def write_map_maker(vcf_fhand, parents_a, parents_b, genos_fhand,
pop_type=DEF_MAPMAKER_POP, phys_map_fhand=None,
coder_threshold=DEF_AB_CODER_THRESHOLD,
smooth_threshold=None, recomb_threshold=None):
sep = '\t'
coder = ABCoder(vcf_fhand, parents_a, parents_b,
parent_index_threshold=coder_threshold,
smooth_threhsold=smooth_threshold,
recomb_threshold=recomb_threshold)
if pop_type not in ['f2 intercross', 'f2 backcross', 'f3 self',
'ri self', 'ri sib']:
msg = 'Defined pop type \'{0}\' does not match an allowed pop_type '
msg += '(f2 intercross, f2 backcross, f3 self, ri self or ri sib)'
raise ValueError(msg.format(pop_type))
samples = coder.offspring
snp_ids = []
snp_genos = []
coding = 'ascii'
if phys_map_fhand is not None:
phys_map_fhand.write('marker\tposition\tChromosome\n')
for snp, genos in coder.recode_genotypes(samples):
snp_id = get_or_create_id(snp).encode(coding)
snp_ids.append(snp_id)
geno_array = array('c')
for geno in genos.values():
geno_array.append(_code_to_one_letter(geno))
snp_genos.append(geno_array)
if phys_map_fhand is not None:
phys_map_fhand.write(snp_id)
phys_map_fhand.write(sep)
phys_map_fhand.write(str(snp.POS))
phys_map_fhand.write(sep)
phys_map_fhand.write(snp.CHROM.encode(coding))
phys_map_fhand.write('\n')
genos_fhand.write('data type ' + pop_type + '\n')
genos_fhand.write('{0} {1} 1\n'.format(len(samples), len(snp_genos)))
for snp_id, snp_geno in zip(snp_ids, snp_genos):
genos_fhand.write('*{0}'.format(snp_id))
genos_fhand.write(sep)
genos_fhand.write(sep.join(snp_geno))
genos_fhand.write('\n')
genos_fhand.write('\n')
genos_fhand.write('*sample_names' + sep)
encoded_samples = [sample.encode(coding) for sample in samples]
genos_fhand.write(sep.join(encoded_samples))
genos_fhand.write('\n')
return coder
def write_parent_checker(vcf_fhand,
parents_a,
parents_b,
genos_fhand,
phys_map_fhand=None,
coder_threshold=DEF_AB_CODER_THRESHOLD,
smooth_threshold=None,
recomb_threshold=None):
sep = '\t'
coder = ABCoder(vcf_fhand,
parents_a,
parents_b,
parent_index_threshold=coder_threshold,
smooth_threhsold=smooth_threshold,
recomb_threshold=recomb_threshold)
samples = coder.offspring
snp_ids = []
snp_genos = []
coding = 'ascii'
if phys_map_fhand is not None:
phys_map_fhand.write('marker\tposition\tChromosome\n')
for snp, genos in coder.recode_genotypes(samples):
snp_id = get_or_create_id(snp).encode(coding)
snp_ids.append(snp_id)
geno_array = array('c')
for geno in genos.values():
geno_array.append(_code_to_one_letter(geno))
snp_genos.append(geno_array)
if phys_map_fhand is not None:
phys_map_fhand.write(snp_id)
phys_map_fhand.write(sep)
phys_map_fhand.write(str(snp.POS))
phys_map_fhand.write(sep)
phys_map_fhand.write(snp.CHROM.encode(coding))
phys_map_fhand.write('\n')
genos_fhand.write('ID')
genos_fhand.write(sep)
genos_fhand.write(sep.join(snp_ids))
genos_fhand.write('\n')
for sample_idx, sample in enumerate(samples):
genos_fhand.write(sample.encode(coding))
genos_fhand.write(sep)
to_write = sep.join(snp_genos[snp_idx][sample_idx]
for snp_idx in range(len(snp_ids)))
genos_fhand.write(to_write)
genos_fhand.write('\n')
return coder
def write_parent_checker(vcf_fhand, parents_a, parents_b, genos_fhand,
phys_map_fhand=None,
coder_threshold=DEF_AB_CODER_THRESHOLD,
smooth_threshold=None, recomb_threshold=None):
sep = '\t'
coder = ABCoder(vcf_fhand, parents_a, parents_b,
parent_index_threshold=coder_threshold,
smooth_threhsold=smooth_threshold,
recomb_threshold=recomb_threshold)
samples = coder.offspring
snp_ids = []
snp_genos = []
coding = 'ascii'
if phys_map_fhand is not None:
phys_map_fhand.write('marker\tposition\tChromosome\n')
for snp, genos in coder.recode_genotypes(samples):
snp_id = get_or_create_id(snp).encode(coding)
snp_ids.append(snp_id)
geno_array = array('c')
for geno in genos.values():
geno_array.append(_code_to_one_letter(geno))
snp_genos.append(geno_array)
if phys_map_fhand is not None:
phys_map_fhand.write(snp_id)
phys_map_fhand.write(sep)
phys_map_fhand.write(str(snp.POS))
phys_map_fhand.write(sep)
phys_map_fhand.write(snp.CHROM.encode(coding))
phys_map_fhand.write('\n')
genos_fhand.write('ID')
genos_fhand.write(sep)
genos_fhand.write(sep.join(snp_ids))
genos_fhand.write('\n')
for sample_idx, sample in enumerate(samples):
genos_fhand.write(sample.encode(coding))
genos_fhand.write(sep)
to_write = sep.join(snp_genos[snp_idx][sample_idx] for snp_idx in range(len(snp_ids)))
genos_fhand.write(to_write)
genos_fhand.write('\n')
return coder