Package: src

• Package : analysis
  • Module : ficusAnalysis
  • Module : internalAnalysis
• Package : data_access
  • Package : data_prepare
    • Module : parseFasta
  • Package : via_DMS
    • Module : DMSDatabase
    • Module : FileOperations
    • Module : Input
    • Module : Query
    • Module : QueryBuilder
    • Module : secure
• Package : processing
  • Module : DatasetsMerger
  • Module : MASICmerger
  • Module : MSGFplusMerger

Module : MetProWorkflowApp

usage: MetProWorkflowApp.py [-h] [-M MODE] [-It {1,2,3}] [-S STORAGE]
                            [-P [PROJECTNAME]] [-I INPUT]
                            [-C [COMBINEDATASETS]] [-Sa {internal,ficus,both}]

Named Arguments

-M, --Mode

Different Modes to run the workflow?

Developer : Automatically generates files at each step! User : Generates CrossTab/Metric only!

-It, --InputType

Possible choices: 1, 2, 3

Type of input 1 : a datapackage ID 2 : a list of dataset IDs 3 : a list of MSGFjobs Nums

-S, --Storage

Path to store data & results of the pipeline.

-P, --ProjectName

FICUS Study name Eg. hess/stegen/blanchard etc.

-I, --Input

A valid input InputType: 1, An Integer InputType: 2, A comma-seperated list of Integers InputType: 3, A comma-seperated list of Integers

-C, --CombineDatasets

Combine all dataset’s MSGF & MASIC jobs to single file for generating crossTabs.

Default: False

-Sa, --SelectAnalysis

Possible choices: internal, ficus, both

internal : Run internal analysis ficus : Run ficus analysis both : Run both analysis

Module : Workflow

class src.Workflow.Workflow(mode=None, InputType=None, path_to_data=None, project_name=None, UserInput=None, CombineDatasets=None, SelectAnalysis=None)

Bases: object

Automate the Meta-proteomics workflow

run_Analysis(on_file, analysis_type)

Run desired analysis on a file. :meta public: :param analysis_type: :return:

start_downStreamAnalysis(result_path)

Decides to run analysis on combined results vs single dataset. :meta public: :param result_path: :return:

start_merging(folder)

Start merging MSGF and MASIC jobs :meta public: :param folder: :return:

download_data_from_DMS(user_obj)

build & execute query to dowload data from DMS :meta public: :param user_obj: input from shell script. :return: path to !!

start_workflow()

Runs the workflow in 3 stages 1. Download relevant datasets from specified source. 2. Aggregation of analysis tools{MSGF+, MASIC} results: to extract useful data from datasets. 3. Generation of experimental report. :meta public: :return: