def test_plot_heterozygous_haplotypes(self):
heterozygous = haplotyper.Zygosity.HET
haplotype_wrapper = genotyper.process(self.vcf_path, self.chrom,
self.parental_sample, self.phase,
heterozygous)
plotter = hplot.Plotter(haplotype_wrapper)
user_conf = list(["show=False", "xtickslabels=False", "size_y=5"])
plotter.plot_haplotypes(override_conf=user_conf)
def test_generate_homozygous_yticks(self):
homozygous = haplotyper.Zygosity.HOM
haplotype_wrapper = genotyper.process(self.vcf_path, self.chrom,
self.parental_sample, self.phase,
homozygous)
plotter = hplot.Plotter(haplotype_wrapper)
labels = plotter.get_ytickslabels()
logger.debug("Parent: {parent}".format(parent=self.parental_sample))
logger.debug(labels)
def main():
args = parse_args()
haplotype_wrapper = genotyper.process(args.vcf, args.chr, args.parental, args.phase,
haplotyper.Zygosity[args.zygosis])
plotter = hplot.Plotter(haplotype_wrapper)
plotter.plot_haplotypes(output_file=args.output, override_conf=args.conf)
if args.phase:
writer.save_phased_variants(haplotype_wrapper, args.vcf)
def test_genotype_filtering(self):
haplotype_wrapper = genotyper.process(self.vcf_one_chr_path,
self.chrom, self.parental_sample,
self.phase, Zygosity.HOM)
genotypes_uc_len = len(haplotype_wrapper.genotypes)
variants_uc_len = len(haplotype_wrapper.variants)
logger.debug(
"Length genotypes: {length}".format(length=genotypes_uc_len))
logger.debug(
"Length variants: {length}".format(length=variants_uc_len))
assert genotypes_uc_len == variants_uc_len
def test_plot_homozygous_haplotypes(self):
homozygous = haplotyper.Zygosity.HOM
haplotype_wrapper = genotyper.process(self.vcf_path, self.chrom,
self.parental_sample, self.phase,
homozygous)
plotter = hplot.Plotter(haplotype_wrapper)
ytickslabels = plotter.get_ytickslabels()
custom_config = hplot.PlotConfig(
title="Parental '{parent}' in '{chrom}'".format(
parent=self.parental_sample, chrom=self.chrom),
xtickslabels=plotter.get_xtickslabels(),
ytickslabels=ytickslabels,
start=0,
end=1000,
size_x=10,
size_y=len(ytickslabels) * .2,
show=True)
plotter.plot_haplotypes(custom_config)
def test_save_phased_variants(self):
haplotype_wrapper = genotyper.process(self.vcf_one_chr_path,
self.chrom, self.parental_sample,
True, Zygosity.HOM)
assert haplotype_wrapper
writer.save_phased_variants(haplotype_wrapper, self.vcf_one_chr_path)
def test_genotype_n_variants(self):
haplotype_wrapper = genotyper.process(self.vcf_one_chr_path,
self.chrom, self.parental_sample,
self.phase, Zygosity.HOM)
assert haplotype_wrapper