cblaster
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API Documentation
cblaster
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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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H
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I
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M
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N
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O
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P
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Q
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R
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S
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T
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V
A
accession (cblaster.classes.Scaffold attribute)
add_binary_arguments() (in module cblaster.parsers)
add_clustering_group() (in module cblaster.parsers)
add_clusters() (cblaster.classes.Scaffold method)
add_config_subparser() (in module cblaster.parsers)
add_extract_clusters_subparser() (in module cblaster.parsers)
add_extract_subparser() (in module cblaster.parsers)
add_field_whitespace() (in module cblaster.formatters)
add_filtering_group() (in module cblaster.parsers)
add_gne_output_group() (in module cblaster.parsers)
add_gne_params_group() (in module cblaster.parsers)
add_gne_subparser() (in module cblaster.parsers)
add_gui_subparser() (in module cblaster.parsers)
add_input_group() (in module cblaster.parsers)
add_intermediate_genes_group() (in module cblaster.parsers)
add_makedb_subparser() (in module cblaster.parsers)
add_output_arguments() (in module cblaster.parsers)
add_output_group() (in module cblaster.parsers)
add_plot_clusters_subparser() (in module cblaster.parsers)
add_search_subparser() (in module cblaster.parsers)
add_searching_group() (in module cblaster.parsers)
B
binary() (in module cblaster.formatters)
bitscore (cblaster.classes.Hit attribute)
C
calculate_score() (cblaster.classes.Cluster method)
cblaster.classes (module)
cblaster.formatters (module)
cblaster.genome_parsers (module)
cblaster.helpers (module)
cblaster.hmm_search (module)
cblaster.local (module)
cblaster.parsers (module)
cblaster.remote (module)
cblaster.sql (module)
check() (in module cblaster.remote)
check_pfam_db() (in module cblaster.hmm_search)
Cluster (class in cblaster.classes)
clusters (cblaster.classes.Organism attribute)
(cblaster.classes.Scaffold attribute)
copy() (cblaster.classes.Hit method)
coverage (cblaster.classes.Hit attribute)
D
diamond() (in module cblaster.local)
dict_to_cluster() (in module cblaster.helpers)
E
efetch_sequences() (in module cblaster.helpers)
end (cblaster.classes.Cluster attribute)
(cblaster.classes.Subject attribute)
evalue (cblaster.classes.Hit attribute)
F
fasta_seqrecords_to_cluster() (in module cblaster.helpers)
fetch_pfam_profiles() (in module cblaster.hmm_search)
find_fasta() (in module cblaster.genome_parsers)
find_feature() (in module cblaster.genome_parsers)
find_files() (in module cblaster.genome_parsers)
find_gene_name() (in module cblaster.genome_parsers)
find_overlapping_location() (in module cblaster.genome_parsers)
find_regions() (in module cblaster.genome_parsers)
find_sqlite_db() (in module cblaster.helpers)
find_translation() (in module cblaster.genome_parsers)
form_command() (in module cblaster.helpers)
format() (cblaster.classes.Session method)
from_dict() (cblaster.classes.Cluster class method)
(cblaster.classes.Hit class method)
(cblaster.classes.Organism class method)
(cblaster.classes.Scaffold class method)
(cblaster.classes.Serializer class method)
(cblaster.classes.Session class method)
(cblaster.classes.Subject class method)
from_file() (cblaster.classes.Session class method)
from_files() (cblaster.classes.Session class method)
from_json() (cblaster.classes.Serializer class method)
full_database_path() (in module cblaster.parsers)
full_name (cblaster.classes.Organism attribute)
full_path() (in module cblaster.parsers)
G
