SYMBOL INDEX (94 symbols across 37 files)

FILE: Chapter02/NumPy.py
  function compute_frac (line 40) | def compute_frac(arr_1d):

FILE: Chapter03/Filtering_SNPs.py
  function do_window (line 42) | def do_window(recs, size, fun):
  function apply_win_funs (line 57) | def apply_win_funs(wins, funs):
  function get_sample (line 93) | def get_sample(rec, annot, my_type):
  function get_sample_relation (line 119) | def get_sample_relation(recs, f1, f2):
  function plot_hz_rel (line 146) | def plot_hz_rel(dps, ax, ax2, name, rel):
  function get_variant_relation (line 181) | def get_variant_relation(recs, f1, f2):
  function eff_to_int (line 202) | def eff_to_int(rec):

FILE: Chapter04/2L.py
  function insert_in_window (line 37) | def insert_in_window(row):

FILE: Chapter04/Mendel.py
  function accept_entry (line 78) | def accept_entry(row):

FILE: Chapter04/Preparation.py
  function compute_mendelian_errors (line 76) | def compute_mendelian_errors(mother, father, offspring):
  function acceptable_position_to_genotype (line 112) | def acceptable_position_to_genotype():
  function acumulate (line 120) | def acumulate(fun):
  function get_family_indexes (line 129) | def get_family_indexes(samples_hdf5, cross_pd):
  function get_mendelian_errors (line 152) | def get_mendelian_errors():
  function get_parent_indexes (line 196) | def get_parent_indexes(samples_hdf5, parents_pd):

FILE: Chapter05/Gene_Ontology.py
  function do_request (line 26) | def do_request(server, service, *args, **kwargs):
  function get_upper (line 75) | def get_upper(go_id):

FILE: Chapter05/Getting_Gene.py
  function get_sequence (line 45) | def get_sequence(chrom_seq, CDSs, strand):

FILE: Chapter05/Orthology.py
  function do_request (line 20) | def do_request(server, service, *args, **kwargs):

FILE: Chapter06/Admixture.py
  function load_Q (line 83) | def load_Q(fname, ind_order):

FILE: Chapter06/Data_Formats.py
  function get_non_auto_SNPs (line 58) | def get_non_auto_SNPs(map_file, exclude_file):

FILE: Chapter06/Pop_Stats.py
  function assign_cohort (line 46) | def assign_cohort(pops, pop_ind, sample_family_id, sample_id):

FILE: Chapter07/Comparison.py
  function do_basic_popgen (line 65) | def do_basic_popgen(seqs):

FILE: Chapter07/Exploration.py
  function get_ebov_2014_sources (line 22) | def get_ebov_2014_sources():
  function get_other_ebov_sources (line 27) | def get_other_ebov_sources():
  function get_other_ebolavirus_sources (line 33) | def get_other_ebolavirus_sources():
  function dump_genes (line 92) | def dump_genes(species, recs, g_dls, p_hdls):
  function describe_seqs (line 129) | def describe_seqs(seqs):

FILE: Chapter07/Trees.py
  function compute_level (line 21) | def compute_level(node, level=0):
  function compute_height (line 31) | def compute_height(node):
  function compute_nofs (line 45) | def compute_nofs(node):
  function print_nodes (line 56) | def print_nodes(node):
  function print_breadth (line 67) | def print_breadth(tree):
  function simplify_tree (line 84) | def simplify_tree(node):

FILE: Chapter07/Visualization.py
  function get_color (line 45) | def get_color(name):
  function color_tree (line 51) | def color_tree(node, fun_color=get_color):

FILE: Chapter08/Distance.py
  function get_closest_atoms (line 41) | def get_closest_atoms(pdb_struct, ref_atom, distance):
  function get_closest_alternative (line 74) | def get_closest_alternative(pdb_struct, ref_atom, distance):

FILE: Chapter08/Intro.py
  function do_request (line 25) | def do_request(server, **kwargs):

FILE: Chapter08/Mass.py
  function get_mass (line 40) | def get_mass(atoms, accept_fun=lambda atom: atom.parent.id[0] != 'W'):
  function get_center (line 55) | def get_center(atoms, weight_fun=lambda atom: 1 if atom.parent.id[0] != ...

