source: orange-bioinformatics/docs/reference/obiGO-yeast.py @ 1634:32373d957326

Revision 1634:32373d957326, 34.6 KB checked in by mitar, 2 years ago (diff)

Renamed addon reference documentation.

Line 
1from __future__ import division
2import obiGO, obiProb
3import orange
4
5data = orange.ExampleTable("../../../../doc/datasets/brown-selected.tab")
6
7ontology = obiGO.Ontology()
8annotations = obiGO.Annotations("yeast", ontology=ontology)
9
10cluster_genes = [str(ex["gene"]) for ex in data if ex.getclass() == "Resp"]
11
12gg = dict([(b, a) for a, b in annotations.GetGeneNamesTranslator(cluster_genes).items()])
13cluster_genes = [gg.get(name, name) for name in cluster_genes]
14gg = dict([(ann.DB_Object_Symbol, ann.DB_Object_ID) for ann in annotations])
15cluster_genes = [gg.get(name, name) for name in cluster_genes]
16cluster_genes = cluster_genes[:10]
17reference_genes = annotations.geneNames
18
19david_date = "August 3, 2009"
20
21david_results_bp = """Category  Term    Count   %   PValue  Genes   List Total  Pop Hits    Pop Total   Fold Enrichment Bonferroni  Benjamini   FDR
22GOTERM_BP_ALL   GO:0015992~proton transport 8   57.14%  1.3041103299910861E-11  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  53  5164    55.676549865229106  3.115524416230642E-8    2.077016336698989E-9    2.2887058914733416E-8
23GOTERM_BP_ALL   GO:0015986~ATP synthesis coupled proton transport   8   57.14%  2.3084091771234847E-12  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  42  5164    70.25850340136054   5.514709577880694E-9    1.8382365629676656E-9   4.051181612396704E-9
24GOTERM_BP_ALL   GO:0044249~cellular biosynthetic process    8   57.14%  0.0026654367159150284   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  878 5164    3.360885128538887   0.9982984740500304  0.14734967010922517 4.5760545698257165
25GOTERM_BP_ALL   GO:0015672~monovalent inorganic cation transport    8   57.14%  6.501499399871959E-11   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  66  5164    44.70995670995671   1.5532080710478624E-7   8.62893434483425E-9 1.1410075106965678E-7
26GOTERM_BP_ALL   GO:0006818~hydrogen transport   8   57.14%  1.3041103299910861E-11  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  53  5164    55.676549865229106  3.115524416230642E-8    2.077016336698989E-9    2.2887058914733416E-8
27GOTERM_BP_ALL   GO:0051234~establishment of localization    9   64.29%  0.004162009675774264    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999, S000003439,     14  1235    5164    2.6880277617119726  0.9999529260234311  0.2111926048706756  7.058073886583582
28GOTERM_BP_ALL   GO:0006812~cation transport 8   57.14%  3.2348983576564486E-8   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  158 5164    18.67631103074141   7.727873692198184E-5    2.5760541179087326E-6   5.677217334021378E-5
29GOTERM_BP_ALL   GO:0009165~nucleotide biosynthetic process  8   57.14%  2.884205297126469E-9    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  112 5164    26.346938775510203  6.8903427785649285E-6   2.460844882312685E-7    5.061755459223605E-6
30GOTERM_BP_ALL   GO:0006811~ion transport    8   57.14%  9.322978491193589E-8    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  184 5164    16.03726708074534   2.2270116490286096E-4   6.960162230784661E-6    1.6361734598291378E-4
31GOTERM_BP_ALL   GO:0006810~transport    9   64.29%  0.003689044915217824    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999, S000003439,     14  1213    5164    2.7367801201271935  0.9998536375393898  0.19374226311229126 6.280333887049161
32GOTERM_BP_ALL   GO:0009058~biosynthetic process 8   57.14%  0.012969438334012132    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  1153    5164    2.5592863337876346  0.9999999999999715  0.49994490614887377 20.47521247842694
33GOTERM_BP_ALL   GO:0042775~organelle ATP synthesis coupled electron transport   3   21.43%  0.001698878089256512    S000003155, S000004997, S000004387,     14  25  5164    44.26285714285714   0.9827866703378599  0.098914987364349   2.93996869915667
34GOTERM_BP_ALL   GO:0006164~purine nucleotide biosynthetic process   8   57.14%  2.1784520172080657E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  78  5164    37.83150183150183   5.20432014816663E-7 2.1684672724120446E-8   3.8231643406660965E-7
