def snp_count_table(options):
""" make a table of snp counts. there are serious problems with this now:
1) don't have snp count for baseline (as it's not gam or vcf)
2) snps counted differenty for gam/vcf (multiple alternates at same site
counted in former but not latter)
"""
# tsv header
count_table = "#\t{}\t\n".format(options.baseline)
count_table += "#graph\tlinear_snp_count\tsample_snp_count\taugmented_snp_count\n"
sums = defaultdict(lambda : (0,0,0))
counts = defaultdict(lambda : 0)
for gam in options.in_gams:
linear_vcf = linear_vcf_path(gam, options) + ".gz"
vg_sample = sample_vg_path(gam, options)
vg_augmented = augmented_vg_path(gam, options)
vcf_snps = count_vcf_snps(linear_vcf, options)
sample_snps = count_vg_paths(vg_sample, options)
augmented_snps = count_vg_paths(vg_augmented, options)
name = graph_path(gam, options)
sums[name] = (sums[name][0] + vcf_snps,
sums[name][1] + sample_snps,
sums[name][2] + augmented_snps)
counts[name] = counts[name] + 1
for name in list(set(map(lambda x : graph_path(x, options), options.in_gams))):
avg_vcf = float(sums[name][0]) / float(counts[name])
avg_sam = float(sums[name][1]) / float(counts[name])
avg_aug = float(sums[name][2]) / float(counts[name])
count_table +="{}\t{}\t{}\t{}\n".format(
os.path.splitext(os.path.basename(name))[0],
avg_vcf,
avg_sam,
avg_aug)
with open(count_tsv_path(options), "w") as ofile:
ofile.write(count_table)
def graph_size_table(options):
""" make a table of sequence lengths for the vg call outputs
"""
# tsv header
length_table = "#\t{}\t\n".format(options.baseline)
length_table += "#graph\tsample_snp_length\taugmented_snp_length\toriginal_length\n"
sums = defaultdict(lambda : (0,0,0))
counts = defaultdict(lambda : 0)
for gam in options.in_gams:
linear_vcf = linear_vcf_path(gam, options) + ".gz"
vg_sample = sample_vg_path(gam, options)
vg_augmented = augmented_vg_path(gam, options)
sample_snps = vg_length(vg_sample, options)
augmented_snps = vg_length(vg_augmented, options)
vg_original = graph_path(gam, options)
original_snps = vg_length(vg_original, options)
name = graph_path(gam, options)
sums[name] = (sums[name][0] + sample_snps,
sums[name][1] + augmented_snps,
sums[name][2] + original_snps)
counts[name] = counts[name] + 1
for name in list(set(map(lambda x : graph_path(x, options), options.in_gams))):
avg_sam = float(sums[name][0]) / float(counts[name])
avg_aug = float(sums[name][1]) / float(counts[name])
avg_ori = float(sums[name][2]) / float(counts[name])
length_table +="{}\t{}\t{}\t{}\n".format(
os.path.splitext(os.path.basename(name))[0],
avg_sam,
avg_aug,
avg_ori)
with open(size_tsv_path(options), "w") as ofile:
ofile.write(length_table)
