A program to retrieve context-dependent core substitution rate constants (Homo sapiens, germline) for DNA sequences and entire genomes.
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Trek.R

README.Rmd

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Trek: a program to retrieve context-dependent core substitution rate constants (Homo sapiens, germline) for DNA sequences and entire genomes

The Trek methodology is described in detail at http://dx.doi.org/10.1101/024257. The name of the package reflects on the fact that we obtained the Transposon Exposed k rate constants (byr$^{-1}$), using the genomic treks of retrotransposon remnants in the human genome. The name additionally salutes the 50$^{th}$ anniversary of the Star Trek franchise.

Installation

1. Install the latest version of R programming language or skip to the next step. Step-wise instructions on R installation and upgrade can be found through the following links: 1, 2.

2. Launch R from the command line and install the R packages shiny (required for the graphical user interface), doMC, foreach and itertools (required for a parallel execution of the program) from within R.

$ R
> install.packages("shiny")
> install.packages("doMC")
> install.packages("foreach")
> install.packages("itertools")

3. Download the Trek source code from the GitHub repository. You can also do that via a Linux/Unix/OSX command line, given that git is installed, by typing the following:

$ git clone https://github.com/aleksahak/Trek

The downloaded folder has the following content:

  • lib/ - the subfolder containing all the source files,
  • TrekGUI/ - the subfolder containing the graphical user interface,
  • Trek.R - the interfacing R script used to execute Trek from command line.

4. Finally, you need to bit compile the package by going into the lib/ subfolder and executing bitcompile.R code from within R.

$ cd lib/
$ R
> source("bitcompile.R")

This generates a single file, Trek.lib, which encapsulates the main Trek code and all its dependencies. At this stage, the subfolder lib/ can be safely removed. You might, however, want to copy the test.fasta file from inside lib/, in order to test the Trek installation.

At this point, the Trek installation folder should contain:

  • Trek.lib - the bit-compiled Trek program,
  • TrekGUI/ - the subfolder containing the graphical user interface,
  • Trek.R - the interfacing R script used to execute Trek from command line,

and, if the test sequence file is preserved,

  • test.fasta - the example DNA sequence fasta file.

Running Trek from R

Trek can be executed as an R program, either from within R, or from the Linux/Unix/OSX command line through R CMD BATCH or Rscript execution. The latter two options allow the usage of Trek from the scripts written via programming languages other than R.

In R, as exemplified in the Trek.R interfacing script, one should load the Trek.lib bit-compiled file, then execute Trek via the R function Trek(). The latter accepts four arguments:

  • FastaFile - the relative or absolute path to the fasta file to analyse,
  • OutFile - the relative or absolute path to the output file to be saved,
  • MutRates - an argument accepting "sym" and "nosym" options for the strand-symmetrised (recommended) and raw parameter usage for substitution rates,
  • nCPU - the number of CPUs to be used for the calculation, where the larger values can markedly speed up the mapping process for entire genomes.

Alternatively, the Trek.R file can be edited to set the desired arguments, and executed from the command line via R CMD BATCH or Rscript.

Running Trek from a GUI

Trek features a browser-based graphical user interface (GUI), written with Shiny that can be executed locally on as many CPUs as desired. To launch the GUI, enter the TrekGUI/ subfolder and double click on TrekGUI file. If the file fails to open a browser, make sure that the permissions are correctly set for the file (as executable):

$ cd TrekGUI/
$ chmod 700 TrekGUI # May require sudo rights.

If double clicking on TrekGUI does not launch your browser after the above step, then, most probably, your Rscript utility of R is not installed on the default /usr/bin/Rscript path. To correct the TrekGUI setup, first find out the installed path for Rscript by typing from the command line:

$ which Rscript

then open the TrekGUI executable file via a usual plain text editor and correct the Rscript path stated at the first line.

Now double click on TrekGUI. As soon as the browser opens, the rest is self explanatory.

License

You may redistribute the Trek source code (or its components) and/or modify/translate it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License (GPL2). You can find the details of GPL2 in the following link: http://www.gnu.org/licenses/gpl-2.0.html.

Questions and bug reports to Aleksandr B. Sahakyan via [as952 at cam dot ac dot uk].