35GOTERM_BP_ALL   GO:0042773~ATP synthesis coupled electron transport 3   21.43%  0.001698878089256512    S000003155, S000004997, S000004387,     14  25  5164    44.26285714285714   0.9827866703378599  0.098914987364349   2.93996869915667
36GOTERM_BP_ALL   GO:0006163~purine nucleotide metabolic process  8   57.14%  2.8583856087082035E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  81  5164    36.430335097001766  6.828681227144529E-7    2.6264167174439024E-8   5.016442483629646E-7
37GOTERM_BP_ALL   GO:0007571~age-dependent general metabolic decline  2   14.29%  0.02491247592376542 S000003882, S000003882,     14  10  5164    73.77142857142856   1.0 0.7226114630464955  35.77322472636095
38GOTERM_BP_ALL   GO:0009152~purine ribonucleotide biosynthetic process   8   57.14%  1.3504564734308501E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  73  5164    40.422700587084144  3.226239850828705E-7    1.5363049277183904E-8   2.3700393869674485E-7
39GOTERM_BP_ALL   GO:0006796~phosphate metabolic process  11  78.57%  6.609360672311857E-11   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000000195, S000005999, S000003882, S000005999, S000004387,     14  290 5164    13.991133004926107  1.578975383775827E-7    8.310397370259182E-9    1.1599365912218218E-7
40GOTERM_BP_ALL   GO:0009260~ribonucleotide biosynthetic process  8   57.14%  1.9849931357144687E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  77  5164    38.32282003710575   4.7421478244213944E-7   2.061803872077661E-8    3.4836461493270576E-7
41GOTERM_BP_ALL   GO:0006793~phosphorus metabolic process 11  78.57%  6.609360672311857E-11   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000000195, S000005999, S000003882, S000005999, S000004387,     14  290 5164    13.991133004926107  1.578975383775827E-7    8.310397370259182E-9    1.1599365912218218E-7
42GOTERM_BP_ALL   GO:0009150~purine ribonucleotide metabolic process  8   57.14%  1.6417078391964835E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  75  5164    39.3447619047619    3.922039358839058E-7    1.7827454956709232E-8   2.8811831809250066E-7
43GOTERM_BP_ALL   GO:0009259~ribonucleotide metabolic process 8   57.14%  2.3877846642490237E-10  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  79  5164    37.35262206148282   5.704415340090918E-7    2.2817667644225992E-8   4.1905411363174494E-7
44GOTERM_BP_ALL   GO:0051188~cofactor biosynthetic process    8   57.14%  3.4773191839524677E-9   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  115 5164    25.659627329192546  8.307281102348796E-6    2.864591178708409E-7    6.102665184304357E-6
45GOTERM_BP_ALL   GO:0046034~ATP metabolic process    8   57.14%  3.870915746856979E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  45  5164    65.57460317460317   9.247588694805131E-9    1.5412647824675219E-9   6.793399176530102E-9
46GOTERM_BP_ALL   GO:0006123~mitochondrial electron transport, cytochrome c to oxygen 3   21.43%  2.6032148376007355E-4   S000003155, S000004997, S000004387,     14  10  5164    110.65714285714284  0.46312446340401836 0.016670004919741466    0.4558791472939139
47GOTERM_BP_ALL   GO:0051186~cofactor metabolic process   8   57.14%  3.7293039277677224E-7   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  225 5164    13.114920634920635  8.905341134267664E-4    2.5454843862848797E-5   6.544876183900428E-4
48GOTERM_BP_ALL   GO:0009145~purine nucleoside triphosphate biosynthetic process  8   57.14%  5.353761737671291E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  47  5164    62.78419452887537   1.2790030923248707E-8   1.4211145593634456E-9   9.39572863956073E-9
49GOTERM_BP_ALL   GO:0009144~purine nucleoside triphosphate metabolic process 8   57.14%  6.261365320746103E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  48  5164    61.476190476190474  1.4958304817014323E-8   1.4958304594969718E-9   1.0988576715220688E-8
50GOTERM_BP_ALL   GO:0006119~oxidative phosphorylation    11  78.57%  2.1818706134527815E-17  S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000000195, S000005999, S000003882, S000005999, S000004387,     14  68  5164    59.668067226890756  5.212488895538695E-14   5.212488895538695E-14   3.829164197571297E-14
