goatools.gosubdag.rpt.write_hierarchy module

Print a GO term’s lower-level hierarchy.

class goatools.gosubdag.rpt.write_hierarchy.WrHierGO(gosubdag, **kws)

Bases: object

Write hierarchy object.

kws_dct = {'dash_len', 'include_only', 'item_marks', 'max_indent', 'sortby'}

kws_set = {'concise', 'no_dup', 'no_indent'}

kws_all = {'concise', 'dash_len', 'include_only', 'item_marks', 'max_indent', 'no_dup', 'no_indent', 'sortby'}

prt_hier_all(prt=sys.stdout)

Write hierarchy for all GO Terms in obo file.

prt_hier_down(goid, prt=sys.stdout)

Write hierarchy for all GO IDs below GO ID in arg, goid.

prt_hier_up(goids, prt=sys.stdout)

Write hierarchy for all GO IDs below GO ID in arg, goid.

static get_goids_all(go2term_ns)

GO IDs from user-specfied GO to root