THAPBI PICT
stable
Documentation contents:
Introduction
Installation
Quick Start
Worked Examples
Reference database
Abundance & Negative Controls
Classifier Assessment
Command Line
Python API
Release History
Development Notes
THAPBI PICT
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
A
abundance_filter_fasta() (in module thapbi_pict.utils)
abundance_from_read_name() (in module thapbi_pict.utils)
abundance_values_in_fasta() (in module thapbi_pict.utils)
apply_method_to_seqs() (in module thapbi_pict.classify)
B
Base (class in thapbi_pict.db_orm)
C
check_rapidfuzz() (in module thapbi_pict.versions)
check_tools() (in module thapbi_pict.versions)
class_list_from_tally_and_db_list() (in module thapbi_pict.assess)
cmd_as_string() (in module thapbi_pict.utils)
color_bands() (in module thapbi_pict.summary)
connect_to_db() (in module thapbi_pict.db_orm)
consoliate_and_sort_taxonomy() (in module thapbi_pict.classify)
D
DataSource (class in thapbi_pict.db_orm)
E
expand_IUPAC_ambiguity_codes() (in module thapbi_pict.utils)
export_sample_biom() (in module thapbi_pict.utils)
export_sample_tsv() (in module thapbi_pict.utils)
extract_binary_tally() (in module thapbi_pict.assess)
extract_global_tally() (in module thapbi_pict.assess)
F
file_to_sample_name() (in module thapbi_pict.utils)
filter_tree() (in module thapbi_pict.taxdump)
find_fastq_pairs() (in module thapbi_pict.prepare)
find_paired_files() (in module thapbi_pict.utils)
find_requested_files() (in module thapbi_pict.utils)
G
genus_species_name() (in module thapbi_pict.utils)
genus_species_split() (in module thapbi_pict.utils)
get_ancestor() (in module thapbi_pict.taxdump)
I
import_fasta_file() (in module thapbi_pict.db_import)
is_spike_in() (in module thapbi_pict.utils)
iskeyword() (in module thapbi_pict.utils)
K
kmers() (in module thapbi_pict.utils)
L
load_fasta_header() (in module thapbi_pict.utils)
load_marker_defs() (in module thapbi_pict.prepare)
load_md5() (in module thapbi_pict.ena_submit)
load_merged() (in module thapbi_pict.taxdump)
load_metadata() (in module thapbi_pict.utils)
load_names() (in module thapbi_pict.taxdump)
load_nodes() (in module thapbi_pict.taxdump)
load_taxonomy() (in module thapbi_pict.db_import)
load_tsv() (in module thapbi_pict.assess)
lookup_genus() (in module thapbi_pict.db_import)
lookup_species() (in module thapbi_pict.db_import)
M
main() (in module thapbi_pict.assess)
(in module thapbi_pict.classify)
(in module thapbi_pict.conflicts)
(in module thapbi_pict.db_import)
(in module thapbi_pict.denoise)
(in module thapbi_pict.dump)
(in module thapbi_pict.edit_graph)
(in module thapbi_pict.ena_submit)
(in module thapbi_pict.fasta_nr)
(in module thapbi_pict.prepare)
(in module thapbi_pict.sample_tally)
(in module thapbi_pict.summary)
(in module thapbi_pict.taxdump)
make_nr_fasta() (in module thapbi_pict.prepare)
marker_cut() (in module thapbi_pict.prepare)
marker_definition (thapbi_pict.db_orm.SeqSource attribute)
marker_seq (thapbi_pict.db_orm.SeqSource attribute)
MarkerDef (class in thapbi_pict.db_orm)
MarkerSeq (class in thapbi_pict.db_orm)
md5_hexdigest() (in module thapbi_pict.utils)
md5seq() (in module thapbi_pict.utils)
merge_paired_reads() (in module thapbi_pict.prepare)
method_blast() (in module thapbi_pict.classify)
method_cleanup() (in module thapbi_pict.classify)
method_dist() (in module thapbi_pict.classify)
method_identity() (in module thapbi_pict.classify)
method_substr() (in module thapbi_pict.classify)
module
thapbi_pict
thapbi_pict.assess
thapbi_pict.classify
thapbi_pict.conflicts
thapbi_pict.db_import
thapbi_pict.db_orm
thapbi_pict.denoise
thapbi_pict.dump
thapbi_pict.edit_graph
thapbi_pict.ena_submit
thapbi_pict.fasta_nr
thapbi_pict.prepare
thapbi_pict.sample_tally
thapbi_pict.summary
thapbi_pict.taxdump