51GOTERM_BP_ALL   GO:0008152~metabolic process    14  100.00% 0.019621353851322847    S000004997, S000004387, S000003159, S000003439, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000004028, S000005999,     14  3818    5164    1.352540597171294   1.0 0.6426933342222417  29.374312706476815
52GOTERM_BP_ALL   GO:0009142~nucleoside triphosphate biosynthetic process 8   57.14%  1.1330305911809188E-11  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  52  5164    56.747252747252745  2.706801482954546E-8    1.933429638611983E-9    1.9884527358016157E-8
53GOTERM_BP_ALL   GO:0006118~electron transport   6   42.86%  1.1045195750922386E-5   S000003155, S000004997, S000004028, S000004387, S000003439, S000003159,     14  132 5164    16.766233766233768  0.026042020409655975    7.327069494768024E-4    0.019382452143623663
54GOTERM_BP_ALL   GO:0051179~localization 9   64.29%  0.005041519242062774    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999, S000003439,     14  1271    5164    2.611891648870406   0.999994297765288   0.23999017511150011 8.48817753150758
55GOTERM_BP_ALL   GO:0009141~nucleoside triphosphate metabolic process    8   57.14%  1.7133267420743854E-11  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  55  5164    53.65194805194805   4.093144034822416E-8    2.40773179172038E-9 3.006878079858666E-8
56GOTERM_BP_ALL   GO:0006754~ATP biosynthetic process 8   57.14%  3.2721626944045396E-12  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  44  5164    67.06493506493506   7.817191005621282E-9    1.954297723649745E-9    5.742617492643376E-9
57GOTERM_BP_ALL   GO:0006753~nucleoside phosphate metabolic process   8   57.14%  3.2721626944045396E-12  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  44  5164    67.06493506493506   7.817191005621282E-9    1.954297723649745E-9    5.742617492643376E-9
58GOTERM_BP_ALL   GO:0055086~nucleobase, nucleoside and nucleotide metabolic process  8   57.14%  1.7766800583227095E-7   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  202 5164    14.608203677510607  4.2435883801938967E-4   1.248371336348697E-5    3.1180536678165893E-4
59GOTERM_BP_ALL   GO:0006091~generation of precursor metabolites and energy   14  100.00% 1.7111195002613388E-16  S000004997, S000004387, S000003159, S000003439, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000004028, S000005999,     14  322 5164    16.03726708074534   5.304645611658998E-13   2.652322805829499E-13   3.885780586188048E-13
60GOTERM_BP_ALL   GO:0009117~nucleotide metabolic process 8   57.14%  5.840328188592497E-8    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  172 5164    17.156146179401993  1.3951571125714324E-4   4.500810660945653E-6    1.0249720883148683E-4
61GOTERM_BP_ALL   GO:0006732~coenzyme metabolic process   8   57.14%  1.081918945782046E-7    S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  188 5164    15.696048632218842  2.584370494638222E-4    7.832407207586378E-6    1.8987567623751644E-4
62GOTERM_BP_ALL   GO:0009108~coenzyme biosynthetic process    8   57.14%  1.3849814685789753E-9   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  101 5164    29.216407355021214  3.3087152432331735E-6   1.2254520420640347E-7   2.430630552385793E-6
63GOTERM_BP_ALL   GO:0001321~age-dependent general metabolic decline during replicative cell aging    2   14.29%  0.005029005617493512    S000003882, S000003882,     14  2   5164    368.85714285714283  0.9999941238340904  0.2442972120915523  8.467976406149823
64GOTERM_BP_ALL   GO:0016310~phosphorylation  11  78.57%  4.944705485834868E-12   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000000195, S000005999, S000003882, S000005999, S000004387,     14  224 5164    18.113520408163268  1.181291520158112E-8    1.6875593145115886E-9   8.677925045219581E-9
65GOTERM_BP_ALL   GO:0009206~purine ribonucleoside triphosphate biosynthetic process  8   57.14%  5.353761737671291E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  47  5164    62.78419452887537   1.2790030923248707E-8   1.4211145593634456E-9   9.39572863956073E-9
