BioProv
stable
Contents:
BioProv - W3C-PROV provenance documents for bioinformatics
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Installation
Dependencies
Source API
BioProv
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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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J
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K
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L
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M
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N
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P
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Q
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R
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T
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U
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V
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W
_
__init__() (bioprov.bioprov.CommandOptionsParser method)
(bioprov.src.config.BioProvDB method)
(bioprov.src.config.Config method)
(bioprov.src.config.Environment method)
(bioprov.src.files.Directory method)
(bioprov.src.files.File method)
(bioprov.src.files.SeqFile method)
(bioprov.src.files.SeqStats method)
(bioprov.src.main.Parameter method)
(bioprov.src.main.PresetProgram method)
(bioprov.src.main.Program method)
(bioprov.src.main.Project method)
(bioprov.src.main.Run method)
(bioprov.src.main.Sample method)
(bioprov.src.prov.BioProvDocument method)
(bioprov.src.workflow.Step method)
(bioprov.src.workflow.Workflow method)
(bioprov.utils.Warnings method)
(bioprov.workflows.workflows.KaijuWorkflow method)
(bioprov.workflows.workflows.WorkflowOptionsParser method)
A
actedOnBehalfOf (bioprov.src.config.Environment property)
add_files() (bioprov.src.main.Project method)
(bioprov.src.main.Sample method)
add_files_to_object() (bioprov.src.files.Directory method)
add_parameter() (bioprov.src.main.Program method)
add_programs() (bioprov.src.main.Project method)
(bioprov.src.main.Sample method)
add_runs() (bioprov.src.main.Program method)
add_step() (bioprov.src.workflow.Workflow method)
assert_tax_rank() (in module bioprov.utils)
auto_update_db() (bioprov.src.main.Project method)
(bioprov.src.main.Sample method)
B
bioprov
module
bioprov.bioprov
module
bioprov.data
module
bioprov.programs
module
bioprov.programs.programs
module
bioprov.src
module
bioprov.src.config
module
bioprov.src.files
module
bioprov.src.main
module
bioprov.src.prov
module
bioprov.src.workflow
module
bioprov.tests
module
bioprov.tests.test_bioprov_imports
module
bioprov.tests.test_bioprov_integration
module
bioprov.tests.test_bioprov_programs
module
bioprov.tests.test_bioprov_workflows
module
bioprov.tests.test_src_config
module
bioprov.tests.test_src_file
module
bioprov.tests.test_src_main
module
bioprov.tests.test_src_prov
module
bioprov.utils
module
bioprov.workflows.blastn_alignment
module
bioprov.workflows.genome_annotation
module
bioprov.workflows.KaijuWorkflow
module
bioprov.workflows.WorkflowOptionsParser
module
bioprov.workflows.workflows
module
BioProvDB (class in bioprov.src.config)
bioprovdocument (bioprov.src.workflow.Workflow property)
BioProvDocument (class in bioprov.src.prov)
blastn() (in module bioprov.programs.programs)
blastn_alignment() (in module bioprov.workflows.workflows)
blastp() (in module bioprov.programs.programs)
build_prov_attributes() (in module bioprov.utils)
build_sample_dict() (bioprov.src.main.Project method)
bundle (bioprov.src.main.Project property)
C
calculate_N50() (in module bioprov.src.files)
clear_db() (bioprov.bioprov.CommandOptionsParser class method)
(bioprov.src.config.BioProvDB method)
(bioprov.src.config.Config method)
CommandOptionsParser (class in bioprov.bioprov)
Config (class in bioprov.src.config)
convert_bytes() (in module bioprov.utils)
create_func() (bioprov.src.main.PresetProgram method)
create_logger() (in module bioprov.utils)
create_provenance() (bioprov.src.workflow.Workflow method)
create_provstore() (bioprov.bioprov.CommandOptionsParser class method)
create_provstore_file() (bioprov.src.config.Config method)
create_sample() (in module bioprov.tests.test_src_main)
D
db (bioprov.src.config.Config property)
db_all() (bioprov.src.config.Config method)
db_path (bioprov.src.config.Config property)
description (bioprov.workflows.workflows.KaijuWorkflow attribute)
deserialize_files_dict() (in module bioprov.src.files)
deserialize_programs_dict() (in module bioprov.src.main)
deserialize_runs_dict() (in module bioprov.src.main)
diamond() (in module bioprov.programs.programs)
dict_to_sample() (in module bioprov.src.main)
dict_to_sha256() (in module bioprov.utils)
dict_to_string() (in module bioprov.utils)
