goatools.cli.wr_sections module

Command-line interface to create an initial Python sections file

Usage:
  goatools wr_sections [GO_FILE]
  goatools wr_sections [GO_FILE] [options]

Options:
  -h --help                                 show this help message and exit

  -i <file.txt>, --ifile=<sections_in.txt>  Read or Write file name [default: sections_in.txt]
  -o <file.txt>, --ofile=<sections.txt>     write file name [default: sections.txt]
  --txt=<file.txt>                          Write file name [default: grouped_gos.txt]

  --py=<file.py>       Write the sections list into a Python file
  --xlsx=<file.xlsx>   Group user GO IDs and write the results into an xlsx file

  --obo=<file.obo>     Ontologies in obo file [default: go-basic.obo].
  --slims=<file.obo>   GO slims in obo file [default: goslim_generic.obo].

  --gaf=<file.gaf>     Annotations from a gaf file
  --gene2go=<gene2go>  Annotations from a gene2go file downloaded from NCBI

class goatools.cli.wr_sections.WrSectionsCli(gosubdag=None)

Bases: object

Class for command-line interface for creating GO term diagrams

kws_dict = {'GO_FILE', 'gaf', 'gene2go', 'ifile', 'obo', 'ofile', 'py', 'slims', 'taxid', 'txt', 'xlsx'}

kws_set = {}

cli(args=None, prt=sys.stdout)

Command-line interface for go_draw script.

goatools.cli.wr_sections.main(args=None)

Create or update sections files from the command line.