Index

_

__annotations__ (specimen.classes.reports.SpecimenModelInfoReport attribute) __init__() (specimen.classes.reports.SpecimenModelInfoReport method)

__module__ (specimen.classes.reports.SpecimenModelInfoReport attribute) __orig_bases__ (specimen.classes.reports.SpecimenModelInfoReport attribute)

B

bdbp_diamond() (in module specimen.hqtb.core.bidirectional_blast)

build_data_directories() (in module specimen.util.set_up)

C

check_unchanged() (in module specimen.hqtb.core.generate_draft_model) CMPB_CONFIG_PATHS_REQUIRED (in module specimen.util.set_up)

create_diamond_db() (in module specimen.hqtb.core.bidirectional_blast) create_DIAMOND_db_from_folder() (in module specimen.util.util) create_NCBIinfo_mapping() (in module specimen.util.util)

D

download_config() (in module specimen.util.set_up)

E

edit_template_identifiers() (in module specimen.hqtb.core.generate_draft_model)

extract_bestbdbp_hits() (in module specimen.hqtb.core.bidirectional_blast) extract_cds() (in module specimen.hqtb.core.bidirectional_blast)

F

format_table() (specimen.classes.reports.SpecimenModelInfoReport method)

G

gen_draft_model() (in module specimen.hqtb.core.generate_draft_model)

H

HQTB_CONFIG_PATH_OPTIONAL (in module specimen.util.set_up)

HQTB_CONFIG_PATH_REQUIRED (in module specimen.util.set_up)

M

module specimen.classes.reports specimen.cmd_access specimen.cmpb.workflow specimen.hqtb.core.analysis specimen.hqtb.core.bidirectional_blast specimen.hqtb.core.generate_draft_model specimen.hqtb.core.refinement.cleanup specimen.hqtb.core.validation specimen.hqtb.workflow specimen.util.set_up specimen.util.util

P

pid_filter() (in module specimen.hqtb.core.generate_draft_model)

PIPELINE_PATHS_OPTIONAL (in module specimen.util.set_up) PIPELINE_PATHS_REQUIRED (in module specimen.util.set_up)

R

remove_absent_genes() (in module specimen.hqtb.core.generate_draft_model) rename_found_homologs() (in module specimen.hqtb.core.generate_draft_model) run() (in module specimen.cmpb.workflow) (in module specimen.hqtb.core.analysis) (in module specimen.hqtb.core.bidirectional_blast) (in module specimen.hqtb.core.generate_draft_model) (in module specimen.hqtb.core.validation) (in module specimen.hqtb.workflow)

run_diamond_blastp() (in module specimen.hqtb.core.bidirectional_blast)

S

save() (specimen.classes.reports.SpecimenModelInfoReport method) save_cmpb_user_input() (in module specimen.util.set_up) specimen.classes.reports module specimen.cmd_access module specimen.cmpb.workflow module specimen.hqtb.core.analysis module specimen.hqtb.core.bidirectional_blast module

specimen.hqtb.core.generate_draft_model module specimen.hqtb.core.refinement.cleanup module specimen.hqtb.core.validation module specimen.hqtb.workflow module specimen.util.set_up module specimen.util.util module SpecimenModelInfoReport (class in specimen.classes.reports)

V

validate_config() (in module specimen.util.set_up)

visualise() (specimen.classes.reports.SpecimenModelInfoReport method)

W

wrapper() (in module specimen.cmpb.workflow) (in module specimen.hqtb.workflow)