directory (bioprov.src.main.Sample property)
Directory (class in bioprov.src.files)
dot (bioprov.src.prov.BioProvDocument property)
duration (bioprov.src.main.Program property)
E
end_time (bioprov.src.main.Program property)
entity (bioprov.src.files.File property)
(bioprov.src.main.Project property)
Environment (class in bioprov.src.config)
exists (bioprov.src.files.Directory property)
(bioprov.src.files.File property)
F
fasttree() (in module bioprov.programs.programs)
File (class in bioprov.src.files)
file_to_sha256() (in module bioprov.utils)
finished (bioprov.src.main.Program property)
from_df() (in module bioprov.src.main)
from_json() (in module bioprov.src.main)
G
GC (bioprov.src.files.SeqStats attribute)
generate_cmd() (bioprov.src.main.PresetProgram method)
(bioprov.src.main.Program method)
generate_param_str() (in module bioprov.src.main)
generate_parser() (bioprov.src.workflow.Workflow method)
generate_project() (bioprov.src.workflow.Workflow method)
generator (bioprov.src.files.SeqFile property)
genome_annotation() (in module bioprov.workflows.workflows)
get_files() (bioprov.src.files.Directory method)
get_size() (in module bioprov.utils)
get_subdirs() (bioprov.src.files.Directory method)
H
has_serializer() (in module bioprov.utils)
I
import_records() (bioprov.src.files.SeqFile method)
is_iterator() (bioprov.src.main.Project static method)
is_sample_and_name() (bioprov.src.main.Project static method)
is_serializable_type() (in module bioprov.utils)
items() (bioprov.src.main.Project method)
J
json_to_dict() (in module bioprov.src.main)
K
kaiju() (in module bioprov.programs.programs)
kaiju2table() (in module bioprov.programs.programs)
KaijuWorkflow (class in bioprov.workflows.workflows)
kallisto_quant() (in module bioprov.programs.programs)
keys() (bioprov.src.main.Project method)
L
list() (bioprov.bioprov.CommandOptionsParser class method)
load_project() (in module bioprov.src.main)
logger (bioprov.src.config.Config property)
M
mafft() (in module bioprov.programs.programs)
main() (bioprov.workflows.workflows.KaijuWorkflow static method)
(in module bioprov.bioprov)
max_bp (bioprov.src.files.SeqStats attribute)
max_seq (bioprov.src.files.SeqFile property)
mean_bp (bioprov.src.files.SeqStats attribute)
min_bp (bioprov.src.files.SeqStats attribute)
min_seq (bioprov.src.files.SeqFile property)
module
bioprov
bioprov.bioprov
bioprov.data
bioprov.programs
bioprov.programs.programs
bioprov.src
bioprov.src.config
bioprov.src.files
bioprov.src.main
bioprov.src.prov
bioprov.src.workflow
bioprov.tests
bioprov.tests.test_bioprov_imports
bioprov.tests.test_bioprov_integration
bioprov.tests.test_bioprov_programs
bioprov.tests.test_bioprov_workflows
bioprov.tests.test_src_config
bioprov.tests.test_src_file
bioprov.tests.test_src_main
bioprov.tests.test_src_prov
bioprov.utils
bioprov.workflows.blastn_alignment
bioprov.workflows.genome_annotation
bioprov.workflows.KaijuWorkflow
bioprov.workflows.WorkflowOptionsParser
bioprov.workflows.workflows
muscle() (in module bioprov.programs.programs)
N
N50 (bioprov.src.files.SeqStats attribute)
name (bioprov.src.main.Project property)
namespace_preffix (bioprov.src.main.Project property)
number_seqs (bioprov.src.files.SeqStats attribute)
P
Parameter (class in bioprov.src.main)
parse_options() (bioprov.workflows.workflows.WorkflowOptionsParser method)
parse_params() (in module bioprov.src.main)
parser() (bioprov.workflows.workflows.KaijuWorkflow class method)
parser_help() (in module bioprov.utils)
pattern_replacer() (in module bioprov.utils)
PresetProgram (class in bioprov.src.main)
prodigal() (in module bioprov.programs.programs)
Program (class in bioprov.src.main)
Project (class in bioprov.src.main)
prokka() (in module bioprov.programs.programs)
prokka_() (in module bioprov.programs.programs)
provn (bioprov.src.prov.BioProvDocument property)
provstore_api (bioprov.src.config.Config property)
provstore_document (bioprov.src.prov.BioProvDocument property)
provstore_file (bioprov.src.config.Config property)
provstore_token (bioprov.src.config.Config property)
provstore_user (bioprov.src.config.Config property)
Q
query_db() (bioprov.src.main.Project method)
R
raw_size (bioprov.src.files.File property)
read_csv() (in module bioprov.src.main)
read_provstore_file() (bioprov.src.config.Config method)
replace_path() (bioprov.src.files.Directory method)
(bioprov.src.files.File method)
replace_paths() (bioprov.src.main.Project method)
Run (class in bioprov.src.main)
run() (bioprov.src.main.PresetProgram method)
(bioprov.src.main.Program method)
(bioprov.src.main.Run method)
run_programs() (bioprov.src.main.Project method)
(bioprov.src.main.Sample method)
run_steps() (bioprov.src.workflow.Workflow method)
