plastid.bin.get_count_vectors module

Fetch vectors of counts at each nucleotide position in one or more regions of interest (ROIs).

Output files

Vectors are saved as individual line-delimited files – one position per line – in a user-specified output folder. Each file is named for the ROI to which it corresponds. If a mask file – e.g. from crossmap – is provided, masked positions will be have value nan in output.

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

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:]. The command-line arguments, if the script is invoked from the command line