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support old version jplace file #25

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Merged
merged 13 commits into from
Nov 25, 2019
Merged

support old version jplace file #25

merged 13 commits into from
Nov 25, 2019

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Description

First question, for old version jplace file, edges of tree are not always in curly braces, they are sometimes in square brackets. Second question, the p field of placements in jplace is not always in the first column, and the n or nm field is not always in second column.

Related Issue

file1 <- system.file("extdata", "upwelling.jplace", package="treeio")
jp1 <- jsonlite::fromJSON(file1)
jp1$tree

[1] "((((chloroplast_Bangiopsis_subsimplex.AY119736_:0.0296744[0],((chloroplast_Erythrotrichia_carnea.AY119739_:0.0669714[1],chloroplast_Rhodochaete_parvula.AY119743_:0.0846451[2]):0.0473989[3],chloroplast_Rhodosorus_marinus.AY119744_:0.06578[4]):0.0135707[5]):0.0125774[6],((((chloroplast_Cyanidium_sp._Monte_Rotaro.AY391365_:0.14225[7],(chloroplast_Cyanidium_caldarium.AY541290_:0.229326[8],(chloroplast_Cyanidioschyzon_merolae_strain_DBV201.AY119729_:2.62716e-06[9],chloroplast_Cyanidioschyzon_merolae.AY119730_:0.00124934[10]):0.0764407[11]):0.0594726[12]):0.0411324[13],(((chloroplast_Vaucheria_litorea.AF227740_:0.0548633[14],(chloroplast_Bumilleriopsis_filiformis.X79223_:0.00713038[15],plastid_Tribonema_aequale.AY528860_:0.013462[16]):0.0188887[17]):0.0307213[18],((chloroplast_Heterosigma_carterae.HCU18090_:2.62716e-06[19],chloroplast_Heterosigma_akashiwo.AY119759_:2.62716e-06[20]):0.0264439[21],((((((((chloroplast_Pavlova_lutheri.AY119755_:0.0155337[22],chloroplast_Pavlova_gyrans.AY119754_:0.031921[23]):0.0284429[24],chloroplast_Pavlova_gyrans.AJ575575_:0.0184771[25]):0.0369803[26],(chloroplast_Phaeocystis_antarctica.AY119756_:0.032481[27],(((chloroplast_Emiliania_huxleyi.AJ575573_:0.00127856[28],(chloroplast_Emiliania_huxleyi.AY675521_:2.62716e-06[29],chloroplast_Emiliania_huxleyi.AY119752_:2.62716e-06[30]):2.62716e-06[31]):0.00987446[32],(chloroplast_Isochrysis_sp._SAG_927-2.AY119753_:0.00129238[33],chloroplast_Isochrysis_galbana.AJ575574_:0.00127939[34]):0.0180921[35]):0.00662445[36],((chloroplast_Prymnesium_parvum.AJ575576_:0.00781698[37],chloroplast_Prymnesium_parvum.AY119758_:0.0107643[38]):0.0264028[39],(chloroplast_Pleurochrysis_carterae.AY119757_:0.0355143[40],(chloroplast_Imantonia_rotunda.EU851963_:0.0471273[41],chloroplast_Chrysochromulina_polylepis.AJ575572_:0.0130868[42]):0.00866583[43]):0.00227491[44]):0.00414201[45]):0.00687632[46]):0.0219329[47]):0.0287832[48],(((chloroplast_Pycnococcus_provasolii.EU851957_:0.0991635[49],(chloroplast_Mantoniella_squamata.EU851964_:0.00735936[50],((chloroplast_Micromonas_pusilla.EU851965_:2.62716e-06[51],plastid_uncultured_Prasinophyceae.AY176639_:2.62716e-06[52]):0.00915325[53],(chloroplast_Ostreococcus_sp._RCC789.EU851970_:0.0155525[54],(((chloroplast_Bathycoccus_prasinos.EU851955_:0.0100228[55],(uncultured_Prasinophyceae.AY509538_:2.62716e-06[56],uncultured_Prasinophyceae.AY509537_:0.00127378[57]):0.018912[58]):0.0387387[59],plastid_uncultured_Prasinophyceae.AY176630_:0.0268697[60]):0.00352364[61],(plastid_uncultured_Prasinophyceae.AY176628_:0.0181777[62],((Ostreococcus_tauri_2_:2.62716e-06[63],Ostreococcus_tauri_:2.62716e-06[64]):0.010015[65],(plastid_uncultured_Prasinophyceae.AY176620_:2.62716e-06[66],chloroplast_Ostreococcus_sp._RCC344.EU851961_:2.62716e-06[67]):0.00559304[68]):0.00536261[69]):0.00155492[70]):0.0103018[71]):0.0195476[72]):0.0116489[73]):0.0572199[74]):0.0500432[75],(((chloroplast_Chlorella_pyrenoidosa.EU043049_:0.00246255[76],chloroplast_Chlorella_vulgaris.EU043044_:0.00128935[77]):0.0754025[78],(Bigelowiella_natans_:0.108317[79],(Chlamydomonas_reinhardtii_:0.0747763[80],(chloroplast_Picochlorum_sp._RCC289.EU851960_:0.0553565[81],(Chlorella_vulgaris_:0.0479649[82],(chloroplast_Chlorella_pyrenoidosa.EU043047_:0.00249514[83],(chloroplast_Chlorella_pyrenoidosa.EU043046_:0.00250654[84],chloroplast_Auxenochlorella_protothecoides.EU043045_:0.00125447[85]):2.62716e-06[86]):0.0170169[87]):0.0187545[88]):0.0162818[89]):0.0140918[90]):0.00695735[91]):0.0236101[92],plastid_Tetraselmis_marina.AY857618_:0.0274149[93]):0.0121743[94]):0.0144071[95],chloroplast_Pseudochlorella_sp._CCAP_211/1A.EU043048_:0.0910399[96]):0.036916[97]):0.0178205[98],((((Microcystis_aerouginosa_gi166362741refNC_010296.1_:0.100689[99],((Cyanothece_sp._ATCC_51142.CAU39610_:0.0139443[100],Cyanothece_sp._CCY_0110___gi126657681refNZ_AAXW01000012.1_:0.0325757[101]):0.0368903[102],(Cyanothece_sp._PCC_7425_gi218437013refNC_011729.1_:0.0799602[103],Cyanothece_sp._PCC_8801_gi218244892refNC_011726.1_:0.06558[104]):0.017916[105]):0.0403653[106]):0.0316316[107],((Lyngbya_sp_PCC_8106___gi119483230refNZ_AAVU01000001.1_:0.174445[108],Mastigocladus_laminosus.AF170924_:0.292674[109]):0.0843939[110],((Nostock_punctiforme_gi186680550refNC_010628.1_:0.118661[111],((Nostoc_sp._PCC_7120_gi17227497refNC_003272.1_:0.00952002[112],Anabaena_variabilis_A_gi75906225refNC_007413.1_:0.0234306[113]):0.0386248[114],(Fremyella_diplosiphon.FDIPSBA_:0.0552418[115],Nodularia_spumige_gi119512239refNZ_AAVW01000065.1_:0.053628[116]):0.0204852[117]):0.0272273[118]):0.0361292[119],(Synechococcus_sp._PCC_7002___gi170076636refNC_010475.1_:0.0899374[120],((Microcoleus_chthonoplastes_PCC_7420___gi224400128refNW_002435220.1_:0.0921412[121],(((Gloeobacter_violaceus_gi37519569refNC_005125.1_:0.287597[122],(Synechococcus_sp._JA-3-3Ab__gi86604733refNC_007775.1_:0.0880842[123],Synechococcus_sp._JA-2-3Ba____gi86607503refNC_007776.1_:0.637056[124]):0.0999416[125]):0.153018[126],(Thermosynechococcus_gi22297544refNC_004113.1_:0.12404[127],((Acaryochloris_marina_MBIC11017.AB303650_2_:2.62716e-06[128],Acaryochloris_marina_MBIC11017.AB303650_:2.62716e-06[129]):0.240343[130],Cyanothece_sp._PCC_7425_gi220905643refNC_011884.1_:0.144677[131]):0.0173981[132]):0.0300352[133]):0.0359263[134],((Prochlorothrix_hollandica.X14308_:2.62716e-06[135],Prochlorothrix_hollandica.X14523_:0.00135654[136]):0.0865866[137],((Synechococcus_elongatus_PCC_7942___gi81298811refNC_007604.1_:0.0113412[138],Synechococcus_elongatus_PCC_6301___gi56750010refNC_006576.1_:0.00283364[139]):0.115006[140],((Synechococcus_sp._WH_5701__gi87303211refNZ_AANO01000010.1_:0.077507[141],((Synechococcus_sp._WH_5701___gi211606500refNZ_CH724159.1_:2.62716e-06[142],Synechococcus_sp._WH_5701_gi87303578refNZ_AANO01000013.1_:2.62716e-06[143]):2.62716e-06[144],(Synechococcus_sp._WH_5701__gi87301761refNZ_AANO01000004.1_:2.62716e-06[145],Synechococcus_sp._WH_5701__gi211606501refNZ_CH724160.1_:2.62716e-06[146]):2.62716e-06[147]):0.0116739[148]):0.0161385[149],((((((Synechococcus_sp.