create_case_lists

genie.create_case_lists

Creates case lists per cancer type

Attributes

CASE_LIST_TEXT_TEMPLATE = 'cancer_study_identifier: {study_id}\nstable_id: {stable_id}\ncase_list_name: {case_list_name}\ncase_list_description: {case_list_description}\ncase_list_ids: {case_list_ids}' module-attribute

Functions

create_case_lists_map(clinical_file_name)

Creates the case list dictionary

PARAMETER	DESCRIPTION
clinical_file_name	clinical file path

RETURNS	DESCRIPTION
dict	key = cancer_type value = list of sample ids
dict	key = seq_assay_id value = list of sample ids
list	Clinical samples

_write_single_oncotree_case_list(cancer_type, ids, study_id, output_directory)

Writes one oncotree case list. Python verisons below 3.6 will sort the dictionary keys which causes tests to fail

PARAMETER	DESCRIPTION
cancer_type	Oncotree code cancer type
ids	GENIE sample ids
study_id	cBioPortal study id
output_directory	case list output directory

RETURNS	DESCRIPTION
	case list file path

write_case_list_files(clinical_file_map, output_directory, study_id)

Writes the cancer_type case list file to case_lists directory

PARAMETER	DESCRIPTION
clinical_file_map	cancer type to sample id mapping from create_case_lists_map
output_directory	Directory to write case lists
study_id	cBioPortal study id

RETURNS	DESCRIPTION
list	oncotree code case list files

create_sequenced_samples(seq_assay_map, assay_info_file_name)

Gets samples sequenced

PARAMETER	DESCRIPTION
seq_assay_map	dictionary containing lists of samples per seq_assay_id
assay_info_file_name	Assay information name

RETURNS	DESCRIPTION
	lists of cna and sv samples

write_case_list_sequenced(clinical_samples, output_directory, study_id)

Writes the genie sequenced and all samples. Since all samples are sequenced, _all and _sequenced are equal

PARAMETER	DESCRIPTION
clinical_samples	List of clinical samples
output_directory	Directory to write case lists
study_id	cBioPortal study id

RETURNS	DESCRIPTION
list	case list sequenced and all

write_case_list_cna(cna_samples, output_directory, study_id)

Writes the cna sequenced samples

PARAMETER	DESCRIPTION
cna_samples	List of cna samples
output_directory	Directory to write case lists
study_id	cBioPortal study id

RETURNS	DESCRIPTION
	cna caselist path

write_case_list_sv(samples, output_directory, study_id)

Writes the structural variant (sv) sequenced samples

PARAMETER	DESCRIPTION
samples	List of sv samples TYPE: list
output_directory (str	Directory to write case lists
study_id	cBioPortal study id TYPE: str

RETURNS	DESCRIPTION
str	sv caselist path TYPE: str

write_case_list_cnaseq(cna_samples, output_directory, study_id)

writes both cna and mutation samples (Just _cna file for now)

PARAMETER	DESCRIPTION
cna_samples	List of cna samples
output_directory	Directory to write case lists
study_id	cBioPortal study id

RETURNS	DESCRIPTION
	cnaseq path

main(clinical_file_name, assay_info_file_name, output_directory, study_id)

Gets clinical file and gene matrix file and processes it to obtain case list files

PARAMETER	DESCRIPTION
clinical_file_name	Clinical file path
assay_info_file_name	Assay information name
output_directory	Output directory of case list files
study_id	cBioPortal study id