ruruya / gtf-to-csv-converter

simple python 2 gtf to csv converter

gtf-to-csv-converter

A simple python 2 gtf to csv converter.

Stores whole GTF in memory thus will fail on relatively big data. Single thread only.

Works with gzip compressed GTF files and pandas (so please have pandas installed).

GTF file format spec: http://useast.ensembl.org/info/website/upload/gff.html

man

python gtf_to_csv.py --help
usage: gtf_to_csv.py [-h] -i INFILE [-o OUTFILE]
                     [-columns COLUMN [COLUMN ...]]

Input GTF file and optional parameters

optional arguments:
  -h, --help            show this help message and exit
  -i INFILE             input gtf file
  -o OUTFILE            output csv file, defaults to `input file name`.csv
  -columns COLUMN [COLUMN ...], -c COLUMN [COLUMN ...]
                        list of columns to write to csv, e. g. `-columns column1 column2 column3`