i = same_subject_idxs[0][sample_pair_idx]
j = same_subject_idxs[1][sample_pair_idx]
sample_i = snp_samples[i]
sample_j = snp_samples[j]
sample_pair = (sample_i, sample_j)
perr = diversity_utils.calculate_fixation_error_rate(
sfs_map, sample_i, sample_j)[0]
snp_perrs[sample_pair] = perr
tracked_private_snp_perrs[sample_pair] = perr
gene_changes[sample_pair].extend(
gene_diversity_utils.calculate_gene_differences_between(
i, j, gene_reads_matrix, gene_depth_matrix,
marker_coverages))
gene_perr = gene_diversity_utils.calculate_gene_error_rate(
i, j, gene_reads_matrix, gene_depth_matrix,
marker_coverages)[0]
gene_opportunities[sample_pair] = gene_depth_matrix.shape[0]
gene_perrs[sample_pair] = gene_perr
sys.stderr.write("Done!\n")
for sample_i, sample_j in snp_changes.keys():
# First output SNPs
if not ((snp_samples[snp_i] in haploid_samples) and
(snp_samples[snp_j] in haploid_samples)):
# both have to be haploids
continue
plower = snp_difference_matrix[snp_i, snp_j]
pupper = plower * 1.1
#plower,pupper = stats_utils.calculate_poisson_rate_interval(snp_difference_matrix[snp_i,snp_j], snp_opportunity_matrix[snp_i, snp_j])
diff_subject_snp_plowers.append(plower)
diff_subject_snp_puppers.append(pupper)
i = diff_subject_gene_idxs[0][sample_pair_idx]
j = diff_subject_gene_idxs[1][sample_pair_idx]
gene_differences = gene_diversity_utils.calculate_gene_differences_between(
i, j, gene_depth_matrix, marker_coverages, include_high_copynum=False)
if snp_substitution_rate[snp_i, snp_j] < clade_divergence_threshold:
for gene_idx, depth_tuple_1, depth_tuple_2 in gene_differences:
if gene_idx not in between_host_gene_idx_map:
between_host_gene_idx_map[gene_idx] = 0
between_host_gene_idxs.append(gene_idx)
between_host_gene_idx_map[gene_idx] += 1
if snp_substitution_rate[snp_i, snp_j] < modification_divergence_threshold:
# A modification, not a replacement!
for gene_idx, depth_tuple_1, depth_tuple_2 in gene_differences:
if gene_idx not in low_divergence_between_host_gene_idx_map:
i = same_subject_snp_idxs[0][sample_pair_idx]
j = same_subject_snp_idxs[1][sample_pair_idx]
plower, pupper = stats_utils.calculate_poisson_rate_interval(
snp_difference_matrix[i, j], snp_opportunity_matrix[i, j], alpha)
same_subject_snp_plowers.append(plower)
same_subject_snp_puppers.append(pupper)
snp_differences = diversity_utils.calculate_snp_differences_between(
i, j, allele_counts_map, passed_sites_map, min_change=min_change)
i = same_subject_gene_idxs[0][sample_pair_idx]
j = same_subject_gene_idxs[1][sample_pair_idx]
gene_differences = gene_diversity_utils.calculate_gene_differences_between(
i, j, gene_depth_matrix, marker_coverages, min_log2_fold_change=4)
plower, pupper = stats_utils.calculate_poisson_rate_interval(
gene_difference_matrix[i, j], gene_opportunity_matrix[i, j])
same_subject_gene_plowers.append(plower)
same_subject_gene_puppers.append(pupper)
if (len(snp_differences) > 0) or (len(gene_differences) > 0):
# Print them out!
print "Changes between pair", sample_pair_idx
print "SNPs:"
if len(snp_differences) > 0:
for snp_diff_idx in xrange(0, len(snp_differences)):
print snp_differences[snp_diff_idx]
print "Genes:"