add a command line argument to extract part of hdf5 files

doc/source/generating_joint_analysis.rst

@@ -35,16 +35,22 @@ By default, all the traits will have the same weight.
 
 If the user wishes to, she/he can specify a vector of weight by using the --custom-loadings option.
 
-Access HDFStore components
---------------------------
+Extract HDFStore components to tsv files
+----------------------------------------
 
-To access each table of the HDFStore you can use `pandas read_hdf functions <https://pandas.pydata.org/docs/reference/api/pandas.read_hdf.html>`_ :
+Each table of the HDFStore is accessible through the command line tool `jass extract-tsv` (see command line reference for complete details).
+
+.. code-block:: shell
+
+  jass extract-tsv --hdf5-table-path ./initTable.hdf5 --tsv-path './test_extract.tsv' --table-key SumStatTab
+
+alternately, you can use directly `pandas read_hdf functions <https://pandas.pydata.org/docs/reference/api/pandas.read_hdf.html>`_ :
 
 For instance if you want to access the Regions table :
 
 .. code-block:: python
 
-   pd.read_hdf("WK_test.hdf5", "Regions")
+  pd.read_hdf("WK_test.hdf5", "Regions")
 
 Note that is you wish that the SumStatTab table to be saved as a csv file you can provide the command lines
 with the --csv-file-path option and a csv will be generated as well. Outputting a csv while lengthen execution
@@ -54,5 +60,7 @@ Command Line example
 --------------------
 
 See command line usage for details
+
 .. code-block:: shell
+
   jass create-project-data --init-table-path init_table/init_table_EUR_not_imputed.hdf5 --phenotype z_MAGIC_GLUCOSE-TOLERANCE z_MAGIC_FAST-GLUCOSE z_MAGIC_FAST-INSULIN z_MAGIC_HBA1C --worktable-path ./work_glycemic.hdf5 --manhattan-plot-path ./manhattan_glycemic.png --quadrant-plot-path ./quadrant_glycemic.png