Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | R | S | U | W

_

__getitem__() (Amplicons method)
(FrequencyMatrix method)
__init__() (AmpliconReadGraph method)
(Amplicons method)
(DecliquedAmpliconReadGraph method)
(FrequencyMatrix method)
(PQueue method)
(ReadGraph method)
(SplitAmpliconReadGraph method)
__iter__() (Amplicons method)
(FrequencyMatrix method)
__len__() (Amplicons method)
(FrequencyMatrix method)
__str__() (Amplicons method)
_get_frequency_pairs() (DecliquedAmpliconReadGraph method)

A

add_node() (PQueue method)
(ReadGraph method)
add_nodes_from() (ReadGraph method)
amplicon_frequency_matrix_strategy() (in module bioa.algorithms.reconstruction)
amplicon_frequency_matrix_strategy_from_graph() (in module bioa.algorithms.reconstruction)
amplicons_from_windows() (bioa.Amplicons class method)
ampreadgraph() (in module bioa)
are_consistent() (in module bioa.util.general)

B

bioa.algorithms.reconstruction (module)
bioa.io.amplicon (module)
bioa.io.readpairs (module)
bioa.io.sam (module)
bioa.util.general (module)
bioa.util.graph (module)
bioa.util.matrix (module)
bioa.util.validation (module)
build_amplicons_from_file() (in module bioa.io.amplicon)
build_amplicons_from_graph() (AmpliconReadGraph method)
build_uniform_amplicons() (bioa.Amplicons class method)
build_uniform_amplicons_from_file() (in module bioa.io.amplicon)

C

calc_score() (Amplicons method)
construct_normalized_freq_matrix() (bioa.FrequencyMatrix class method)
convert_decliqued_readgraph() (bioa.SplitAmpliconReadGraph class method)
convert_networkx_to_read_graph() (in module bioa.util.general)

D

dcampreadgraph() (in module bioa)
decrease_key() (PQueue method)
delete_node() (PQueue method)

E

error_tolerance (AmpliconReadGraph attribute)
estimate_amplicons() (bioa.Amplicons class method)

F

find_amplicons_by_primers() (in module bioa.io.amplicon)
frequency_matrix() (in module bioa)

G

get_amplicons() (AmpliconReadGraph method)
get_edge_freq() (ReadGraph method)
get_fork_nodes() (DecliquedAmpliconReadGraph method)
get_forks() (ReadGraph method)
get_max() (PQueue method)
get_min() (PQueue method)
get_node_freq() (ReadGraph method)
get_node_position() (ReadGraph method)
get_node_read() (ReadGraph method)
get_node_read_len() (ReadGraph method)
get_pairs_from_file() (in module bioa.io.readpairs)
get_read_and_fork_nodes() (DecliquedAmpliconReadGraph method)
get_read_nodes() (DecliquedAmpliconReadGraph method)
(SplitAmpliconReadGraph method)
get_reference_len() (Amplicons method)
get_start_end_position() (Amplicons method)
get_start_end_position_by_amplicon() (AmpliconReadGraph method)
get_start_end_positions() (AmpliconReadGraph method)
(Amplicons method)
graph_rank() (in module bioa.util.graph)
greedy_fork_resolution() (in module bioa.algorithms.reconstruction)

H

hamming_distance() (in module bioa.util.validation)

I

is_fork() (ReadGraph method)
is_valid() (bioa.Amplicons class method)

J

jensen_shannon_divergence() (in module bioa.util.validation)

K

kullback_leibler_divergence() (in module bioa.util.validation)

L

least_squares_fork_balance() (in module bioa.algorithms.reconstruction)

M

matrix_rank() (in module bioa.util.matrix)
max() (PQueue method)
max_bandwidth() (in module bioa.util.graph)
max_bandwidth_strategy() (in module bioa.algorithms.reconstruction)
max_frequency_strategy() (in module bioa.algorithms.reconstruction)
mean_diversity() (in module bioa.util.validation)
min() (PQueue method)
min_coverage (Amplicons attribute)
min_forest_fork_resolution() (in module bioa.algorithms.reconstruction)
min_unsplittable_flows_resolution() (in module bioa.algorithms.reconstruction)

N

next() (Amplicons method)

P

parse_pairs() (in module bioa.io.readpairs)
positive_predictive_value() (in module bioa.util.validation)
predecessors() (ReadGraph method)
predecessors_iter() (ReadGraph method)

R

random_amplicons() (bioa.Amplicons class method)
random_bandwidth_strategy() (in module bioa.algorithms.reconstruction)
random_fork_resolution() (in module bioa.algorithms.reconstruction)
read_frequency_correlation() (DecliquedAmpliconReadGraph method)
read_frequency_squared_euclidean_distance() (DecliquedAmpliconReadGraph method)
readgraph() (in module bioa)
reads_from_sam() (in module bioa.io.sam)
reads_from_sam_quick() (in module bioa.io.sam)
reconstruct_sequence() (in module bioa.util.general)
reconstruct_uniform_sequence() (in module bioa.util.general)
remove_node() (ReadGraph method)
remove_nodes_from() (ReadGraph method)
root_mean_square_deviation() (in module bioa.util.validation)

S

score (Amplicons attribute)
sensitivity() (in module bioa.util.validation)
set_amplicons() (AmpliconReadGraph method)
set_edge_freq() (ReadGraph method)
set_node_freq() (ReadGraph method)
set_node_position() (ReadGraph method)
set_node_read() (ReadGraph method)
shannon_entropy() (in module bioa.util.validation)
shape (FrequencyMatrix attribute)
sink (ReadGraph attribute)
source (ReadGraph attribute)
span (Amplicons attribute)
split_edge() (DecliquedAmpliconReadGraph method)
split_fork() (DecliquedAmpliconReadGraph method)
splitampreadgraph() (in module bioa)
successors() (ReadGraph method)
successors_iter() (ReadGraph method)

U

update_freq_matrix_from_lp_output() (in module bioa.algorithms.reconstruction)

W

write_amplicons_to_fasta() (in module bioa.io.amplicon)
write_pairs() (in module bioa.io.readpairs)
write_pairs_to_file() (in module bioa.io.readpairs)