__WH_7805__gi88807077refNZ_AAOK01000001.1_:0.00282307[150],(Synechococcus_sp._WH_7805__gi88807768refNZ_AAOK01000002.1_:2.62716e-06[151],(Synechococcus_sp._WH_7805_gi211594037refNZ_CH724168.1_:2.62716e-06[152],Synechococcus_sp._WH_7805__gi88809542refNZ_AAOK01000006.1_:2.62716e-06[153]):0.00138873[154]):0.00276638[155]):0.00844882[156],Synechococcus_sp._WH_7803___gi148238336refNC_009481.1_:0.00801814[157]):0.0180692[158],(Synechococcus_sp._RS9917___gi87125174refNZ_AANP01000006.1_:2.62716e-06[159],(Synechococcus_sp._RS9917___gi87124875refNZ_AANP01000005.1_:2.62716e-06[160],Synechococcus_sp._RS9__gi211606499refNZ_CH724158.1_:2.62716e-06[161]):0.00278788[162]):0.00874388[163]):0.00421837[164],((Synechococcus_sp._RCC307_gi148241099refNC_009482.1_:0.0436787[165],(Synechococcus_sp._CC9605_gi78211558refNC_007516.1_:0.0292645[166],((Synechococcus_sp._CC9902_gi78183584refNC_007513.1_:0.00569178[167],(Synechococcus_sp.__BL107__gi116072546refNZ_AATZ01000004.1_:2.62716e-06[168],Synechococcus_sp._BL107_gi211594587refNZ_DS022298.1_:2.62716e-06[169]):0.00260315[170]):0.0417448[171],Synechococcus_sp._WH_8102_gi33864539refNC_005070.1_:0.0213766[172]):0.00906289[173]):0.0225313[174]):0.0359511[175],(Synechococcus_sp._gi87123618refNZ_AANP01000002.1_:0.0436975[176],(Prochlorococcus_marinus_str._MIT_9303___gi124021714refNC_008820.1_:0.213286[177],(Synechococcus_sp.__RS9916__gi116074999refNZ_AAUA01000003.1_:2.62716e-06[178],Synechococcus_sp._RS9__gi211594588refNZ_DS022299.1_:2.62716e-06[179]):0.0326556[180]):0.018698[181]):0.0201245[182]):0.0123275[183]):0.0171659[184],Synechococcus_sp._RS9917__gi87124182refNZ_AANP01000003.1_:0.206502[185]):0.0124936[186],Cyanobium_sp._PCC_70_gi223490194refNW_002243451.1_:0.0349915[187]):0.0244749[188]):0.0552727[189]):0.0484564[190]):0.0330387[191]):0.053081[192]):0.0322305[193],Synechocystis_sp_PCC_6803___gi16329170refNC_000911.1_:0.055271[194]):0.0342032[195]):0.0313[196]):0.003393[197]):0.0208115[198]):0.0544215[199],Trichodesmium_erythr_gi113473942refNC_008312.1_:0.115405[200]):0.0393095[201],(((Prochlorococcus_marinus_str._NATL1A___gi124024712refNC_008819.1_:2.62716e-06[202],Procholococcus_marinus_str._NATL2A___gi162958048refNC_007335.2_:0.00387272[203]):0.0652348[204],(Prochlorococcus_marinus_subsp._marinus_str._CCMP1375_gi33239452refNC_005042.1_:0.107069[205],Procholococcus_marinus_str._MIT_9211___gi159902540refNC_009976.1_:0.0648332[206]):0.0645389[207]):0.0732978[208],((Prochlorococcus_marinus_subsp._pastoris_str._CCMP1986_gi33860560refNC_005072.1_:0.00386442[209],Prochlorococcus_marinus_str._MIT_9515___gi123965234refNC_008817.1_:0.00513584[210]):0.0108901[211],(Prochlorococcus_marinus_str._AS9601_gi123967536refNC_008816.1_:2.62716e-06[212],(Prochlorococcus_marinus_str._MIT_9301__gi126