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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
#!R install.packages(c("bio3d", "seqinr", "optparse"), dependencies=TRUE) source("http://bioconductor.org/biocLite.R") biocLite("Biostrings")
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Software
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R packages
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Database
Installation
- 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
. - 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. - 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. - Export the environment variables of the external softwares, for this add next line in the "~/.bashrc" file,
export PATH="path:$PATH";
. Wherepath
must be replaced by location obtained in the item 3. - Detect directory location with PDBfam script by
> system.file("script",package = "PDBfam")
. - Give execute permissions to the directory with PDBfam script
$ chmod -R +x path
, Wherepath
must be replaced by location obtained in the item 5. - 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
Updated