view release on metacpan or  search on metacpan

scripts/manipulate_wig.pl  view on Meta::CPAN

Discard lines with a score value of zero.

=back

=head2 BigWig support

=over 4

=item chromo E<lt>fileE<gt>

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

=item db E<lt>fileE<gt>

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 F<wigToBigWig> 
utility. If a bigWig input file was specified, it will be conveniently 
substituted as a database. B<Note> that the C<--skip> option will be 
applied to the generated chromosome file.

=item bw2w E<lt>pathE<gt>

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

=item w2bw E<lt>pathE<gt>

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

=back

=head2 General functions

=over 4

=item --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.

=item --version

Print the version number of the program and exit.

=item --help

Display the POD documentation using perldoc. 

=back

=head1 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.

B<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.

=head1 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.