final_line_number = 0
while final_line_number >= 0:
sys.stderr.write("Loading chunk starting @ %d...\n" % final_line_number)
dummy_samples, allele_counts_map, passed_sites_map, final_line_number = parse_midas_data.parse_snps(
species_name,
debug=debug,
allowed_samples=snp_samples,
chunk_size=chunk_size,
initial_line_number=final_line_number)
sys.stderr.write("Done! Loaded %d genes\n" % len(allele_counts_map.keys()))
# Calculate fixation matrix
sys.stderr.write("Calculating matrix of snp differences...\n")
chunk_snp_difference_matrix, chunk_snp_opportunity_matrix = diversity_utils.calculate_fixation_matrix(
allele_counts_map, passed_sites_map, min_change=min_change)
sys.stderr.write("Done!\n")
if snp_difference_matrix.shape[0] == 0:
snp_difference_matrix = numpy.zeros_like(
chunk_snp_difference_matrix) * 1.0
snp_opportunity_matrix = numpy.zeros_like(snp_difference_matrix) * 1.0
snp_difference_matrix += chunk_snp_difference_matrix
snp_opportunity_matrix += chunk_snp_opportunity_matrix
sys.stderr.write("Calculating genotype matrix for chunk...\n")
for gene_name in allele_counts_map.keys():
for variant_type in allele_counts_map[gene_name].keys():
if len(allele_counts_map[gene_name][variant_type]['alleles']) == 0:
median_coverages = numpy.array(
[sample_coverage_map[samples[i]] for i in xrange(0, len(samples))])
# Calculate full matrix of synonymous pairwise differences
sys.stderr.write("Calculate synonymous pi matrix...\n")
pi_matrix_syn, avg_pi_matrix_syn = diversity_utils.calculate_pi_matrix(
allele_counts_map,
passed_sites_map,
variant_type='4D',
allowed_genes=metaphlan2_genes)
# Calculate fixation matrix
fixation_matrix_syn = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
variant_type='4D',
min_change=min_change,
allowed_genes=metaphlan2_genes)
sys.stderr.write("Done!\n")
# Calculate full matrix of nonsynonymous pairwise differences
sys.stderr.write("Calculate nonsynonymous pi matrix...\n")
# Calculate allele count matrices
pi_matrix_non, avg_pi_matrix_non = diversity_utils.calculate_pi_matrix(
allele_counts_map,
passed_sites_map,
variant_type='1D',
allowed_genes=metaphlan2_genes)
# Calculate fixation matrix
fixation_matrix_non = diversity_utils.calculate_fixation_matrix(
sys.stderr.write("Loading chunk starting @ %d...\n" % final_line_number)
snp_samples, allele_counts_map, passed_sites_map, final_line_number = parse_midas_data.parse_snps(
species_name,
debug=debug,
allowed_variant_types=allowed_variant_types,
allowed_samples=largest_clade_samples,
allowed_genes=core_genes,
chunk_size=chunk_size,
initial_line_number=final_line_number)
sys.stderr.write("Done! Loaded %d genes\n" % len(allele_counts_map.keys()))
# Calculate fixation matrix
sys.stderr.write("Calculating matrix of snp differences...\n")
chunk_snp_difference_matrix, chunk_snp_opportunity_matrix = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
allowed_genes=core_genes,
min_change=min_change)
sys.stderr.write("Done!\n")
if snp_difference_matrix.shape[0] == 0:
snp_difference_matrix = numpy.zeros_like(
chunk_snp_difference_matrix) * 1.0
snp_opportunity_matrix = numpy.zeros_like(snp_difference_matrix) * 1.0
synonymous_difference_matrix = numpy.zeros_like(snp_difference_matrix)
synonymous_opportunity_matrix = numpy.zeros_like(snp_difference_matrix)
nonsynonymous_difference_matrix = numpy.zeros_like(
snp_difference_matrix)
nonsynonymous_opportunity_matrix = numpy.zeros_like(
snp_difference_matrix)
sys.stderr.write("Analyzing %d haploid samples...\n" %
len(desired_samples))
species_idx += 1
# Load SNP information for species_name
sys.stderr.write("Loading %s...\n" % species_name)
dummy_samples, allele_counts_map, passed_sites_map = parse_midas_data.parse_snps(
species_name, debug=debug, allowed_samples=desired_samples)
sys.stderr.write("Done!\n")
# Calculate fixation matrices
sys.stderr.write("Calculating 4D fixation matrix...\n")
fixation_matrix_syn, fixation_opportunities_syn = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
allowed_variant_types=set(['4D']),
min_change=min_change)
sys.stderr.write("Calculating 1D fixation matrix...\n")
fixation_matrix_non, fixation_opportunities_non = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
allowed_variant_types=set(['1D']),
min_change=min_change)
sys.stderr.write("Calculating total fixation matrix...\n")
fixation_matrix_all, fixation_opportunities_all = diversity_utils.calculate_fixation_matrix(
allele_counts_map, passed_sites_map, min_change=min_change)
sys.stderr.write("Done!\n")
# Calculate fraction nonsynonymous
dummy_samples, allele_counts_map, passed_sites_map, final_line_number = parse_midas_data.parse_snps(
species_name,
debug=debug,
allowed_samples=snp_samples,
allowed_genes=core_genes,
chunk_size=chunk_size,
initial_line_number=final_line_number)
sys.stderr.write("Done! Loaded %d genes\n" % len(allele_counts_map.keys()))
print len(dummy_samples), "dummy samples!"
# Calculate fixation matrix
sys.stderr.write("Calculating matrix of snp differences...\n")
chunk_snp_difference_matrix, chunk_snp_opportunity_matrix = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
min_change=min_change,
allowed_genes=core_genes,
allowed_variant_types=allowed_variant_types) #
sys.stderr.write("Done!\n")
if snp_difference_matrix.shape[0] == 0:
snp_difference_matrix = numpy.zeros_like(
chunk_snp_difference_matrix) * 1.0
snp_opportunity_matrix = numpy.zeros_like(snp_difference_matrix) * 1.0
snp_difference_matrix += chunk_snp_difference_matrix
snp_opportunity_matrix += chunk_snp_opportunity_matrix
sys.stderr.write("Calculating singletons...\n")
chunk_singletons = diversity_utils.calculate_singletons(
allele_counts_map, passed_sites_map, allowed_genes=core_genes)
species_name, debug)
sys.stderr.write("Done!\n")
median_coverages = numpy.array(
[sample_coverage_map[samples[i]] for i in xrange(0, len(samples))])
# Calculate full matrix of synonymous pairwise differences
sys.stderr.write("Calculate synonymous pi matrix...\n")
pi_matrix_syn, avg_pi_matrix_syn = diversity_utils.calculate_pi_matrix(
allele_counts_map, passed_sites_map, variant_type='4D')
pis = numpy.diag(pi_matrix_syn)
# Calculate fixation matrix
fixation_matrix_syn, persite_fixation_matrix_syn = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
variant_type='4D',
min_change=min_change)
sys.stderr.write("Done!\n")
# Calculate full matrix of nonsynonymous pairwise differences
sys.stderr.write("Calculate nonsynonymous pi matrix...\n")
# Calculate allele count matrices
pi_matrix_non, avg_pi_matrix_non = diversity_utils.calculate_pi_matrix(
allele_counts_map, passed_sites_map, variant_type='1D')
# Calculate fixation matrix
fixation_matrix_non, persite_fixation_matrix_non = diversity_utils.calculate_fixation_matrix(
allele_counts_map,
passed_sites_map,
variant_type='1D',