695337refNC_009091.1_:0.0115344[213],(Prochlorococcus_marinus_str._MIT_9312_gi78778385refNC_007577.1_:0.00402475[214],(Procholococcus_marinus_str._MIT_9215___gi157412338refNC_009840.1_:2.62716e-06[215],Procholococcus_marinus_str._MIT_9202_gi225077649refNW_002467725.1_:0.00254717[216]):0.00627816[217]):0.005283[218]):0.00140083[219]):0.0116153[220]):0.0461325[221]):0.158153[222]):0.0598755[223]):0.0735348[224],(Fragilariopsis_psbA_:0.0261132[225],Pmultiseries_psbA_:0.0139712[226]):0.0137913[227]):0.0138551[228],(plastid_Ballia_callitricha.DQ787635_:0.0643769[229],Phaeodactylum_tricornutum_:0.0212228[230]):0.0108685[231]):0.0220385[232],(chloroplast_Skeletonema_costatum.AY119761_:0.0037475[233],(Thalassiosira_pseudonana_2_:2.62716e-06[234],Thalassiosira_pseudonana_:2.62716e-06[235]):0.00128936[236]):0.0148686[237]):0.0413777[238]):0.00677313[239]):0.0181954[240],(((chloroplast_Fucus_vesiculosus.DQ307679_:0.0363344[241],chloroplast_Ectocarpus_siliculosus.X56695_:0.0425758[242]):0.0409036[243],(chloroplast_Padina_crassa.AY422643_:0.00945597[244],(plastid_Padina_japonica.AY430360_:0.0151942[245],(plastid_Padina_arborescens.AY430357_:0.0172454[246],(plastid_Padina_crassa.AY430358_:2.62716e-06[247],(plastid_Padina_crassa.AY430359_:2.62716e-06[248],plastid_Padina_crassa.AY430361_:2.62716e-06[249]):2.62716e-06[250]):0.00738025[251]):0.00531298[252]):0.00363975[253]):0.0184925[254]):0.0115372[255],(chloroplast_Pachydictyon_coriaceum.AY422614_:0.0259434[256],((chloroplast_Dictyota_dichotoma.AY748320_:2.62716e-06[257],chloroplast_Dictyota_dichotoma.AY748319_:2.62716e-06[258]):0.00249624[259],((chloroplast_Dictyota_dichotoma_var._linearis.AY422632_:2.62716e-06[260],chloroplast_Dictyota_dichotoma.AY748321_:2.62716e-06[261]):2.62716e-06[262],chloroplast_Dictyota_dichotoma_var._linearis.AY422631_:2.62716e-06[263]):2.62716e-06[264]):0.00881923[265]):0.0248245[266]):0.0409737[267]):0.029059[268]):0.0193884[269],(((Synechococcus_sp._PCC_7335_gi225144522refNW_002475532.1_:0.432534[270],Cyanothece_sp._CC_gi126660325refNZ_AAXW01000053.1_:0.278199[271]):0.119517[272],(gi|5821419|dbj|AB025589.1|:0.454275[273],(chloroplast_Galdieria_sulphuraria.AY541295_:0.0610795[274],((chloroplast_Galdieria_sulphuraria.AY541294_:0.00123271[275],chloroplast_Galdieria_sulphuraria.AY541293_:2.62716e-06[276]):0.0217312[277],(chloroplast_Cyanidium_caldarium.X52758_:0.0207176[278],chloroplast_Galdieria_sulphuraria.AY119731_:4.5192e-05[279]):0.0300301[280]):0.0529495[281]):0.0732256[282]):0.0354697[283]):0.0691202[284],(Mesostigma_viride_:0.101394[285],Cyanophora_paradoxa_:0.0702149[286]):0.0248976[287]):0.014028[288]):0.0258734[289],(chloroplast_Flintiella_sanguinaria.AY119740_:0.0513641[290],chloroplast_Porphyridium_aerugineum.AY119741_:0.0495445[291]):0.0174643[292]):0.020752[293]):0.050369[294],(chloroplast_Palmaria_palmata.PPU28165_:0.104631[295],(plastid_Antithamnionella_sp._A31.DQ787640_:0.0202479[296],(chloroplast_Antithamnion_sp.X55364_:0.0292228[297],plastid_Carpoblepharis_flaccida.DQ787643_:0.112145[298]):0.00887985[299]):0.0324329[300]):0.0175603[301]):0.0769895[302],Porphyra_yezoensis_:0.0134362[303],Porphyra_purpurea_:0.022228[304]):0[305];"

