gff2table.py - compute features for intersection of two gff files

Tags

Genomics Intervals Annotation Comparison GFF

Purpose

collect intervals from two gff files and compute features based on their intersection. The script is intended to compute properties for a set of non-overlapping windows.

Transforms:

  • none: no transform

  • overlap: overlap between set1 and set2

  • complement: part of set1 that is not covered by set2

  • third_codon: only takes every third position. Needs frame information

    in the gff file.

Decorators:

  • GC: G+C content of intervals

  • count: number of windows

  • mean-length: mean length of intervals overlapping with window

Usage

Example:

python gff2table.py --help

Type:

python gff2table.py --help

for command line help.

Command line options

usage: gff2table [-h] [--version] [-g GENOME_FILE] [-w FILENAME_WINDOWS]
                 [-d FILENAME_DATA] [--is-gtf] [-f {GC}]
                 [-c {counts,gc,gc3,mean-length,median-length,percent-coverage,median-score,mean-score,stddev-score,min-score,max-score}]
                 [-e] [-t {none,overlap,complement,third_codon}]
                 [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
                 [--timeit-header] [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                 [--log-config-filename LOG_CONFIG_FILENAME]
                 [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                 [-E STDERR] [-S STDOUT]
gff2table: error: argument -?: expected one argument