Updates for GnomAD 4.1.

docs/input-preparation.rst

@@ -72,8 +72,6 @@ a3m and fasta files are too long. We have to shorten them. We can do that with
  .. code:: bash
 
    awk 'BEGIN{FS=" "}{if(NF>1) {printf(">%s\n", $1)}else{print $0}}' AKE_nogaps.fasta > AKE_nogaps_short_names.fasta
-   # Recheck this command if you can remove extra >
-
 
 Congratulations! Now, you have all the input files required for PRESCOTT:
 

docs/introduction.rst

@@ -60,7 +60,7 @@ folder of this repository.
 Below, you will find examples of the most basic usage. Consult to the
 documentation for further details.
 
-Running the escott program
+Running escott program
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Let’s assume that our input MSA is inputAli.fasta and input.pdb is our
@@ -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 with gnomAD frequency data
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Running prescott program with gnomAD frequency data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 A quick help can be accessed by typing
 
@@ -98,15 +98,10 @@ Run the program by issuing the following command in a bash terminal:
 
 .. code:: bash
 
-   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
-
-GnomAD v4.0.0 is the most comprehensive, publicly available human population dataset as far as we know. However,
-if you would like to use GnomAD v2.1.1, you should specify the version with '--gnomadversion' parameter as below:
-
-.. code:: bash
+   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.1.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
 
-   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 2
 
+GnomAD v4.1.0 is the most comprehensive, publicly available human population dataset as far as we are aware of. 
 The most important output is prescott-scores.csv file, which produces entire single point mutational landscape for the protein. 
 
 In addition, there is a file called prescott-scores-details.csv. The file contains all information about the points modulated by population 
@@ -138,7 +133,23 @@ 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
+Running prescott program with older versions of GnomAD data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you would like to use GnomAD v4.0.0 data in prescott, you should specify GnomAD version with '--gnomadversion' parameter as follows:
+
+.. code:: bash
+
+   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 40
+
+However, if you would like to use GnomAD v2.1.1, you should specify the version with '--gnomadversion' parameter as below:
+
+.. code:: bash
+
+   prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 2
+
+
+Running 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. 
@@ -188,6 +199,6 @@ and structural model accurately predicts missense effect. medRxiv. doi:10.1101/2
 https://www.medrxiv.org/content/10.1101/2024.02.03.24302219v1 
 
 
-.. |License: CC BY-NC-SA 4.0| image:: https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-lightgrey.svg
-   :target: http://creativecommons.org/licenses/by-nc-sa/4.0/
+.. |License: GPLv3| image:: https://img.shields.io/badge/license-GPLv3-blue
+   :target: https://www.gnu.org/licenses/gpl-3.0.html
 

examples/example-prescott-script.sh

@@ -4,7 +4,10 @@
 #prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 2
 
 #If you are using GnomAD v4.0.0 data.
-prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
+#prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta  --gnomadversion 40
+
+#If you are using GnomAD v4.1.0 data.
+prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.1.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta
 
 #If you have a custom frequency file
 #prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/custom-frequency-file.txt -s ../data/MLH1.fasta