generate_header_string() (in module cblaster.formatters)
get_cell_values() (in module cblaster.formatters)
get_maximum_row_lengths() (in module cblaster.formatters)
get_parser() (in module cblaster.parsers)
get_pfam_accession() (in module cblaster.hmm_search)
get_profile_names() (in module cblaster.hmm_search)
get_program_path() (in module cblaster.helpers)
get_project_root() (in module cblaster.helpers)
get_sequences() (in module cblaster.helpers)
gne_summary() (in module cblaster.formatters)
group_profiles() (in module cblaster.hmm_search)
H
Hit (class in cblaster.classes)
hits (cblaster.classes.Subject attribute)
humanise() (in module cblaster.formatters)
I
identity (cblaster.classes.Hit attribute)
indices (cblaster.classes.Cluster attribute)
intermediate_end (cblaster.classes.Cluster attribute)
intermediate_genes (cblaster.classes.Cluster attribute)
intermediate_start (cblaster.classes.Cluster attribute)
ipg (cblaster.classes.Subject attribute)
iter_overlapping_features() (in module cblaster.genome_parsers)
M
max_cpus() (in module cblaster.parsers)
merge_cds_features() (in module cblaster.genome_parsers)
N
name (cblaster.classes.Organism attribute)
names (cblaster.classes.Cluster attribute)
NUMBER (cblaster.classes.Cluster attribute)
number (cblaster.classes.Cluster attribute)
O
Organism (class in cblaster.classes)
organisms (cblaster.classes.Session attribute)
organisms_to_tuples() (in module cblaster.genome_parsers)
P
params (cblaster.classes.Session attribute)
parse() (in module cblaster.local)
(in module cblaster.remote)
parse_args() (in module cblaster.parsers)
parse_cds_features() (in module cblaster.genome_parsers)
parse_file() (in module cblaster.genome_parsers)
parse_gff() (in module cblaster.genome_parsers)
parse_hmmer_output() (in module cblaster.hmm_search)
parse_infile() (in module cblaster.genome_parsers)
parse_query_sequences() (in module cblaster.helpers)
perform_hmmer() (in module cblaster.hmm_search)
poll() (in module cblaster.remote)
Q
queries (cblaster.classes.Session attribute)
query (cblaster.classes.Hit attribute)
(cblaster.classes.Session attribute)
R
read_profiles() (in module cblaster.hmm_search)
remove_subject() (cblaster.classes.Cluster method)
(cblaster.classes.Scaffold method)
retrieve() (in module cblaster.remote)
return_file_handle() (in module cblaster.genome_parsers)
run_hmmsearch() (in module cblaster.hmm_search)
S
Scaffold (class in cblaster.classes)
scaffolds (cblaster.classes.Organism attribute)
search() (in module cblaster.local)
(in module cblaster.remote)
seqrecord_to_cluster() (in module cblaster.helpers)
seqrecord_to_tuples() (in module cblaster.genome_parsers)
sequences (cblaster.classes.Cluster attribute)
(cblaster.classes.Session attribute)
sequences_to_fasta() (in module cblaster.helpers)
Serializer (class in cblaster.classes)
Session (class in cblaster.classes)
set_decimals() (in module cblaster.formatters)
start (cblaster.classes.Cluster attribute)
(cblaster.classes.Subject attribute)
start() (in module cblaster.remote)
strain (cblaster.classes.Organism attribute)
strand (cblaster.classes.Subject attribute)
subject (cblaster.classes.Hit attribute)
Subject (class in cblaster.classes)
subjects (cblaster.classes.Cluster attribute)
(cblaster.classes.Scaffold attribute)
summarise_cluster() (in module cblaster.formatters)
summarise_gne() (in module cblaster.formatters)
summarise_organism() (in module cblaster.formatters)
summarise_scaffold() (in module cblaster.formatters)
summary() (cblaster.classes.Organism method)
(cblaster.classes.Scaffold method)
(in module cblaster.formatters)
T
to_dict() (cblaster.classes.Cluster method)
(cblaster.classes.Hit method)
(cblaster.classes.Organism method)
(cblaster.classes.Scaffold method)
(cblaster.classes.Serializer method)
(cblaster.classes.Session method)
(cblaster.classes.Subject method)
to_json() (cblaster.classes.Serializer method)
total_hit_clusters (cblaster.classes.Organism attribute)
V
values() (cblaster.classes.Hit method)
(cblaster.classes.Subject method)
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