1. Andrés Felipe Giraldo Forero Avatar Andrés Felipe Giraldo Forero
  2. Untitled project
  3. Profs

Wiki

Clone wiki

Profs / Tutorial

View History

Requirements

Profs is written in R, a high-level programming language that is widely used in bioinformatics and data analysis. Currently, Profs works only on Linux. Profs makes use of some software, these are available from the official Ubuntu repository:

#!bash
sudo apt-get install r-base r-base-core cd-hit hmmer ncbi-blast+ muscle
A number of additional R packages are used: bio3d, seqinr and Biostrings. These can be most easily installed from within R with the command:

#!R
install.packages(c("bio3d", "seqinr", "optparse"), dependencies=TRUE)
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
Additionally, we use popular bioinformatics databases: PDB, CATH and Pfam. The version of software, R packages and database are listed below:

Installation

  1. Building PDBfam package, for this clone repository by
    $ git clone git@bitbucket.org:afgiraldofo/profs.git, and navigate to the directory and write next command: $ R CMD build profs.
  2. Install PDBfam package, for this open a terminal, navigate to file location and enter the following command: $ sudo R CMD INSTALL ./PDBfam_0.99.tar.gz, if package is successfully installed go to next step.
  3. Get into R terminal, load PDBfam package by > require("PDBfam") and write next command: > system.file("bin",package = "PDBfam"), for know the location of external softwares.
  4. Export the environment variables of the external softwares, for this add next line in the "~/.bashrc" file, export PATH="path:$PATH";. Where path must be replaced by location obtained in the item 3.
  5. Detect directory location with PDBfam script by > system.file("script",package = "PDBfam").
  6. Give execute permissions to the directory with PDBfam script $ chmod -R +x path , Where path must be replaced by location obtained in the item 5.
  7. Change script headers with the R locate, by defect is #!/usr/bin/Rscript --vanilla --slave. NOTE: The R version was testing with the 3.10 version, 2.14.1 or lower have compatibility problems.

Usage

Code

  • parsepfam.R
  • extfasta.R
  • getpfam.R
  • postprocess.R
  • parsecath.R
  • genepdbfam.R
  • genelib.R
  • doalignment.R
  • exportcsv.R

Script connexion

BACK

Updated