Docs update for the custom frequency file.

docs/introduction.rst

@@ -85,8 +85,8 @@ line of the file should contain a mutation (e.g. D136R) or combination
 of mutations separated by colons and ordered according to their
 positions in the sequence (e.g. D136R,V271A).
 
-Running the prescott program
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Running the prescott program with gnomAD frequency data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 A quick help can be accessed by typing
 
@@ -117,6 +117,39 @@ variants are affected by population information.
 
 Please note that the example input files of MLH1 protein for prescott acalculations are in the data directory of this repository.
 
+
+Running the prescott program with custom frequency data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+What if you have your own frequencies for a set of missense mutations that you or another researcher measured?
+prescott module can do calculations with custom frequency files as well. The first step is to prepare a plain text file with ".txt" extension. 
+Note: Saving the custom frequency file with .txt extension is very important to distinguish it from gnomad .csv extension. 
+
+You must have two columns separated by a space character for each missense mutation in a custom frequency file. The first column is the missense mutation and the second 
+column is the frequency (number of observations divided by total number of samples). A few example lines for the format of the custom frequency file is given below:
+
+.. code:: bash
+
+   S2A 2.5607342137e-06
+   S2L 6.1954797779e-06
+   S2W 6.840647125218045e-07
+   F3L 1.5903965494e-06
+   F3S 1.2003274493e-06
+   F3L 1.67277954004e-05
+
+We provide an sample custom frequency file for MLH1 in the data folder of this repository. You can download that file to your computer with the following Linux/Unix command:
+
+.. code:: bash
+
+   wget http://gitlab.lcqb.upmc.fr/tekpinar/PRESCOTT/raw/master/data/custom-frequency-file.txt
+
+If you have already downloaded the repository, go to the examples directory and run the following command to use the custom frequency file:
+
+.. code:: bash
+
+   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/custom-frequency-file.txt -s ../data/MLH1.fasta
+
+
+
 Installation
 ------------