goatools.cli.compare_gos module

Compare two or more sets of GO IDs. Best done using sections.

Usage:
  goatools compare_gos [GO_FILE] ...
  goatools compare_gos [GO_FILE] ... [options]

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

  -s <sections.txt> --sections=<sections.txt>  Sections file for grouping
  -S <sections module str>                     Python module with SECTIONS variable

  -o <file.txt>, --ofile=<file.txt>    write comparison of GO IDs into ASCII file
  --xlsx=<file.xlsx>   write comparison of GO IDs into an xlsx file
  -v --verbose         Print sections as GO headers followed by each header's user GOs

  --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.compare_gos.CompareGOsCli(args=None, **kws)

Bases: object

Class for command-line interface for creating GO term diagrams

kws_dict = {'GO_FILE', 'S', 'gaf', 'gene2go', 'obo', 'ofile', 'sections', 'slims', 'taxid', 'xlsx'}

kws_set = {'verbose'}

excl_flds = {'D1', 'REL', 'REL_short', 'alt', 'childcnt', 'format_txt', 'hdr1usr01', 'hdr_idx', 'id', 'is_hdrgo', 'is_usrgo', 'level', 'num_usrgos', 'rel', 'reldepth'}

write(fout_xlsx=None, fout_txt=None, verbose=False)

Command-line interface for go_draw script.

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

Compare two or more GO ID sets from the command line.