same_subject_snp_plowers = []
same_subject_snp_puppers = []
same_subject_gene_plowers = []
same_subject_gene_puppers = []
for sample_pair_idx in xrange(0, len(same_subject_snp_idxs[0])):
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
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]
avg_depth_i = sample_coverage_map[sample_i]
avg_depth_j = sample_coverage_map[sample_j]
chunk_tracked_private_snps = diversity_utils.calculate_tracked_private_snvs(
i, j, allele_counts_map, passed_sites_map, avg_depth_i,
avg_depth_j, private_snv_map)
chunk_snp_changes = diversity_utils.calculate_snp_differences_between(
i, j, allele_counts_map, passed_sites_map, avg_depth_i,
avg_depth_j)
sample_pair = (sample_i, sample_j)
if sample_pair not in snp_changes:
snp_changes[sample_pair] = []
gene_changes[sample_pair] = []
snp_opportunities[sample_pair] = 0
gene_opportunities[sample_pair] = 0
snp_perrs[sample_pair] = -1
gene_perrs[sample_pair] = -1
tracked_private_snps[sample_pair] = []
tracked_private_snp_opportunities[sample_pair] = 0
tracked_private_snp_perrs[sample_pair] = -1
# Calculate fixation matrix
sys.stderr.write("Calculating joint freqs...\n")
for pair_idx in xrange(0,len(desired_sample_pairs)):
initial_sample_idx, final_sample_idx = desired_sample_pair_idxs[pair_idx]
chunk_gene_names, chunk_chromosomes, chunk_positions, chunk_initial_freqs, chunk_final_freqs, chunk_initial_depths, chunk_final_depths = diversity_utils.calculate_temporal_sample_freqs(allele_counts_map, passed_sites_map, initial_sample_idx, final_sample_idx) #
joint_passed_sites = (chunk_initial_depths>0)*(chunk_final_depths>0)
gene_names[pair_idx].extend(chunk_gene_names[joint_passed_sites])
initial_freqs[pair_idx].extend(chunk_initial_freqs[joint_passed_sites])
initial_depths[pair_idx].extend(chunk_initial_depths[joint_passed_sites])
final_freqs[pair_idx].extend(chunk_final_freqs[joint_passed_sites])
snp_changes[pair_idx].extend(diversity_utils.calculate_snp_differences_between(initial_sample_idx, final_sample_idx, allele_counts_map, passed_sites_map, lower_threshold=snv_lower_threshold,
upper_threshold=snv_upper_threshold))
sys.stderr.write("Done!\n")
for pair_idx in xrange(0,len(desired_sample_pairs)):
gene_names[pair_idx] = numpy.array(gene_names[pair_idx])
initial_freqs[pair_idx] = numpy.array(initial_freqs[pair_idx])
final_freqs[pair_idx] = numpy.array(final_freqs[pair_idx])
sys.stderr.write("Done!\n")
highlighted_gene_colors = {}
highlighted_gene_depths = {}
# Plot joint SFS!