file2 <- system.file("extdata", "ref35extend.jplace", package="treeio")
jp2 <- jsonlite::fromJSON(file2)
colnames(jp2$placements)

[1] "n" "p"

Example

For First question, I checked the tree format in jplace_treetext_to_phylo using grepl("\\{(\\d+)\\}", tree.text) and grepl("\\[(\\d+)\\]", tree.text). For second question, I used the colnames of placements instead of the number of column in extract.placement, when the column number is two, I used placements[,-match("p", colnames(placements))] to obtain the names field of placements.

@GuangchuangYu GuangchuangYu merged commit aaf64fd into YuLab-SMU:master Nov 25, 2019
@GuangchuangYu
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  1. document the differences of different jplace versions as I mentioned in wechat group.
  2. pls fixed tests.
> 
> test_check("treeio")
── 1. Failure: offspring works on bifurcating trees (@test-access-related-nodes.
`offspring(bi_tree, 1)` did not throw an error.

── 2. Failure: offspring works on non-bifurcating trees (@test-access-related-no
`offspring(multi_tree, 1)` did not throw an error.

{
	"tree": "(K:0.081785{11},N:0.062341{14},(D:0.082021{4},(L:0.005508{12},(J:0.013996{10},(G:0.045746{7},((C:0.02773{3},(E:0.031104{5},O:0.048389{15})23:0.008328{23})22:0.015959{22},(H:0.021007{8},(I:0.014739{9},(B:0.031643{2},(A:0.01034{1},(F:0.006649{6},M:0.009195{13})28:0.028303{28})27:0.008072{27})26:0.0035{26})25:0.020359{25})24:0.000555{24})21:0.023675{21})20:0.045745{20})19:0.014684{19})18:0.059308{18})17:0.231628{17})16{16};",
	"data":[
  {
    "edge_num": 1,
    "subs": "C214T / G294T / T966C / C1641T / A1808G / C1941T / C2070T",
    "AA_subs": "K603R",
    "t": 0.01,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0646,
    "dN": 0.0007,
    "dS": 0.0101,
    "N_x_dN": 1,
    "S_x_dS": 6.4
  },
  {
    "edge_num": 2,
    "subs": "C222T / G555A / C732A / C828T / G939T / T999C / A1047G / G1083A / C1263T / G1329A / A1341G / A1344T / T1405C / T1440C / C1752T / A1827G / C1911T / C1941T / G2013A / T2022C / C2043T",
    "AA_subs": "",
    "t": 0.032,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0001,
    "dN": 0,
    "dS": 0.0358,
    "N_x_dN": 0,
    "S_x_dS": 22.7
  },
  {
    "edge_num": 3,
    "subs": "A204G / C222T / G504A / A815G / C891T / G1023T / T1061C / G1101A / G1176A / C1299T / C1545T / C1584T / T1626C / A1668G / G1878A / G1884T / C1944T / A1947G",
    "AA_subs": "N272S / I354T",
    "t": 0.028,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0461,
    "dN": 0.0013,
    "dS": 0.0282,
    "N_x_dN": 2,
    "S_x_dS": 17.9
  },
  {
    "edge_num": 4,
    "subs": "A111G / A168G / T211C / A213G / T214C / G243A / A311G / T315A / G369A / G423A / A477C / G504A / G555A / G585A / C621T / C636T / A768G / T771C / G774A / T780C / C825T / A867G / A870G / G885A / C888T / G897A / C987T / C1006T / G1017A / A1047G / C1062T / A1146T / G1197A / A1230G / A1281G / T1365C / C1392T / T1439C / A1443G / T1512C / T1530C / T1539C / T1560C / A1608G / G1671A / G1689A / G1695A / A1761G / T1776C / T1787C / A1914G / G2052A",
