[Bioperl-l] fail to obtain node-to-node distance from a newick file

Ross KK Leung ross at cuhk.edu.hk
Sat Sep 10 19:06:44 EDT 2011 

Hi Greg,

 

The values are correct! However, how to install this bioperl-live module? my
bioperl is 1.6.1 but there's an error:

 

Can't locate object method "find" via package "Bio::Tree::Tree" at
TreeCalDist.pl line 32, <GEN0> line 1.

my $mt = $tree->find($keyword);  #line 32

 

 

From: gjuggler at gmail.com [mailto:gjuggler at gmail.com] On Behalf Of Gregory
Jordan
Sent: 2011Äê9ÔÂ10ÈÕ 23:40
To: bioperl-l List; Ross KK Leung
Subject: Re: [Bioperl-l] fail to obtain node-to-node distance from a newick
file

 

Hi Ross,

 

Which version of BioPerl are you using?

 

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree
/NodeFunctionsI.pm#L406) the following script works for me. Do those values
look sensible to you? The code on the new branch is a bit experimental, so I
wouldn't be surprised if all the edge cases for calculations like this
aren't covered.

 

--greg

 

use Bio::TreeIO;

 

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");

my $tree = $treeio->next_tree;

my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");

my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");

my $ma = $tree->find("Mycobacterium_abscessus");

my $distance = $mt->distance($ma);

print "MT - MA: ".$mt->distance($ma)."\n";

print "MT - MS: ".$mt->distance($ms)."\n";

print "MS - MA: ".$ms->distance($ma)."\n";

# MT - MA: 0.24326

# MT - MS: 0.18573

# MS - MA: 0.20729

 

--greg

 

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"



What's the problem?



use Bio::TreeIO;



($treefh) = @ARGV;



my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;



$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);



my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);



my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";





#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;

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