hapsburg.PackagesSupport.parallel_runs.helper_functions
=======================================================

.. py:module:: hapsburg.PackagesSupport.parallel_runs.helper_functions

.. autoapi-nested-parse::

   Helper Functions for Notebook Runs on Cluster
   @ Author: Harald Ringbauer, 2019



Functions
---------

.. autoapisummary::

   hapsburg.PackagesSupport.parallel_runs.helper_functions.prepare_path
   hapsburg.PackagesSupport.parallel_runs.helper_functions.multi_run
   hapsburg.PackagesSupport.parallel_runs.helper_functions.split_up_roh_df
   hapsburg.PackagesSupport.parallel_runs.helper_functions.get_sep_from_extension
   hapsburg.PackagesSupport.parallel_runs.helper_functions.combine_individual_data
   hapsburg.PackagesSupport.parallel_runs.helper_functions.move_X_to_parent_folder
   hapsburg.PackagesSupport.parallel_runs.helper_functions.create_folders
   hapsburg.PackagesSupport.parallel_runs.helper_functions.split_up_inferred_roh
   hapsburg.PackagesSupport.parallel_runs.helper_functions.postprocess_iid


Module Contents
---------------

.. py:function:: prepare_path(base_path, iid, ch, prefix_out, logfile=True)

   Prepare the path and pipe printing for one Individual.
   Create Path if not already existing.
   logfile: Whether to pipe output to log-file


.. py:function:: multi_run(fun, prms, processes=4, output=False)

   Implementation of running in Parallel.
   fun: Function
   prms: The Parameter Files
   processes: How many Processes to use


.. py:function:: split_up_roh_df(base_path, path_out, iid, file_in='roh_info.csv', file_out='roh_gt.csv')

   Splits up the ROH-dataframe from base_path/file_in into file_out.
   Picks out Individual iid. Done to pass on "ground truth"
   base_path: Where to find roh_info.csv
   path_out: Where to save roh_gt to
   iid: Which Individual to extract from roh_info.csv.


.. py:function:: get_sep_from_extension(path)

   Get Seperator for csv/tsv from file extensions.
   Either comma or tab. Return delimiter


.. py:function:: combine_individual_data(base_path, iid, delete=False, chs=range(1, 23), prefix_out='', file='roh.csv', file_result='_roh_full.csv')

   Function to merge data from one Individual Analysis (all Chromosome)
   chs: Which Chromosomes to combine"
   file: Which files to combine. Either roh or ibd.csv
   delete: Whether to delete individual folder and contents after combining.


.. py:function:: move_X_to_parent_folder(base_path, iid, delete=False, ch=23, prefix_out='', file_result='_roh_full.csv')

   Take ROH result table from X folder, and move it to parent folder.
   Delete the original result folder


.. py:function:: create_folders(input_base_folder, outfolder='plink_out/')

   Create Folders for ROH analysis with Plink/BCFTOOLs.
   Operates within HAPSBURG Mosaic Data Structure. Return
   h5 path, vcf path, and folder for intermediary output


.. py:function:: split_up_inferred_roh(df_t, iid, save_path)

   Extract only ROH from Individual iid and saves it to save_path


.. py:function:: postprocess_iid(df_plink, input_base_folder, iids, ch=3, prefix_out='')

   Split up results into roh.csv and roh_gt.csv for each IID.
   df_plink: Data Frame with Plink results, formated correctly