gff2histogram.py - compute histograms from intervals in gff or bed format

Tags

Genomics Intervals GFF Summary

Purpose

This script computes distributions of interval sizes, intersegmental distances and interval overlap from a list of intervals in gff or bed format.

The output will be written into separate files. Filenames are given by --ouput-filename-pattern.

Available methods are:

hist

Output a histogram of interval sizes and distances between intervals in nucleotides.

stats

Output summary statistics of interval sizes and distances between intervals

values

Output distances, sizes, and overlap values to separate files.

all

all of the above.

Usage

For example, a small gff file such as this (note that intervals need to be sorted by position):

chr19   processed_transcript    exon    60105   60162   .       -       .
chr19   processed_transcript    exon    60521   60747   .       -       .
chr19   processed_transcript    exon    65822   66133   .       -       .
chr19   processed_transcript    exon    66346   66416   .       -       .
chr19   processed_transcript    exon    66346   66509   .       -       .

will give when called as:

cgat gff2histogram < in.gff

the following output files:

hist

Histogram of feature sizes and distances between adjacent features

residues	size	distance
58.0	1	na
71.0	1	na
164.0	1	na
212.0	na	1
227.0	1	na
312.0	1	na
358.0	na	1
5074.0	na	1

stats

Summary statistics of the distribution of feature size and distance between adjacent features.

data	nval	min	max	mean	median	stddev	sum	q1	q3
size	5	58.0000	312.0000	166.4000	164.0000	95.6339	832.0000	71.0000	227.0000
distance	3	212.0000	5074.0000	1881.3333	358.0000	2258.3430	5644.0000	212.0000	5074.0000

overlaps

A file with features that overlap other features, here:

chr19   processed_transcript    exon    66346   66416   .       -       .       chr19   processed_transcript    exon    66346   66509   .       -       .

Type:

python gff2histogram.py --help

for command line help.

Command line options

usage: gff2histogram [-h] [--version] [-b BIN_SIZE] [--min-value MIN_VALUE]
                     [--max-value MAX_VALUE] [--no-empty-bins]
                     [--with-empty-bins] [--ignore-out-of-range]
                     [--missing-value MISSING_VALUE] [--use-dynamic-bins]
                     [--format {gff,gtf,bed}]
                     [--method {all,hist,stats,overlaps,values}]
                     [--output-section {all,size,distance}]
                     [--timeit TIMEIT_FILE] [--timeit-name TIMEIT_NAME]
                     [--timeit-header] [--random-seed RANDOM_SEED]
                     [-v LOGLEVEL] [--log-config-filename LOG_CONFIG_FILENAME]
                     [--tracing {function}] [-? ?]
                     [-P OUTPUT_FILENAME_PATTERN] [-F] [-I STDIN] [-L STDLOG]
                     [-E STDERR] [-S STDOUT]
gff2histogram: error: argument -?: expected one argument