66GOTERM_BP_ALL   GO:0009205~purine ribonucleoside triphosphate metabolic process 8   57.14%  6.261365320746103E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  48  5164    61.476190476190474  1.4958304817014323E-8   1.4958304594969718E-9   1.0988576715220688E-8
67GOTERM_BP_ALL   GO:0009201~ribonucleoside triphosphate biosynthetic process 8   57.14%  8.476650445053009E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  50  5164    59.01714285714286   2.0250749632744203E-8   1.68756253415836E-9 1.4876466725155524E-8
68GOTERM_BP_ALL   GO:0009199~ribonucleoside triphosphate metabolic process    8   57.14%  9.815138922270817E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  51  5164    57.85994397759104   2.3448390007452247E-8   1.803722282645026E-9    1.7225498805117923E-8
69"""
70
71david_results_cc = """Category  Term    Count   %   PValue  Genes   List Total  Pop Hits    Pop Total   Fold Enrichment Bonferroni  Benjamini   FDR
72GOTERM_CC_ALL   GO:0044444~cytoplasmic part 12  85.71%  0.006088819536079676    S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000005999, S000003882, S000004028, S000004387, S000003439, S000003159,     14  2641    5632    1.827879050143344   0.9814660869691836  0.13275524314652598 8.72075140466545
73GOTERM_CC_ALL   GO:0031090~organelle membrane   10  71.43%  3.029187860465467E-6    S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  700 5632    5.746938775510205   0.0019761075921682636   1.0410314240905105E-4   0.004525594357451812
74GOTERM_CC_ALL   GO:0031975~envelope 10  71.43%  4.78624197919905E-8 S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  434 5632    9.269256089532588   3.125367247458488E-5    2.8412833162905216E-6   7.15077466795222E-5
75GOTERM_CC_ALL   GO:0043234~protein complex  13  92.86%  2.603956264388198E-7    S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  1316    5632    3.973947025618758   1.7002391047071796E-4   1.2145523826445626E-5   3.890375158688286E-4
76GOTERM_CC_ALL   GO:0044429~mitochondrial part   10  71.43%  1.0957063379250622E-7   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  477 5632    8.433662773285414   7.154706817014134E-5    5.503802375850242E-6    1.6370141305843688E-4
77GOTERM_CC_ALL   GO:0031967~organelle envelope   10  71.43%  4.503200851575421E-8    S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  431 5632    9.333775273450447   2.9405469906707005E-5   2.9405859021114367E-6   6.727903724135231E-5
78GOTERM_CC_ALL   GO:0005754~mitochondrial proton-transporting ATP synthase, catalytic core   3   21.43%  1.4737764835078688E-5   S000003882, S000000195, S000003882,     14  3   5632    402.2857142857143   0.009577670489531065    4.1833992163242684E-4   0.0220163639806481
79GOTERM_CC_ALL   GO:0031966~mitochondrial membrane   10  71.43%  1.080240517000826E-9    S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  283 5632    14.215042907622413  7.05396839717487E-7 1.4107940771168614E-7   1.613909073050479E-6
80GOTERM_CC_ALL   GO:0005753~mitochondrial proton-transporting ATP synthase complex   5   35.71%  9.998508143708598E-8    S000003882, S000002706, S000000195, S000005999, S000003882,     14  21  5632    95.78231292517006   6.528813007933287E-5    5.440840318726714E-6    1.493803553298534E-4
81GOTERM_CC_ALL   GO:0005751~mitochondrial respiratory chain complex IV   5   35.71%  8.365377472985592E-9    S000003155, S000004997, S000004028, S000004387, S000003159,     14  12  5632    167.61904761904765  5.462576611603431E-6    6.82823708353375E-7 1.2498103152402962E-5
82GOTERM_CC_ALL   GO:0044425~membrane part    13  92.86%  4.362609746181852E-7    S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  1375    5632    3.8034285714285714  2.848379045127247E-4    1.8991718223948517E-5   6.517839032826878E-4
83GOTERM_CC_ALL   GO:0016469~proton-transporting two-sector ATPase complex    8   57.14%  2.9258138389520786E-12  S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  47  5632    68.4741641337386    1.910528291126923E-9    9.552640900523102E-10   4.3711811947844126E-9
84GOTERM_CC_ALL   GO:0005746~mitochondrial respiratory chain  5   35.71%  9.653058317842064E-7    S000003155, S000004997, S000004028, S000004387, S000003159,     14  36  5632    55.87301587301587   6.30146386737862E-4 3.707843095557273E-5    0.0014421837375766522
