Commit e1284daa by Mustafa Tekpinar

Docs update for the custom frequency file.

parent d1e78426
...@@ -85,8 +85,8 @@ line of the file should contain a mutation (e.g. D136R) or combination ...@@ -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 of mutations separated by colons and ordered according to their
positions in the sequence (e.g. D136R,V271A). positions in the sequence (e.g. D136R,V271A).
Running the prescott program Running the prescott program with gnomAD frequency data
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A quick help can be accessed by typing A quick help can be accessed by typing
...@@ -117,6 +117,39 @@ variants are affected by population information. ...@@ -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. 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 Installation
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