    "AA_subs": "K104R / F105L / E382D / F480S / I596T",
    "t": 0.082,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0385,
    "dN": 0.0033,
    "dS": 0.0849,
    "N_x_dN": 5,
    "S_x_dS": 53.8
  },
  {
    "edge_num": 5,
    "subs": "C174T / G243A / G321A / A622T / T831C / A894G / G948T / C960T / A984G / C1041T / G1135A / T1215C / T1249C / A1401G / T1527A / T1594C / A1826G / A1848G / T1950C / G1986A",
    "AA_subs": "T208S / V379I / K609R",
    "t": 0.031,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.0641,
    "dN": 0.002,
    "dS": 0.0305,
    "N_x_dN": 3,
    "S_x_dS": 19.3
  },
  {
    "edge_num": 6,
    "subs": "T829C / C1353T / A1443G / T1548C / C1645A",
    "AA_subs": "S277P / L549I",
    "t": 0.007,
    "N": 1514.9,
    "S": 633.1,
    "dN_vs_dS": 0.298,
    "dN": 0.0013,
    "dS": 0.0044,
    "N_x_dN": 2,
    "S_x_dS": 2.8
  },
  {
    "edge_num": 7,
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    "subs": "C16A / G96A / C169A / A286C / A344G / C531T / A534C / G537A / A789T / T822A / G879A / A962T / C1005T / G1074A / A1090G / C1110T / A1125T / A1146G / C1164T / C1182T / G1239A / T1410C / T1413C / C1428T / C1473A / C1641T / T1764C / A1851G / T1932G / C1965A / A1983G / T2022C",
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    "edge_num": 23,
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    "edge_num": 25,
    "subs": "G96A / T162C / T214C / G303A / T318C / A366G / C390T / G498A / A1146G / G1425A / C1461T / G1677A / A1902G / A1959G",
    "AA_subs": "",
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  {
    "edge_num": 26,
    "subs": "G785A / A1067G / C1548T",
    "AA_subs": "R262K / K356R",
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    "S_x_dS": 0.5
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  {
    "edge_num": 27,
    "subs": "C1168T / G1180A / A1242G / T1249C / T1257C",
    "AA_subs": "D394N",
    "t": 0.008,
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    "S": 633.1,
    "dN_vs_dS": 0.0863,
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    "dS": 0.0076,
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  },
  {
    "edge_num": 28,
    "subs": "A21G / T186A / T211C / G294A / T299C / A348T / C438T / C444T / C582T / A744G / C771T / A785G / G786A / C1374T / C1467T / A1500G / A1869G / G1878A / C2043T",
    "AA_subs": "V100A / K262R",
    "t": 0.028,
    "N": 1514.9,
    "S": 633.1,
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    "dS": 0.0289,
    "N_x_dN": 2,
    "S_x_dS": 18.3
  }
],
	"metadata": {"info": "R-package treeio", "data": "Mon Nov 25 23:40:14 2019"}
}
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 130 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
1. Failure: offspring works on bifurcating trees (@test-access-related-nodes.R#70) 
2. Failure: offspring works on non-bifurcating trees (@test-access-related-nodes.R#76) 

Error: testthat unit tests failed
Execution halted

1 error ✖ | 0 warnings ✔ | 0 notes ✔

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2 participants
@xiangpin @GuangchuangYu