85GOTERM_CC_ALL   GO:0044422~organelle part   10  71.43%  0.0368673468391256  S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  2301    5632    1.7483081889861551  0.9999999999777655  0.5353835078549395  42.94864604210752
86GOTERM_CC_ALL   GO:0033178~proton-transporting two-sector ATPase complex, catalytic domain  4   28.57%  6.414463893121058E-6    S000003882, S000002706, S000000195, S000003882,     14  17  5632    94.65546218487394   0.0041798981622530595   1.994400309182076E-4    0.009582956878873006
87GOTERM_CC_ALL   GO:0033177~proton-transporting two-sector ATPase complex, proton-transporting domain    3   21.43%  0.0010077286045780168   S000002706, S000005999, S000005999,     14  21  5632    57.469387755102034  0.4823099464317113  0.024089493962627162    1.4950448954651918
88GOTERM_CC_ALL   GO:0000276~mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) 2   14.29%  0.027376315885587123    S000002706, S000005999,     14  12  5632    67.04761904761905   0.9999999865729374  0.4427322586888206  33.94699076606338
89GOTERM_CC_ALL   GO:0000275~mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)  3   21.43%  7.340126705958842E-5    S000003882, S000000195, S000003882,     14  6   5632    201.14285714285714  0.04680214738322663 0.001915474595515665    0.1096074222371568
90GOTERM_CC_ALL   GO:0005743~mitochondrial inner membrane 10  71.43%  3.133119092481637E-11   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  191 5632    21.062079281974572  2.0459247185300455E-8   6.819749098774253E-9    4.680961174230447E-8
91GOTERM_CC_ALL   GO:0000274~mitochondrial proton-transporting ATP synthase, stator stalk 2   14.29%  0.006909968533425321    S000002706, S000005999,     14  3   5632    268.1904761904762   0.9891963501737456  0.14455501193220344 9.840977861323552
92GOTERM_CC_ALL   GO:0005740~mitochondrial envelope   10  71.43%  3.1435985004983136E-9   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  319 5632    12.610837438423646  2.0527677120352195E-6   2.932527882748559E-7    4.6966224354072494E-6
93GOTERM_CC_ALL   GO:0005739~mitochondrion    12  85.71%  1.328977450330144E-6    S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000005999, S000003882, S000004028, S000004387, S000003439, S000003159,     14  1154    5632    4.183213666749195   8.674464023651351E-4    4.821121845244303E-5    0.0019855104412713764
94GOTERM_CC_ALL   GO:0045277~respiratory chain complex IV 5   35.71%  8.365377472985592E-9    S000003155, S000004997, S000004028, S000004387, S000003159,     14  12  5632    167.61904761904765  5.462576611603431E-6    6.82823708353375E-7 1.2498103152402962E-5
95GOTERM_CC_ALL   GO:0044455~mitochondrial membrane part  10  71.43%  3.5280572783016857E-13  S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  117 5632    34.38339438339438   2.303972568284962E-10   2.303972568284962E-10   5.271338920920243E-10
96GOTERM_CC_ALL   GO:0045267~proton-transporting ATP synthase, catalytic core 3   21.43%  1.4737764835078688E-5   S000003882, S000000195, S000003882,     14  3   5632    402.2857142857143   0.009577670489531065    4.1833992163242684E-4   0.0220163639806481
97GOTERM_CC_ALL   GO:0032991~macromolecular complex   13  92.86%  6.200301918298537E-6    S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  1725    5632    3.0317184265010355  0.0040406243253358065   2.0241999553805012E-4   0.00926302113514188
98GOTERM_CC_ALL   GO:0019866~organelle inner membrane 10  71.43%  5.203286066955664E-11   S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  202 5632    19.915134370579917  3.39774325341935E-8 8.494358216815101E-9    7.773847121583799E-8
99GOTERM_CC_ALL   GO:0045265~proton-transporting ATP synthase, stator stalk   2   14.29%  0.006909968533425321    S000002706, S000005999,     14  3   5632    268.1904761904762   0.9891963501737456  0.14455501193220344 9.840977861323552
100GOTERM_CC_ALL   GO:0045263~proton-transporting ATP synthase complex, coupling factor F(o)   3   21.43%  4.406829632417675E-4    S000002706, S000005999, S000005999,     14  14  5632    86.20408163265306   0.2501104878313618  0.011009310594931931    0.6563739649655287
101GOTERM_CC_ALL   GO:0045261~proton-transporting ATP synthase complex, catalytic core F(1)    4   28.57%  8.008761082313701E-7    S000003882, S000002706, S000000195, S000003882,     14  9   5632    178.79365079365078  5.228355818966968E-4    3.268523508093146E-5    0.0011965242358913386
