Bio::ToolBox - manipulate_wig

Home

Install

Libraries

Applications

Examples

FAQ

manipulate_wig.pl

A progam to manipulate wiggle files.

SYNOPSIS

manipulate_wig.pl [options] -i <file1.wig> -o <file1.out.wig>

File Options: 
-i --in <file>            Input file. Accepts 'stdin'.
-o --out <file>           Output file. Accepts 'stdout'.

Selection functions:
-k --skip <regex>         Skip lines where chromosomes match regex 
-y --apply <regex>        Only apply manipulations to matching chromosomes 

Manipulation functions (in order of execution):
-u --null                 Convert null, NA, N/A, NaN, inf values to 0
-d --delog [2|10]         Delog values of given base 
-b --abs                  Convert to the absolute value 
-m --mult <float>         Multiply score by the given value
-a --add <float>          Add the given value to the score
-l --log [2|10]           Convert to log2 or log10. 
-n --min <float>          Set the minimum score
-x --max <float>          Set the maximum score
-p --place <int>          Format score to decimal positions
-z --zero                 Discard lines with zero values

BigWig support:
--chromo <file>           Chromosome sizes file for writing bigWig
--db <file>               Indexed file to obtain chromosome info
--bw2w <path>             Path to UCSC bigWigToWig utility
--w2bw <path>             Path to UCSC wigToBigWig utility

General functions:
-t --stats                Calculate statistics 
-v --version              print version and exit
-h --help                 show extended documentation

OPTIONS

The command line flags and descriptions:

File options

• –in <file>

  Specify the input wig file. All three formats, variableStep, fixedStep, and bedGraph, are supported. Files may be gzipped. BigWig files are supported, so long as the UCSC bigWigToWig utility is available. Alternatively, the input may be read from standard input by specifying ‘stdin’ as the file name.

• –out <file>

  Specify the output wig file. The output format will be the same format as the input. The file may be gzipped by appending .gz to the name. BigWig files are supported, so long as the UCSC wigToBigWig utility is available and a chromosome file is provided. Alternatively, the output may be sent to standard output by specifying ‘stdout’ as the file name.

Selection functions

• –skip <regex>

  Selectively skip (discard) lines corresponding to certain chromosomes that match the provided regular expression. For example, skip the mitochondrial and random contigs, use “chrM|chrUn|random”.

• –apply <regex>

  Selectively apply manipulation functions to certain chromosomes that match provided regular expression, leaving remaining lines untouched. For example, to apply a normalization to the X chromosome, use ‘chrX’.

Manipulation functions

• –null

  Convert lines with a score of null, NA, N/A, NaN, or inf to a value of 0.

• –delog [2

  10]

  Convert lines from log space in the indicated base.

• –abs

  Convert line scores to absolute values.

• –mult <float>

  Multiply line scores by the indicated value.

• –add <float>

  Add the indicated value to each line score.

• –log [2

  10]

  Convert the line score to a log equivalent in the indicated base space.

• –min <float>

  Set the minimum floor score. Any score below the indicated value will be set to the indicated value.

• –max <float>

  Set the maximum ceiling score. Any score above the indicated value will be set to the indicated value.

• –place <integer>

  Format the score value to the indicated number of decimal positions.

• –zero

  Discard lines with a score value of zero.

BigWig support

• chromo <file>

  When writing to a bigWig output file, provide a chromosome sizes text file for use with the wigToBigWig utility. Alternatively, use a database file, below.

• db <file>

  When writing to a bigWig output file, provide an indexed database file, such as another bigWig file, Bam, indexed Fasta, etc, for automatically generating a chromosome sizes text file to use with the wigToBigWig utility. If a bigWig input file was specified, it will be conveniently substituted as a database. Note that the --skip option will be applied to the generated chromosome file.

• bw2w <path>

  If the UCSC bigWigToWig utility is not in your environment PATH, provide the path with this option.

• w2bw <path>

  If the UCSC wigToBigWig utility is not in your environment PATH, provide the path with this option.

General functions

• –stats

  Calculate the statistics across the genome at base pair resolution. Statistics are calculated after any processing indicated above are performed. Only applied chromosomes are calculated. Results are printed to STDOUT, or STDERR if standard out is used as an output.

• –version

  Print the version number of the program and exit.

• –help

  Display the POD documentation using perldoc.

DESCRIPTION

A program to manipulate the score value of wig files. This will process all forms of text based wig files, including fixedStep, variableStep, and bedGraph. Files may be gzip compressed. BigWig files are also transparently supported as both input and output, provided that the appropriate UCSC utility files are available.

NOTE: More than one option may be specified! The options above are the order in which the score is manipulated. If they are not in the order you want, you may have to pipe to sequential instances. Use ‘stdin’ and ‘stdout’ for filenames.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.