goatools.grouper.wr_sections module

Prints a Python sections file.

class goatools.grouper.wr_sections.WrSectionsBase(grprobj, ver_list=None)

Bases: object

Tasks for writing a sections file.

prt_ver(prt)

Print version of GO-DAG for the GO and for GO slims.

prt_col_hdr(prt)

Print a comment line describing the columns in the output.

get_sections_2dnt(sec2d_go)

Return a sections list containing sorted lists of namedtuples.

get_ntgos_sorted(hdrgos)

Return sorted Grouper namedtuples if there are user GO IDs underneath.

prt_ntgos(prt, ntgos)

Print the Grouper namedtuples.

get_summary_data(sec2d_nt)

Get placed/unplaced GO IDs and sections.

get_summary_str(sec2d_nt)

Get string describing counts of placed/unplaced GO IDs and count of sections.

class goatools.grouper.wr_sections.WrSectionsPy(grprobj, ver_list=None)

Bases: WrSectionsBase

Holds formatting information for printing sections into a Python file.

wr_py_sections_new(fout_py, doc=None)

Write the first sections file.

wr_py_sections(fout_py, sections, doc=None)

Write sections 2-D list into a Python format list.

class goatools.grouper.wr_sections.WrSectionsTxt(grprobj, ver_list=None)

Bases: WrSectionsBase

Manages GO group headers and optionally sections containing GO group headers.

static prt_sections(prt, sections, prtfmt, secspc=False)

Print GO namedtuples in their sections.

prt_info(prt, sections=None)

Print GO namedtuples in their sections.

prt_goid_cnt(prt=sys.stdout)

Get number of hdrgos and usrgos in each section.

wr_txt_grouping_gos()

Write one file per GO group.

wr_txt_section_hdrgos(fout_txt, sortby=None, prt_section=True)

Write high GO IDs that are actually used to group current set of GO IDs.