plastid.bin.gff_parent_types module

Exports a table of parent-child feature relationships for all feature types found in a GFF3 file. Features with multiple parents are sorted into a category called Multiple.


Command-line arguments

Positional arguments

Argument Description
infile.gff Input GFF3 file
outfile.txt Name of output file

Optional arguments

Argument Description
-h, --help show this help message and exit
--exclude  EXCLUDE [EXCLUDE ...] Feature types to exclude from consideration

Warning/error options

Argument Description
-q, --quiet Suppress all warning messages. Cannot use with ‘-v’.
-v, --verbose Increase verbosity. With ‘-v’, show every warning. With ‘-vv’, turn warnings into exceptions. Cannot use with ‘-q’. (Default: show each type of warning once)

Script contents

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

Command-line program

Parameters:
argv : list, 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