FILE: Chapter08/PDB.py
  function print_pdb_headers (line 29) | def print_pdb_headers(headers, indent=0):
  function describe_model (line 51) | def describe_model(name, pdb):
  function get_fasta (line 77) | def get_fasta(pdb_file, fasta_file, transfer_ids=None):

FILE: Chapter08/Parser.py
  function parse_pdb (line 41) | def parse_pdb(hdl):
  function process_multi_lines (line 72) | def process_multi_lines(hdl):
  function get_spec_list (line 105) | def get_spec_list(my_str):
  function process_struct_types (line 118) | def process_struct_types(hdl):

FILE: Chapter08/PyMol_Intro.py
  function dump_thread (line 2) | def dump_thread():

FILE: Chapter08/Stats.py
  function get_bounds (line 57) | def get_bounds(my_atoms):

FILE: Chapter08/mmCIF.py
  function describe_model (line 24) | def describe_model(name, pdb):

FILE: Chapter09/galaxy/api.py
  function summarize_contents (line 92) | def summarize_contents(contents):
  function dataset_to_param (line 122) | def dataset_to_param(dataset):

FILE: Chapter10/Clustering.py
  function plot_kmeans_pca (line 89) | def plot_kmeans_pca(trans, kmeans):

FILE: Chapter11/Dask_Distributed.py
  function calc_stats (line 54) | def calc_stats(my_chunk):

FILE: Chapter11/Dask_Intro.py
  function calc_stats (line 42) | def calc_stats(variant):

FILE: Chapter11/MP_intro.py
  function calc_stats (line 47) | def calc_stats(my_chunk):
  function compute_interval (line 71) | def compute_interval(interval):

FILE: Chapter11/Zarr_Intro.py
  function calc_stats (line 61) | def calc_stats(my_chunk):

FILE: Chapter12/Builtin.py
  function fibo (line 5) | def fibo(n):
  function gene_min_reads (line 16) | def gene_min_reads(source, min_reads):

FILE: Chapter12/Lazy.py
  function load (line 4) | def load(file_name):
  function get_min_reads (line 9) | def get_min_reads(all_data, min_reads):
  function has_min_observations (line 17) | def has_min_observations(subset_data, min_observations):
  function get_rec (line 27) | def get_rec(file_name):
  function gene_min_reads (line 35) | def gene_min_reads(source, min_reads):
  function gene_min_observations (line 41) | def gene_min_observations(subset_source, min_observations):

FILE: Chapter12/Mutability.py
  function restore_db (line 5) | def restore_db(file_name):
  function load (line 9) | def load(file_name):
  function save (line 14) | def save(dict_db, file_name):
  function add_sample_dict (line 19) | def add_sample_dict(dict_db, gene_list):
  function add_sample_new_dict (line 24) | def add_sample_new_dict(dict_db, gene_list):

FILE: Chapter12/Persistence1.py
  function restore_db (line 5) | def restore_db(file_name):
  function load (line 9) | def load(file_name):
  function save (line 14) | def save(dict_db, file_name):
  function add_sample_csv (line 19) | def add_sample_csv(gene_list):

FILE: Chapter12/Persistence2.py
  function restore_db (line 5) | def restore_db(file_name):
  function load (line 9) | def load(file_name):
  function save (line 14) | def save(dict_db, file_name):
  function add_sample_new_dict (line 19) | def add_sample_new_dict(dict_db, gene_list):

FILE: Chapter12/Pure.py
  function restore_db (line 5) | def restore_db(file_name):
  function load (line 9) | def load(file_name):
  function save (line 14) | def save(dict_db, file_name):
  function add_sample_csv (line 19) | def add_sample_csv(gene_list):
  function add_sample_global_dict (line 26) | def add_sample_global_dict(gene_list):
  function add_sample_dict (line 32) | def add_sample_dict(dict_db, gene_list):

FILE: Chapter12/Recursion.py
  function fibo_iter (line 1) | def fibo_iter(n):
  function fibo_naive (line 13) | def fibo_naive(n):
  function factorial (line 31) | def factorial(n):

FILE: Chapter12/Tools.py
  function fibo_iter (line 4) | def fibo_iter(n):
  function fibo_naive (line 18) | def fibo_naive(n):
  function fibo (line 27) | def fibo(n):
  function factorial (line 40) | def factorial(n):