CMUW10X_0008', 'Z:/HOME/Waples/Stacks_mapping/Chum_data/psv/chum_08_switched_3_mstmap.txt', switched_mappable_3[0], switched_mappable_3[1])
# Go to Rqtl, rebuild linkage groups
#Parameters
genotypes_of_locus = switchAlleles.combine_mappable_loci(mappable)
ini_map, loci_on_lg = switchAlleles.parse_map_file(linkage_map_file)
int_arr = switchAlleles.convert_genotypes_to_int_array(genotypes_of_locus, ini_map)
num_loci = int_arr.shape[0]
num_pairs = int((num_loci * (num_loci-1))/2)
pairs = itertools.combinations(int_arr, 2)
#import timeit
#timeit.timeit('next(switchAlleles.getR(pairs))', setup = "import switch_allele_functions as switchAlleles; from __main__ import int_arr; from __main__ import pairs", number = 100000)
R = numpy.fromiter(switchAlleles.getR(pairs), dtype = numpy.float64, count = num_pairs)
pairs = itertools.combinations(int_arr, 2)
NR = numpy.fromiter(switchAlleles.getNR(pairs), dtype = numpy.float64, count = num_pairs)
