gtf2tab

Simple command-line application to convert GTF fields + attributes to a simple tab-delimited format.

Installation instructions

The simplest method is to download the appropriate binary for your platform. Download the appropriate binary from here and place it in the appropriate folder:

Platform	Path
Linux	/usr/bin
Mac OSX	/usr/bin
Windows	C:\Windows

If you're using cygwin on Windows, simply place the binary in the bin folder of your cygwin installation.

Important instructions for Windows users!!

To run gtf2tab, you need to download the Visual C++ Redistributable package for Visual Studio 2015. You can get that from Microsoft's website by following this link.

Build Instructions

Unless you really want to compile the program yourself, please ignore these instructions. It is much easier to simply download the pre-compiled binary by following the instructions above. You need to install the appropriate CMake version for your platform. To build:

On Mac OSX / Linux:

Clone the gtf2tab repository, and run the following commands to build and install gtf2tab:

cd gtf2tab
mkdir bin
cd bin
cmake ..
make
sudo make install

To build test executables, do:

cmake -DBUILD_TESTS=ON ..
make
cd tests
ctest

On Windows

1. Download the zip file of the repository, and extract it to a folder of your choosing.
2. Create a new folder called bin in the gtf2tab directory.
3. Open CMake-GUI, and point it to the source directory gtf2tab and the binary directory gtf2tab/bin.
4. Click Configure, select your build system, then click Generate.
5. Navigate to the bin directory. You will then need to follow the instructions appropriate for your build system to build the binary.

Usage Instructions

Usage: gtf2tab OPTIONS INPUT_FILE

Options:
    If no input file is specified, standard input is used

    -a ATTRIBUTE_LIST    Comma-separated list of attributes. Examples
                         for an Ensembl GTF are gene_id and gene_biotype.

    -f FIELDLIST         GTF fields to print, as a comma-separated list of
                         integers. Hyphens can also be used to specify a range
                         of values

    -t FEATURETYPE       Type of GTF feature to print.

    -o OUTPUTFILE        Output filename. Default is standard output

    -h                   Display help

Example:
     To extract columns 1-4 and gene_id, gene_biotype
     from file.gtf the command would be:

     gtf2tab -f 1-4 -a gene_id,gene_biotype file.gtf