DTarray_pro

Combine DTASelect-filter files.

DTarray_pro extracts Uniprot ID numbers, molecular weights, and spectral counts from .dtafilter files stored in the working directory. Protein data is combined into one dataset and written to the working directory as a tab delimitated text file (.tsv). At runtime, a file list named dtarray_pro_flist.txt, containing all the valid DTASelect-filter files found in the working directory, is generated. If a file list already exists, the existing file list is used. Various options are available to, modify how files are treated in the working directory, extract additional data from the DTASelect-filter files, and to change the output file format.

Installation

DTarray_pro is written in c++ 11 and can be compiled on linux or OS-X with gcc.

DTarray_pro expects to be installed in ~/local. The program needs data stored in text files in ~local/<program_dir>/db for some features to work. First make ~/local if it doesn't exist.

mkdir -p ~/local

If you do not wish to build the program in ~/local, you can run the configure script from the desired location with the --progdir ./ option.

DTarray_pro depends on the utils c++ library which is included as a submodule in this repository. To clone this repository and the utils submodule, run:

git clone --recurse-submodules --single-branch --branch stable https://github.com/ajmaurais/DTarray_pro

To build the executable, run:

cd ~/local/DTarray_pro
./configure
make

After compilation, the bin directory should contain two files:

• DTarray - the DTarray_pro executable.
• DTSetup - a bash script which can optionally be used to automatically setup the input directory for DTarray

Usage

From a folder containing DTASelect-filter files with the format <sample_name>.dtafilter.

DTarray

See ~/local/<program_directory>/helpFile.pdf for a detailed explanation of optional arguments or use DTarray -h to see the help file from the terminal.