thapbi_pict.utils
thapbi_pict.versions
N
none_str() (in module thapbi_pict.dump)
not_top_species() (in module thapbi_pict.taxdump)
O
onebp_deletions() (in module thapbi_pict.utils)
onebp_inserts() (in module thapbi_pict.utils)
onebp_substitutions() (in module thapbi_pict.utils)
P
parse_curated_fasta_entry() (in module thapbi_pict.db_import)
parse_cutadapt_stdout() (in module thapbi_pict.prepare)
parse_flash_stdout() (in module thapbi_pict.prepare)
parse_ncbi_fasta_entry() (in module thapbi_pict.db_import)
parse_ncbi_taxid_entry() (in module thapbi_pict.db_import)
parse_obitools_fasta_entry() (in module thapbi_pict.db_import)
parse_sample_tsv() (in module thapbi_pict.utils)
parse_sintax_fasta_entry() (in module thapbi_pict.db_import)
parse_species_tsv() (in module thapbi_pict.utils)
perfect_match_in_db() (in module thapbi_pict.classify)
perfect_substr_in_db() (in module thapbi_pict.classify)
prepare_sample() (in module thapbi_pict.prepare)
primer_clean() (in module thapbi_pict.utils)
R
read_correction() (in module thapbi_pict.denoise)
read_summary() (in module thapbi_pict.summary)
reject_species_name() (in module thapbi_pict.utils)
run() (in module thapbi_pict.utils)
run_cutadapt() (in module thapbi_pict.prepare)
run_flash() (in module thapbi_pict.prepare)
S
sample_summary() (in module thapbi_pict.summary)
save_confusion_matrix() (in module thapbi_pict.assess)
save_mapping() (in module thapbi_pict.assess)
save_nr_fasta() (in module thapbi_pict.prepare)
SeqSource (class in thapbi_pict.db_orm)
setup_blast() (in module thapbi_pict.classify)
setup_dist2() (in module thapbi_pict.classify)
setup_dist3() (in module thapbi_pict.classify)
setup_dist4() (in module thapbi_pict.classify)
setup_dist5() (in module thapbi_pict.classify)
setup_dist6() (in module thapbi_pict.classify)
setup_dist7() (in module thapbi_pict.classify)
setup_dist8() (in module thapbi_pict.classify)
setup_dist9() (in module thapbi_pict.classify)
setup_onebp() (in module thapbi_pict.classify)
setup_seqs() (in module thapbi_pict.classify)
source (thapbi_pict.db_orm.SeqSource attribute)
sp_for_sample() (in module thapbi_pict.assess)
sp_in_tsv() (in module thapbi_pict.assess)
species_level() (in module thapbi_pict.utils)
species_or_species_groups() (in module thapbi_pict.taxdump)
split_read_name_abundance() (in module thapbi_pict.utils)
Synonym (class in thapbi_pict.db_orm)
T
tally_files() (in module thapbi_pict.assess)
taxid_and_sp_lists() (in module thapbi_pict.classify)
Taxonomy (class in thapbi_pict.db_orm)
taxonomy (thapbi_pict.db_orm.SeqSource attribute)
thapbi_pict
module
thapbi_pict.assess
module
thapbi_pict.classify
module
thapbi_pict.conflicts
module
thapbi_pict.db_import
module
thapbi_pict.db_orm
module
thapbi_pict.denoise
module
thapbi_pict.dump
module
thapbi_pict.edit_graph
module
thapbi_pict.ena_submit
module
thapbi_pict.fasta_nr
module
thapbi_pict.prepare
module
thapbi_pict.sample_tally
module
thapbi_pict.summary
module
thapbi_pict.taxdump
module
thapbi_pict.utils
module
thapbi_pict.versions
module
U
unique_or_separated() (in module thapbi_pict.classify)
unoise() (in module thapbi_pict.denoise)
usearch() (in module thapbi_pict.denoise)
V
valid_marker_name() (in module thapbi_pict.utils)
version_blast() (in module thapbi_pict.versions)
version_cutadapt() (in module thapbi_pict.versions)
version_flash() (in module thapbi_pict.versions)
version_graphviz_fdp() (in module thapbi_pict.versions)
version_usearch() (in module thapbi_pict.versions)
version_vsearch() (in module thapbi_pict.versions)
vsearch() (in module thapbi_pict.denoise)
W
write_pdf() (in module thapbi_pict.edit_graph)
write_table() (in module thapbi_pict.ena_submit)
write_xgmml() (in module thapbi_pict.edit_graph)
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