summarizeWigPerFeature.py

common.ngseq.summarizeWigPerFeature.py

This stand-alone script reads a wig or bigwig file and a gff or gtf annotation file and then sumarizes the data in the wig file for a specified feature type from the annotation file. The result is output as a tab delimited text file. Options are available to control the feature type and the numbers that are output in the file.

module_version:1.0 created_on:2014-01-07

Command-line Arguments

usage:

summarizeWigPerFeature.py :param: <output tsv file> :param: <input wig/bigwig file> :param: <input gtf/gff file> -l|--log <file> [--tmpdir] [-v|--verbose] [--version] [--help]

Required Parameters

param:

<output tsv file>

The filename of the output text file. Tab-seperated values.

param:

<input wig/bigwig file>

The input file in wig or bigwig format

param:

<input gtf/gff file>

The input annotation file. Currently only gff v3 is supported.

--logfile|-l

The name (inc. path) of the log file from the wrapper.

Optional Parameter

--help|-h

Print a basic description of the tool and its options to STDOUT.

--version

Show program’s version number and exit.

--verbose|-v

Turn on verbose logging (recommended).

Output

A tsv file with the summarization stats for each feature in the annotation.