plastid.bin.make_wiggle module

Create genome browser tracks from read alignments, using mapping rules to extract the biology of interest (e.g. ribosomal P-sites, et c) from the alignments.

Output files

Tracks can be output in wiggle and bedGraph formats. Because these formats are unstranded, two files are created:

OUTBASE_fw.wig

Counts at each position for the plus/forward strand of each chromosome

OUTBASE_rc.wig

Counts at each position for the minus/reverse strand of each chromosome

where OUTBASE is given by the user.

See also

Read mapping functions

Explanations of mapping rules and why they can be useful

plastid.genomics.map_factories

For lists of mapping rules and their parameters

plastid.bin.make_wiggle.main(argv=['-T', '-E', '-b', 'html', '-d', '_build/doctrees', '-D', 'language=en', '.', '_build/html'])[source]

Command-line program

Parameters
argvlist, optional

A list of command-line arguments, which will be processed as if the script were called from the command line if main() is called directly.

Default: sys.argv[1:] (actually command-line arguments)