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Setup_Instructions.txt
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Setup_Instructions.txt
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vkabat.jar and entropy.jar are scripts designed to provide users with a simple way to get e6, e20, and vkbat values for each residue.
The output_to_csv.py script was written by Richard Pearson and is a tool to take the raw command line outputs and transfer them to a csv file.
The entropy.jar and vkbat.jar files were written by Benjy Strauss. This readme file was written by Richard Pearson and is
intended to provide a quick start up guide and provide users with some information on setup.
This document will cover setup first and then simple use instructions. You can contact [email protected] if you have questions.
######################################################################################################
# SETUP AND DEPENDENCIES #
######################################################################################################
Note: This should work equally well on Windows, Mac, and Linux OS and on both 32-bit and 62-bit arch.
However, my install was successfully accomplished using a 64-bit Mac with High Sierra installed.
\\ Java
Most importantly, you will need Java installed on your computer.
To check if you have Java installed enter the following into the terminal window:
java -version
This should return some basic information about which version of java is installed.
Now check to see if it is on your PATH by typing the following:
which java
\\ Python
Python and Perl are both required to be installed and should be on your computer's PATH.
To check if you have Python enter the following into your terminal window:
python --version
To check if you have Python on your PATH enter the following into your terminal window:
which python
I used Python 3.8.3 which can be downloaded at python.org
\\ Python libraries
Two known python library dependencies are the libraries called biopython and pandas.
Check to see if your computer has the biopython and pandas library by entering the following into
your terminal window:
pip list
-or-
conda list
A list will be returned and check to see if biopython is in this list. If it is not, type
the following into the command line:
pip install biopython
pip install pandas
-or-
conda install biopython
conda install pandas
\\ Perl
To check if you have Perl enter the following into your terminal window:
perl -v
To check if you have Perl on your PATH enter the following into your terminal window:
which perl
I used Perl 5.28.0 which can be downloaded at perl.org
If you have a mac you can use the following to install perl:
curl -L http://xrl.us/installperlosx | bash
\\ Perl modules
The known Perl module dependencies are the following, HTTP::Request and LWP::MediaTypes
To check this enter the following in the terminal:
instmodsh
Then type l and hit ENTER.
Check to see if these are
To install run the following commands:
\curl -L https://install.perlbrew.pl | bash
cpan App::cpanminus
cpanm HTTP::Request
cpanm LWP::MediaTypes
ONLY INSTALL THESE PERL MODULES IF THE FOLLOWING TERMINAL COMMANDS DO NOT WORK:
curl http://www.compbio.dundee.ac.uk/jpred/downloads/jpredapi.tar.gz -o ./jredapi.tar.gz
tar xzf jpredapi.tar.gz
Test using the following command:
perl jpredapi submit mode=single format=raw [email protected] name=TestJob1 seq=MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC
If this runs successfully, proceed to the following VERY IMPORTANT STEP (MUST DO IN ORDER):
java -jar vkbat.jar [enter raw sequence here]
IMPORTANT NOTE: If the above did not properly set-up the files, please feel free to reach out via email at [email protected] so I can help.
#######################################################################################################
# USING THE SCRIPTS #
#######################################################################################################
How to use entropy.jar (This script provides e6 and e20 values for each residue position)
java -jar entropy.jar [ENTER RAW SEQUENCE HERE NO BRACKETS]
How to use vkbat.jar (This script provides vkbat values for each residue position)
java -jar vkbat.jar [ENTER RAW SEQUENCE HERE NO BRACKETS]
How to use output_to_csv.py (Converts input to a csv file)
python output_to_csv.py [OUTPUT TYPE FOR EXAMPLE, E6, E20, or VKBAT] [SEQUENCE NAME FOR EXAMPLE 1AA7] [RAW SEQUENCE INPUT]