Given a list of gene/attribute ids or names and a GTF or GFF formatted file, parse the input file to find entries with the names or ids in attribute section. The input list of ids/names must be one per line. Supports reading gzipped (.gz) files.
- gcc (version >=4.8 for c++11 standard support)
- boost library ( for gzip support)
- boost-dev
- boost-iostreams-dev
On a Debian/Ubuntu machine install boost libraries using:
sudo apt-get install libboost-dev libboost-iostreams-dev
For other distros and unix variants, see boost library installation
Clone the repository to your local disk:
git clone https://github.com/sudeepsahadevan/gtf_parser.git
Change to directory and make
cd gtf_parser
make
The executable gtf_parser will be created in the folder bin
Call the executable as:
/path/to/gtfparser --ids /path/to/ids --gff /path/to/gtf > gff_filtered
For more usage options see:
/path/to/gtfparser -h