Workflow description:
Overview of components:
Overview datasets:
Project: nmdc-proteomics-workflow
Meta-Proteomics Workflow
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C
check_url() (src.data_access.via_DMS.FileOperations.FileOperations method)
cleansequence() (src.analysis.internalAnalysis.downStreamAnalysis method)
Config (class in src.data_access.via_DMS.secure)
consolidate_syn_files() (src.processing.MSGFplusMerger.MSGFplusMerger method)
create_dir() (src.data_access.via_DMS.FileOperations.FileOperations method)
current_local_datetime() (in module utility.utils)
current_UTC_datetime() (in module utility.utils)
D
DATASET (src.data_access.via_DMS.Query.Query attribute)
DATASET_MASIC (src.data_access.via_DMS.Query.Query attribute)
DATASET_MSFG (src.data_access.via_DMS.Query.Query attribute)
DatasetsMerger (class in src.processing.DatasetsMerger)
db_name (src.data_access.via_DMS.secure.Config attribute)
db_password (src.data_access.via_DMS.secure.Config attribute)
db_server (src.data_access.via_DMS.secure.Config attribute)
db_user (src.data_access.via_DMS.secure.Config attribute)
DMSDatabase (class in src.data_access.via_DMS.DMSDatabase)
download_data_from_DMS() (src.Workflow.Workflow method)
download_fasta_param_files() (src.data_access.via_DMS.FileOperations.FileOperations method)
download_masic_jobs() (src.data_access.via_DMS.FileOperations.FileOperations method)
download_msgf_jobs() (src.data_access.via_DMS.FileOperations.FileOperations method)
download_over_http() (src.data_access.via_DMS.FileOperations.FileOperations method)
download_raw_files() (src.data_access.via_DMS.FileOperations.FileOperations method)
downStreamAnalysis (class in src.analysis.internalAnalysis)
E
execute() (src.data_access.via_DMS.QueryBuilder.QueryBuilder method)
F
FileOperations (class in src.data_access.via_DMS.FileOperations)
fill_holes() (src.processing.MSGFplusMerger.MSGFplusMerger method)
findproteinname() (src.analysis.internalAnalysis.downStreamAnalysis method)
G
get_files() (src.data_access.via_DMS.FileOperations.FileOperations method)
get_protein_info() (src.processing.MSGFplusMerger.MSGFplusMerger method)
group_files() (src.processing.MSGFplusMerger.MSGFplusMerger method)
I
improve_FDR() (src.processing.MSGFplusMerger.MSGFplusMerger method)
Input (class in src.data_access.via_DMS.Input)
J
JOB_INFO (src.data_access.via_DMS.Query.Query attribute)
K
keep_best_scoring_peptide() (src.processing.MSGFplusMerger.MSGFplusMerger method)
M
MASIC_loc (src.data_access.via_DMS.Query.Query attribute)
MASICmerger (class in src.processing.MASICmerger)
merge_all_jobs_in_UserInput() (src.processing.DatasetsMerger.DatasetsMerger method)
merge_msgfplus_msaic() (src.processing.MASICmerger.MASICmerger method)
module
src.analysis.internalAnalysis
src.data_access.via_DMS.DMSDatabase
src.data_access.via_DMS.FileOperations
src.data_access.via_DMS.Input
src.data_access.via_DMS.Query
src.data_access.via_DMS.QueryBuilder
src.data_access.via_DMS.secure
src.processing.DatasetsMerger
src.processing.MASICmerger
src.processing.MSGFplusMerger
src.Workflow
utility.utils
MSGF (src.data_access.via_DMS.Query.Query attribute)
MSGF_loc (src.data_access.via_DMS.Query.Query attribute)
MSGFplusMerger (class in src.processing.MSGFplusMerger)
O
open_connection() (src.data_access.via_DMS.DMSDatabase.DMSDatabase method)
other_input() (src.data_access.via_DMS.Input.Input method)
P
parameter_optimization() (in module src.analysis.internalAnalysis)
parse_fileserverpath_to_web_url() (src.data_access.via_DMS.FileOperations.FileOperations method)
process_data() (src.analysis.internalAnalysis.downStreamAnalysis method)
Q
Query (class in src.data_access.via_DMS.Query)
QueryBuilder (class in src.data_access.via_DMS.QueryBuilder)
R
run_Analysis() (src.Workflow.Workflow method)
run_query() (src.data_access.via_DMS.DMSDatabase.DMSDatabase method)
S
save_to_disk() (src.data_access.via_DMS.QueryBuilder.QueryBuilder method)
src.analysis.internalAnalysis
module
src.data_access.via_DMS.DMSDatabase
module
src.data_access.via_DMS.FileOperations
module
src.data_access.via_DMS.Input
module
src.data_access.via_DMS.Query
module
src.data_access.via_DMS.QueryBuilder
module
src.data_access.via_DMS.secure
module
src.processing.DatasetsMerger
module
src.processing.MASICmerger
module
src.processing.MSGFplusMerger
module
src.Workflow
module
stack_files() (src.processing.MSGFplusMerger.MSGFplusMerger method)
start_downStreamAnalysis() (src.Workflow.Workflow method)
start_merging() (src.Workflow.Workflow method)
start_with_datapackage_id() (src.data_access.via_DMS.QueryBuilder.QueryBuilder method)
start_with_dataset_ids() (src.data_access.via_DMS.QueryBuilder.QueryBuilder method)
start_with_job_nums() (src.data_access.via_DMS.QueryBuilder.QueryBuilder method)
start_workflow() (src.Workflow.Workflow method)
str2bool() (in module utility.utils)
T
tackle_Unique_Seq_ID_holes_() (src.processing.MSGFplusMerger.MSGFplusMerger method)
timeit() (in module utility.utils)
U
use_df() (src.data_access.via_DMS.FileOperations.FileOperations method)
user_input() (src.data_access.via_DMS.Input.Input method)
utility.utils
module
W
Workflow (class in src.Workflow)
write_to_disk() (src.data_access.via_DMS.FileOperations.FileOperations method)
(src.processing.MSGFplusMerger.MSGFplusMerger method)
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