102GOTERM_CC_ALL   GO:0016020~membrane 13  92.86%  7.628592576013883E-6    S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  1756    5632    2.978197201431826   0.004969102909115897    2.26405727854595E-4 0.011396720953205097
103GOTERM_CC_ALL   GO:0045259~proton-transporting ATP synthase complex 6   42.86%  1.4166066493008505E-9   S000003882, S000002706, S000000195, S000005999, S000005999, S000003882,     14  25  5632    96.54857142857142   9.250436889818303E-7    1.541740075605702E-7    2.116449182576474E-6
104GOTERM_CC_ALL   GO:0044446~intracellular organelle part 10  71.43%  0.0368673468391256  S000003882, S000002706, S000003155, S000000195, S000005999, S000004997, S000003882, S000004028, S000004387, S000003159,     14  2301    5632    1.7483081889861551  0.9999999999777655  0.5353835078549395  42.94864604210752
105"""
106
107david_results_mf = """Category  Term    Count   %   PValue  Genes   List Total  Pop Hits    Pop Total   Fold Enrichment Bonferroni  Benjamini   FDR
108GOTERM_MF_ALL   GO:0046961~hydrogen ion transporting ATPase activity, rotational mechanism  7   50.00%  1.357188625187203E-10   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  35  4927    70.38571428571429   2.4076526516925156E-7   2.1887753720584158E-8   2.3007645788553077E-7
109GOTERM_MF_ALL   GO:0022804~active transmembrane transporter activity    7   50.00%  4.561468131602496E-6    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  193 4927    12.764248704663212  0.00805941031507107 3.517669381594146E-4    0.0077325147965212615
110GOTERM_MF_ALL   GO:0017111~nucleoside-triphosphatase activity   7   50.00%  1.354991458548405E-4    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  349 4927    7.058739255014327   0.21368025699328053 0.009203226040080392    0.22945586557691078
111GOTERM_MF_ALL   GO:0008553~hydrogen-exporting ATPase activity, phosphorylative mechanism    2   14.29%  0.015735007517678746    S000003882, S000003882,     14  6   4927    117.30952380952381  0.9999999999993964  0.5849039042925119  23.575548401812018
112GOTERM_MF_ALL   GO:0046933~hydrogen ion transporting ATP synthase activity, rotational mechanism    8   57.14%  1.504413377749123E-12   S000003882, S000002706, S000000195, S000005999, S000000195, S000005999, S000003882, S000005999,     14  38  4927    74.09022556390977   2.668917753467781E-9    2.965464540594098E-10   2.550426536629402E-9
113GOTERM_MF_ALL   GO:0015078~hydrogen ion transmembrane transporter activity  13  92.86%  8.312898389343022E-21   S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  90  4927    50.83412698412699   1.474708174269452E-17   1.474708174269452E-17   1.4092381372956447E-17
114GOTERM_MF_ALL   GO:0015077~monovalent inorganic cation transmembrane transporter activity   13  92.86%  1.6571922570429097E-20  S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  95  4927    48.15864661654136   2.939859063994122E-17   1.469929531997061E-17   2.809343288076066E-17
115GOTERM_MF_ALL   GO:0015075~ion transmembrane transporter activity   13  92.86%  1.3266048405395307E-16  S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  195 4927    23.461904761904762  1.9695356456850277E-13  3.941291737419306E-14   1.887379141862766E-13
116GOTERM_MF_ALL   GO:0016887~ATPase activity  7   50.00%  2.851574368180932E-5    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  265 4927    9.29622641509434    0.04932940179671719 0.002021460114576268    0.04833011644592711
117GOTERM_MF_ALL   GO:0015405~P-P-bond-hydrolysis-driven transmembrane transporter activity    7   50.00%  9.769490154343295E-8    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  101 4927    24.39108910891089   1.7329574628732747E-4   9.628329410094061E-6    1.6561645203028164E-4
118GOTERM_MF_ALL   GO:0015399~primary active transmembrane transporter activity    7   50.00%  9.769490154343295E-8    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  101 4927    24.39108910891089   1.7329574628732747E-4   9.628329410094061E-6    1.6561645203028164E-4
