goatools.rpt.rpt_lev_depth module

Report the level/depth summaries of all GO terms or a subset of GO terms.

Level is the length of a shortest path to a GO term. Depth is the length of a longest path to a GO term.

Example:

>>> godag = GODag("go-basic.obo")
>>> reporter = RptLevDepth(godag)
>>> reporter.write_summary_cnts_all()
    go-basic.obo: format-version(1.2) data-version(releases/2016-03-01)
    46162 nodes imported
    Dep <-Depth Counts->  <-Level Counts->
    Lev   BP    MF    CC    BP    MF    CC
    --- ----  ----  ----  ----  ----  ----
    00     1     1     1     1     1     1
    01    24    19    24    24    19    24
    02   126   131   195   222   154   336
    03   955   493   502  1913   739  1145
    04  1950  1464   566  4506  1812  1300
    05  3371  3765   994  6958  3985   763
    06  4275  1784   748  6945  1888   268
    07  4634  1005   549  4890   903    53
    08  4125   577   216  2022   352     6
    09  3478   315    86   739   109     1
    10  2364   164    12   188    38     0
    11  1583   170     3    37    21     0
    12  1014    68     1     1     0     0
    13   400    49     0     0     0     0
    14   107    13     0     0     0     0
    15    28     3     0     0     0     0
    16    11     0     0     0     0     0

goatools.rpt.rpt_lev_depth.prt_lev_depth(godag, prt=sys.stdout)

Write the counts of GO terms found at each level and depth of the GO DAG.

class goatools.rpt.rpt_lev_depth.RptLevDepth(obodag, log=sys.stdout)

Bases: object

Reports a summary of GO term levels in depths.

nss = ['biological_process', 'molecular_function', 'cellular_component']

wr_xlsx(fout_xlsx)

Write counts of GO terms at all levels and depths.

wr_txt(fout_txt)

Write counts of GO terms at all levels and depths.

prttex_summary_cnts_all(prt=sys.stdout)

Print LaTeX format summary of level and depth counts for all active GO Terms.

write_summary_cnts_all()

Write summary of level and depth counts for all active GO Terms.

write_summary_cnts(go_ids)

Write summary of level and depth counts for specific GO ids.

write_summary_cnts_goobjs(goobjs)

Write summary of level and depth counts for active GO Terms.

static get_cnts_levels_depths_recs(recs)

Collect counts of levels and depths in a Group of GO Terms.

get_data()

Collect counts of GO terms at all levels and depths.