FEAT #96

doc/source/data_import.rst

@@ -106,10 +106,26 @@ Creation of the JASS inittable
 Once, GWAS summary statistics are harmonized, they are integrated into
 one file by the using jass command (see detail in command line usage)
 
-```
-jass create-inittable --input-data-path '$GWAS_files_glob_pattern' --init-covariance-path $path_to_covariance_file  --regions-map-path $path_to_LD_regions --description-file-path $path_to_gwas_meta_data.csv --init-table-path $path_to_output_inittable
+.. code-block:: shell
+
+	jass create-inittable --input-data-path '$GWAS_files_glob_pattern' --init-covariance-path $path_to_covariance_file  --regions-map-path $path_to_LD_regions --description-file-path $path_to_gwas_meta_data.csv --init-table-path $path_to_output_inittable
+
+Add genes and exons annotation to initTable (optional)
+------------------------------------------------------
+If you want to avoid a (non-blocking) error in the JASS web interface when performing a local analysis on a region of the genome, 
+you must add the genes and exons to the InitTable
+
+To do this, you need to download the file: RefSeq Reference Genome Annotation GRCh37 from the website: https://www.ncbi.nlm.nih.gov/genome/guide/human/ 
+before unzipping it on your computer and saving it in the JASS_DATA_DIR folder. Then you can run in a terminal the following command:
+
+.. code-block:: shell
+
+	jass add-gene-annotation --gene-data-path GRCh37_latest_genomic.gff --init-table-path $path_to_initTable.hdf5 --gene-csv-path df_gene.csv --exon-csv-path df_exon.csv
 
-```
+.. warning::
+	For this command, it is necessary to specify the full path of initTable.hdf5 even if this file is in the JASS_DATA_DIR folder. You can use the environment variable $JASS_DATA_DIR (Linux) or %JASS_DATA_DIR% (Windows) 
 
+The advantage of adding genes and exons in the initTable is to have an additional graph in the web page of the results of the local analysis: 
+the position of genes and exons in the studied genomic region (see paragraph: **web usage, section B - Analysis by region**)
 
 .. bibliography:: reference.bib