119GOTERM_MF_ALL   GO:0015662~ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism    2   14.29%  0.06406743892539128 S000003882, S000003882,     14  25  4927    28.154285714285713  1.0 0.9684032470122852  67.45191745405069
120GOTERM_MF_ALL   GO:0046872~metal ion binding    5   35.71%  0.07719554090708378 S000003882, S000002706, S000003155, S000000195, S000003882,     14  640 4927    2.7494419642857144  1.0 0.9829564745750087  74.38322655397852
121GOTERM_MF_ALL   GO:0043492~ATPase activity, coupled to movement of substances   7   50.00%  4.8652622253470385E-8   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  90  4927    27.372222222222224  8.630602941672727E-5    5.753967045607489E-6    8.24779769370565E-5
122GOTERM_MF_ALL   GO:0015002~heme-copper terminal oxidase activity    5   35.71%  7.691253005950271E-7    S000003155, S000004997, S000004028, S000004387, S000003159,     14  30  4927    58.654761904761905  0.0013634983981221094   6.201756809931513E-5    0.0013038461507353105
123GOTERM_MF_ALL   GO:0042626~ATPase activity, coupled to transmembrane movement of substances 7   50.00%  4.8652622253470385E-8   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  90  4927    27.372222222222224  8.630602941672727E-5    5.753967045607489E-6    8.24779769370565E-5
124GOTERM_MF_ALL   GO:0042625~ATPase activity, coupled to transmembrane movement of ions   7   50.00%  3.290094897579469E-9    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  58  4927    42.47413793103448   5.836611263854152E-6    4.48971306687973E-7 5.577509576415451E-6
125GOTERM_MF_ALL   GO:0042623~ATPase activity, coupled 7   50.00%  5.780183298730377E-6    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  201 4927    12.256218905472638  0.010201681018396247    4.2716185735414136E-4   0.009798362529434002
126GOTERM_MF_ALL   GO:0008324~cation transmembrane transporter activity    13  92.86%  1.244185803793163E-17   S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  161 4927    28.41659272404614   2.207185615929071E-14   5.517964039822678E-15   2.1091970603597518E-14
127GOTERM_MF_ALL   GO:0005215~transporter activity 13  92.86%  9.331263693917314E-12   S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  488 4927    9.375146370023419   1.6553750037395787E-8   1.65537505925073E-9 1.581884623291785E-8
128GOTERM_MF_ALL   GO:0019829~cation-transporting ATPase activity  7   50.00%  2.7146665610749877E-10  S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  39  4927    63.166666666666664  4.81581680311649E-7 4.0131815537414184E-8   4.60201854401987E-7
129GOTERM_MF_ALL   GO:0043167~ion binding  5   35.71%  0.08465249594692495 S000003882, S000002706, S000003155, S000000195, S000003882,     14  660 4927    2.666125541125541   1.0 0.9872049046718362  77.67510380858903
130GOTERM_MF_ALL   GO:0016491~oxidoreductase activity  6   42.86%  0.0016156535426757536   S000003155, S000004997, S000004028, S000004387, S000003439, S000003159,     14  361 4927    5.849228333992876   0.9432152372099303  0.08837982165926195 2.703911735463682
131GOTERM_MF_ALL   GO:0016820~hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances   7   50.00%  5.934326909367205E-8    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  93  4927    26.489247311827956  1.0526942125099747E-4   6.579663508032851E-6    1.0060120366750525E-4
132GOTERM_MF_ALL   GO:0016818~hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides   7   50.00%  1.8772210180800466E-4   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  370 4927    6.658108108108109   0.28326583700053276 0.012259428518476279    0.3177584959434432
133GOTERM_MF_ALL   GO:0016817~hydrolase activity, acting on acid anhydrides    7   50.00%  1.9634482734341306E-4   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  373 4927    6.604557640750671   0.2941481609246992  0.011940209452176997    0.3323313942078632
134GOTERM_MF_ALL   GO:0003824~catalytic activity   13  92.86%  0.0012913234405410655   S000004997, S000004387, S000003159, S000003439, S000003882, S000002706, S000000195, S000003155, S000000195, S000005999, S000003882, S000005999, S000004028,     14  2405    4927    1.9023166023166025  0.8989649855976286  0.0735633440992598  2.1667037480417095