runs (bioprov.src.main.Program property)
S
Sample (class in bioprov.src.main)
samples (bioprov.src.main.Project property)
SeqFile (class in bioprov.src.files)
seqfile_formats (bioprov.src.files.SeqFile attribute)
seqrecordgenerator() (in module bioprov.src.files)
seqstats (bioprov.src.files.SeqFile property)
SeqStats (class in bioprov.src.files)
serializer() (bioprov.src.config.Config method)
(bioprov.src.config.Environment method)
(bioprov.src.files.Directory method)
(bioprov.src.files.File method)
(bioprov.src.files.SeqFile method)
(bioprov.src.main.Parameter method)
(bioprov.src.main.Program method)
(bioprov.src.main.Project method)
(bioprov.src.main.Run method)
(bioprov.src.main.Sample method)
(in module bioprov.utils)
serializer_filter() (in module bioprov.utils)
sha256 (bioprov.src.files.File property)
(bioprov.src.main.Project property)
show_config() (bioprov.bioprov.CommandOptionsParser class method)
show_db() (bioprov.bioprov.CommandOptionsParser class method)
show_provstore() (bioprov.bioprov.CommandOptionsParser class method)
size (bioprov.src.files.File property)
start_logging() (bioprov.src.main.Project method)
(bioprov.src.workflow.Workflow method)
start_time (bioprov.src.main.Program property)
status (bioprov.src.main.Program property)
(bioprov.src.main.Run property)
stderr (bioprov.src.main.Program property)
stdin (bioprov.src.main.Program property)
stdout (bioprov.src.main.Program property)
Step (class in bioprov.src.workflow)
T
test_BioProvDB() (in module bioprov.tests.test_src_config)
test_BioProvDocument() (in module bioprov.tests.test_src_prov)
test_blastn() (in module bioprov.tests.test_bioprov_programs)
test_blastn_workflow() (in module bioprov.tests.test_bioprov_workflows)
test_blastp() (in module bioprov.tests.test_bioprov_programs)
test_CLI() (in module bioprov.tests.test_bioprov_integration)
test_Config() (in module bioprov.tests.test_src_config)
test_diamond() (in module bioprov.tests.test_bioprov_programs)
test_empty_runs_attr() (in module bioprov.tests.test_src_main)
test_EnvProv() (in module bioprov.tests.test_src_prov)
test_fasttree() (in module bioprov.tests.test_bioprov_programs)
test_File_and_Directory() (in module bioprov.tests.test_src_file)
test_from_df() (in module bioprov.tests.test_src_main)
test_generate_param_str() (in module bioprov.tests.test_src_main)
test_genome_annotation() (in module bioprov.tests.test_bioprov_workflows)
test_import_bioprov() (in module bioprov.tests.test_bioprov_imports)
test_import_classes_and_functions() (in module bioprov.tests.test_bioprov_imports)
test_import_packages() (in module bioprov.tests.test_bioprov_imports)
test_integration() (in module bioprov.tests.test_bioprov_integration)
test_json_Sample() (in module bioprov.tests.test_src_main)
test_kaiju() (in module bioprov.tests.test_bioprov_programs)
test_kaiju2table() (in module bioprov.tests.test_bioprov_programs)
test_kaiju_workflow() (in module bioprov.tests.test_bioprov_workflows)
test_kallisto() (in module bioprov.tests.test_bioprov_programs)
test_mafft() (in module bioprov.tests.test_bioprov_programs)
test_muscle() (in module bioprov.tests.test_bioprov_programs)
test_Parameter() (in module bioprov.tests.test_src_main)
test_parse_params() (in module bioprov.tests.test_src_main)
test_preset_extra_flags() (in module bioprov.tests.test_src_main)
test_prodigal() (in module bioprov.tests.test_bioprov_programs)
test_Program() (in module bioprov.tests.test_src_main)
test_Project() (in module bioprov.tests.test_src_main)
test_project_json_and_prov() (in module bioprov.tests.test_src_main)
test_prokka() (in module bioprov.tests.test_bioprov_programs)
test_Run() (in module bioprov.tests.test_src_main)
test_Sample() (in module bioprov.tests.test_src_main)
test_SeqFile() (in module bioprov.tests.test_src_file)
to_csv() (bioprov.src.main.Project method)
to_df() (bioprov.src.main.Project method)
to_json() (bioprov.src.main.Project method)
(bioprov.src.main.Sample method)
(in module bioprov.src.main)
to_series() (bioprov.src.main.Sample method)
total_bps (bioprov.src.files.SeqStats attribute)
U
update() (bioprov.src.config.Environment method)
update_db() (bioprov.src.main.Project method)
upload_to_provstore() (bioprov.src.prov.BioProvDocument method)
V
validate_program() (bioprov.src.main.PresetProgram method)
validate_sample() (bioprov.src.main.PresetProgram method)
values() (bioprov.src.main.Project method)
version() (bioprov.bioprov.CommandOptionsParser class method)
W
Warnings (class in bioprov.utils)
Workflow (class in bioprov.src.workflow)
WorkflowOptionsParser (class in bioprov.workflows.workflows)
write_json() (in module bioprov.src.main)
write_provn() (bioprov.src.prov.BioProvDocument method)
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