goatools.grouper.read_goids module

Functions to read text or tsv files containing GO IDs and sections of GO IDs.

goatools.grouper.read_goids.read_sections(sections_file, exclude_ungrouped=False, prt=sys.stdout)

Get sections and GO grouping hdrgos from file, if sections exist.

goatools.grouper.read_goids.read_goids(fin_txt, get_goids_only=False, exclude_ungrouped=False, prt=sys.stdout)

Get user list of GO IDs either from a list or from GO IDs on the command-line

class goatools.grouper.read_goids.ReadGoids

Bases: object

Get user list of GO IDs either from a list or from GO IDs on the command-line

srch_section = re.compile('^#?\\s*SECTION:\\s*(\\S.*\\S)\\s*$', re.IGNORECASE)

srch_py_section = re.compile('^\\s*(\\(|\\[)\\s*(\\\'|")(.*)\\s*(\\\'|")\\s*,\\s*\\[')

srch_py_goids = re.compile('^\\s*(\\\'|")(GO:\\d{7})(\\\'|")\\s*,?')

read_txt(fin_txt, get_goids_only, exclude_ungrouped, prt=sys.stdout)

Get user list of GO IDs either from a list or from GO IDs on the command-line

read_py(fin_txt, get_goids_only, exclude_ungrouped, prt=sys.stdout)

Read GO IDs or sections data from a Python file.

read_sections(sections_file, get_goids_only, exclude_ungrouped)

Read sections variable from a text file of from a Python file.

internal_get_goids_or_sections()

Return GO IDs, Sections/GOs, or None.