Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
O
|
P
|
R
|
S
|
T
|
W
A
add_otu() (physcraper.aligntreetax.AlignTreeTax method)
align_new_seqs() (physcraper.scrape.PhyscraperScrape method)
AlignTreeTax (class in physcraper.aligntreetax)
B
bulk_tnrs_load() (in module physcraper.opentree_helpers)
C
calculate_bootstrap() (physcraper.scrape.PhyscraperScrape method)
calculate_final_tree() (physcraper.scrape.PhyscraperScrape method)
check_complement() (physcraper.scrape.PhyscraperScrape method)
check_if_ottid_in_synth() (in module physcraper.opentree_helpers)
check_taxonomy() (physcraper.configobj.ConfigObj method)
check_tre_in_aln() (physcraper.aligntreetax.AlignTreeTax method)
config_str() (physcraper.configobj.ConfigObj method)
ConfigObj (class in physcraper.configobj)
conflict_tree() (in module physcraper.opentree_helpers)
count_match_tree_to_aln() (in module physcraper.opentree_helpers)
D
debug() (in module physcraper.opentree_helpers)
(in module physcraper.scrape)
deconcatenate_aln() (in module physcraper.opentree_helpers)
E
entrez_efetch() (physcraper.ids.IdDicts method)
est_full_tree() (physcraper.scrape.PhyscraperScrape method)
F
filter_seqs() (physcraper.scrape.PhyscraperScrape method)
G
generate_ATT_from_files() (in module physcraper.aligntreetax)
generate_ATT_from_phylesystem() (in module physcraper.opentree_helpers)
generate_ATT_from_run() (in module physcraper.aligntreetax)
generate_TreeTax_from_run() (in module physcraper.treetaxon)
get_acc_from_blast() (in module physcraper.ncbi_data_parser)
get_citations_from_json() (in module physcraper.opentree_helpers)
get_dataset_from_treebase() (in module physcraper.opentree_helpers)
get_downtorank_id() (physcraper.ncbi_data_parser.Parser method)
get_full_seq() (physcraper.scrape.PhyscraperScrape method)
get_gi_from_blast() (in module physcraper.ncbi_data_parser)
get_id_from_name() (physcraper.ncbi_data_parser.Parser method)
get_id_from_synonym() (physcraper.ncbi_data_parser.Parser method)
get_max_match_aln() (in module physcraper.opentree_helpers)
get_mrca_ott() (in module physcraper.opentree_helpers)
get_name_from_id() (physcraper.ncbi_data_parser.Parser method)
get_ncbi_tax_id() (in module physcraper.ncbi_data_parser)
get_ncbi_tax_name() (in module physcraper.ncbi_data_parser)
get_ncbiid_from_acc() (physcraper.ids.IdDicts method)
get_nexson() (in module physcraper.opentree_helpers)
get_ott_taxon_info() (in module physcraper.opentree_helpers)
get_ottid_from_gbifid() (in module physcraper.opentree_helpers)
get_otu_for_acc() (physcraper.aligntreetax.AlignTreeTax method)
get_rank() (physcraper.ncbi_data_parser.Parser method)
get_tax_info_from_acc() (in module physcraper.ncbi_data_parser)
get_tax_seq_acc() (physcraper.ids.IdDicts method)
get_tree_from_study() (in module physcraper.opentree_helpers)
get_tree_from_synth() (in module physcraper.opentree_helpers)
I
IdDicts (class in physcraper.ids)
is_number() (in module physcraper.configobj)
L
load_names() (in module physcraper.ncbi_data_parser)
load_nodes() (in module physcraper.ncbi_data_parser)
load_synonyms() (in module physcraper.ncbi_data_parser)
M
make_sp_dict() (physcraper.scrape.PhyscraperScrape method)
map_taxa_to_ncbi() (physcraper.scrape.PhyscraperScrape method)
match_id_to_mrca() (physcraper.ncbi_data_parser.Parser method)
O
ottids_in_synth() (in module physcraper.opentree_helpers)
OtuJsonDict() (in module physcraper.opentree_helpers)
P
Parser (class in physcraper.ncbi_data_parser)
physcraper (module)
physcraper.aligntreetax (module)
physcraper.configobj (module)
physcraper.ids (module)
physcraper.ncbi_data_parser (module)
physcraper.opentree_helpers (module)
physcraper.scrape (module)
physcraper.treetaxon (module)
PhyscraperScrape (class in physcraper.scrape)
prune_short() (physcraper.aligntreetax.AlignTreeTax method)
R
read_blast_wrapper() (physcraper.scrape.PhyscraperScrape method)
read_config() (physcraper.configobj.ConfigObj method)
read_in_aln() (physcraper.aligntreetax.AlignTreeTax method)
read_in_tree() (physcraper.aligntreetax.AlignTreeTax method)
read_local_blast_query() (physcraper.scrape.PhyscraperScrape method)
read_webbased_blast_query() (physcraper.scrape.PhyscraperScrape method)
remove_blocklistitem() (physcraper.scrape.PhyscraperScrape method)
remove_identical_seqs() (physcraper.scrape.PhyscraperScrape method)
remove_taxa_aln_tre() (physcraper.aligntreetax.AlignTreeTax method)
replace_aln() (physcraper.scrape.PhyscraperScrape method)
replace_tre() (physcraper.scrape.PhyscraperScrape method)
reset_markers() (physcraper.scrape.PhyscraperScrape method)
root_tree_from_synth() (in module physcraper.opentree_helpers)
run_blast_wrapper() (physcraper.scrape.PhyscraperScrape method)
run_local_blast_cmd() (physcraper.scrape.PhyscraperScrape method)
run_muscle() (physcraper.scrape.PhyscraperScrape method)
run_web_blast_query() (physcraper.scrape.PhyscraperScrape method)
S
scraper_from_opentree() (in module physcraper.opentree_helpers)
select_seq_at_random() (physcraper.scrape.PhyscraperScrape method)
seq_dict_build() (physcraper.scrape.PhyscraperScrape method)
set_defaults() (physcraper.configobj.ConfigObj method)
set_local() (physcraper.configobj.ConfigObj method)
set_verbose() (in module physcraper.aligntreetax)
(in module physcraper.opentree_helpers)
(in module physcraper.scrape)
strip() (in module physcraper.ncbi_data_parser)
summarize_boot() (physcraper.scrape.PhyscraperScrape method)
T
TreeTax (class in physcraper.treetaxon)
trim() (physcraper.aligntreetax.AlignTreeTax method)
W
write_aln() (physcraper.aligntreetax.AlignTreeTax method)
write_file() (physcraper.configobj.ConfigObj method)
write_files() (physcraper.aligntreetax.AlignTreeTax method)
write_labelled() (physcraper.aligntreetax.AlignTreeTax method)
(physcraper.treetaxon.TreeTax method)
write_labelled_aln() (in module physcraper.aligntreetax)
(physcraper.aligntreetax.AlignTreeTax method)
write_labelled_tree() (in module physcraper.aligntreetax)
(physcraper.aligntreetax.AlignTreeTax method)
write_mrca() (physcraper.scrape.PhyscraperScrape method)
write_new_seqs() (physcraper.scrape.PhyscraperScrape method)
write_otu_file() (in module physcraper.aligntreetax)
write_otus() (physcraper.aligntreetax.AlignTreeTax method)
write_papara_files() (physcraper.aligntreetax.AlignTreeTax method)
write_random_resolve_tre() (physcraper.aligntreetax.AlignTreeTax method)
Physcraper
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