Python parse_subject_sample_time_map Beispiele

Beispiel #1

Datei: statistics_correlated_with_piS.py Projekt: zhiru-liu/microbiome_evolution

sys.stderr.write("Loading core genes...\n")
core_genes = parse_midas_data.load_core_genes(species_name)
sys.stderr.write("Done! %d core genes\n" % len(core_genes))

#################
# Load metadata #
#################

# Load subject and sample metadata
sys.stderr.write("Loading HMP metadata...\n")
subject_sample_map = parse_midas_data.parse_subject_sample_map()
sys.stderr.write("Done!\n")

# Load time metadata
subject_sample_time_map_all_samples = parse_midas_data.parse_subject_sample_time_map(
)

######################
# Load coverage data #
######################

# Load genomic coverage distributions
sample_coverage_histograms, samples = parse_midas_data.parse_coverage_distribution(
    species_name)
median_coverages = numpy.array([
    stats_utils.calculate_median_from_histogram(sample_coverage_histogram)
    for sample_coverage_histogram in sample_coverage_histograms
])
sample_coverage_map = {
    samples[i]: median_coverages[i]
    for i in xrange(0, len(samples))

Beispiel #2

Datei: plot_piS_ordered_by_time.py Projekt: zhiru-liu/microbiome_evolution

min_change = 0.8
# Minimum median coverage of sample to look at
min_coverage = 20

#################
# Load metadata #
#################

# Load subject and sample metadata
sys.stderr.write("Loading HMP metadata...\n")
subject_sample_map = parse_midas_data.parse_subject_sample_map()
sys.stderr.write("Done!\n")

# Load time metadata
subject_sample_time_map = parse_midas_data.parse_subject_sample_time_map()

######################
# Load coverage data #
######################

# Load genomic coverage distributions
sample_coverage_histograms, samples = parse_midas_data.parse_coverage_distribution(
    species_name)
median_coverages = numpy.array([
    stats_utils.calculate_median_from_histogram(sample_coverage_histogram)
    for sample_coverage_histogram in sample_coverage_histograms
])
sample_coverage_map = {
    samples[i]: median_coverages[i]
    for i in xrange(0, len(samples))