135GOTERM_MF_ALL   GO:0016462~pyrophosphatase activity 7   50.00%  1.8772210180800466E-4   S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  370 4927    6.658108108108109   0.28326583700053276 0.012259428518476279    0.3177584959434432
136GOTERM_MF_ALL   GO:0016676~oxidoreductase activity, acting on heme group of donors, oxygen as acceptor  5   35.71%  7.691253005950271E-7    S000003155, S000004997, S000004028, S000004387, S000003159,     14  30  4927    58.654761904761905  0.0013634983981221094   6.201756809931513E-5    0.0013038461507353105
137GOTERM_MF_ALL   GO:0016675~oxidoreductase activity, acting on heme group of donors  5   35.71%  7.691253005950271E-7    S000003155, S000004997, S000004028, S000004387, S000003159,     14  30  4927    58.654761904761905  0.0013634983981221094   6.201756809931513E-5    0.0013038461507353105
138GOTERM_MF_ALL   GO:0022892~substrate-specific transporter activity  13  92.86%  1.045535361873502E-12   S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  407 4927    11.24096174096174   1.8547117175415906E-9   2.3183899244827444E-10  1.7723711387418462E-9
139GOTERM_MF_ALL   GO:0022891~substrate-specific transmembrane transporter activity    13  92.86%  1.1436221376671628E-13  S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  339 4927    13.495785924989466  2.0286217150555785E-10  3.381039892502713E-11   1.9385604232979858E-10
140GOTERM_MF_ALL   GO:0022890~inorganic cation transmembrane transporter activity  13  92.86%  2.6125070468606044E-18  S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  142 4927    32.21881287726358   4.634587501130712E-15   1.544862500376904E-15   4.428833833827902E-15
141GOTERM_MF_ALL   GO:0004129~cytochrome-c oxidase activity    5   35.71%  7.691253005950271E-7    S000003155, S000004997, S000004028, S000004387, S000003159,     14  30  4927    58.654761904761905  0.0013634983981221094   6.201756809931513E-5    0.0013038461507353105
142GOTERM_MF_ALL   GO:0016787~hydrolase activity   7   50.00%  0.030218055645008027    S000003882, S000002706, S000000195, S000000195, S000005999, S000003882, S000005999,     14  988 4927    2.493421052631579   1.0 0.8078538878815004  40.55798333297395
143GOTERM_MF_ALL   GO:0022857~transmembrane transporter activity   13  92.86%  6.05182729099852E-13    S000004997, S000004387, S000003159, S000003882, S000002706, S000000195, S000003155, S000005999, S000000195, S000005999, S000003882, S000005999, S000004028,     14  389 4927    11.761109070877708  1.0735938804629086E-9   1.5337053849151516E-10  1.0259348925956147E-9
144"""
145
146def proces_david(dav):
147    lines = [line.split("\t") for line in dav.split("\n") if line]
148    keys = lines[0]
149    return dict([(line[1].split("~")[0], dict(zip(keys, line))) for line in lines])
150
151terms = [["GO:0009058", "GO:0006119"], ["GO:0031967", "GO:0044455"], ["GO:0046933", "GO:0003824"]]
152print "Genes:"
153print "\n".join(cluster_genes)
154
155for aspect, terms, david in zip(["P", "C", "F"], terms, [proces_david(david_results_bp), proces_david(david_results_cc), proces_david(david_results_mf)]):
156    enriched_terms = annotations.GetEnrichedTerms(cluster_genes, reference_genes, aspect=aspect, prob=obiProb.Hypergeometric())
157#    print enriched_terms
158    for term in terms:
159        print "Term: %s - %s" % (term, ontology[term].name)
160        print "    Annotated genes in reference: %i from %i" % (enriched_terms[term][2], len(reference_genes))
161        print "    Annotated genes in cluster: %i from %i" % (len(enriched_terms[term][0]), len(cluster_genes))
162        print "    Enrichment: %.3f" % ((len(enriched_terms[term][0]) / len(cluster_genes)) / (enriched_terms[term][2]/len(reference_genes)))
163        print "    p-value (hypergeometric distribution): %f" % (enriched_terms[term][1])
164        print "    Comment: results from NCBI David (%s):" % david_date
165        print "        Annotated genes in reference: %s from %s" % (david[term]["Pop Hits"], david[term]["Pop Total"])
166        print "        Annotated genes in cluster: %s from %s" % (david[term]["Count"], david[term]["List Total"])
167        print "        Enrichment: %s" % david[term]["Fold Enrichment"]
168        print "        p-value: %s" % david[term]["PValue"]
169   
170
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