split Treefile with thousand individual trees
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Entering edit mode
6 days ago
Oscar ▴ 30

Hello to all.

I have an issue with a .treefile.

The output from an IQtree analysis contains phylogenetic trees in a single locus.treefile, so, I want to split this locus.treefile into single files to obtain 2060 individual files (gene_1.tree, gene_2.tree, gene_3.tree ... gene_2060.tree).

The estructure of the locus.treefile separate each tree with an " ; ". The following contains information for two of the trees (the file contains 2058 additional trees):

(AcspLA:0.0550850024,(((((((((((Amphipsocus_japonicus:1.5771368581,(Mesopsocus_unipunctatus:0.8365383843,Ptycta_johnsoni:0.0000025621):1.4774447149):4.8541249689,Eochi:0.0000022329):0.1344174527,((Asson:0.4126609598,(PocorIL:0.1836688674,Tecon:0.2418666321):0.0704386481):0.0280942648,((Dycol:0.1961781585,(FuspCA:0.1769105247,Valenzuela_badiostigma:0.1228532870):0.0368946618):0.1181803754,Pajap:0.2365433670):0.0336218799):0.0989756183):0.0275876256,NespEL:0.3799904864):0.0269265276,((((Bertkauia_sp:0.1996835619,Heterocaecilius_solocipennis:0.2810839219):0.1223689652,KaspPE:0.4073061209):0.0435778837,(((((Hemoc:0.0037848634,Hesmi:0.0039819046):0.0632385839,(Lachesilla_contraforcepeta:0.0457735376,LaspGHN:0.0685122622):0.0097144339):0.0108621111,(((Lapic:0.0409583342,(LarufMEX:0.0174576318,Lasp7Q:0.0233519081):0.0237937365):0.0129996555,Lapun:0.0711267075):0.0071725659,Latex:0.0290190965):0.0335594774):0.0198046870,Laped:0.0812291217):0.0096622032,LaspMLY:0.0616375041):0.1644360762):0.0200978861,(Eccry:0.2533730982,Ectopsocus_briggsi:0.0972539113):0.1569484594):0.0363384695):0.0495779929,(((Anama:0.4951611270,Idori:0.1406206376):0.0578980461,Xasom:1.6911980061):0.3626265631,KispEL:0.0673328073):0.1909529197):0.0245502365,(Elipsocus_kuriliensis:0.1812454931,Prpul:0.2501024166):0.0070727122):0.1581322264,(GRA1sp1LA:0.0565059253,Grint:0.0860243458):0.0343478571):0.0719184687,AnspLA:0.1231998418):0.1158243461,((Anpal:0.0377743706,PrspLA:0.0746790203):0.0128505872,((GRA2sp1LA:0.0433712951,GRAspLA:0.0116273364):0.0416790880,Wajar:0.1327100784):0.0165778607):0.0264912004):0.0311045638,Dacal:0.0083742870):0.0077716369,Daanc:0.0084948721); (AcspLA:0.0379350549,((((((((((((Amphipsocus_japonicus:0.1642865189,PocorIL:0.1997053515):0.1722065132,(((Dycol:0.3834131188,(FuspCA:0.2114511523,Valenzuela_badiostigma:0.2770859591):0.0463773738):0.0514403967,((Tecon:0.1006012119,Matsumuraiella_radiopicta:0.0499927965):0.1550516942,Graphopsocus_cruciatus:0.2057583464):0.1171203545):0.0443764170,(Pajap:0.3604314657,Xasom:0.2461379116):0.0688824437):0.0191288451):0.0792404837,Asson:0.4319538940):0.3197999993,(KaspPE:0.3052930718,Peripsocus_phaeopterus:0.1838043688):0.2703568320):0.0474314778,(Eccry:0.2663960114,Ectopsocus_briggsi:0.2460982767):0.1337472595):0.0385258672,((((Hemoc:0.0226485683,Hesmi:0.0206254129):0.1342505608,(Lachesilla_contraforcepeta:0.2090130012,LaspGHN:0.2298257799):0.1036318426):0.0396288984,((Lapic:0.0758480974,(((LarufMEX:0.0017301144,Lachesilla_abiesicola:0.0026905720):0.0299939566,Lasp7Q:0.0402756397):0.0334689461,Latex:0.0773631299):0.0270828381):0.0304605185,Lapun:0.1516689743):0.0542199019):0.0528901382,(Laped:0.2721550187,LaspMLY:0.2152446242):0.0241130509):0.3037300351):0.0255452620,((((Elipsocus_kuriliensis:0.2183555966,((Eochi:0.2621431376,Prpul:0.1927386607):0.0395580421,Mesopsocus_unipunctatus:0.1971171911):0.0342170127):0.0282165916,NespEL:0.2688196832):0.0271236508,KispEL:0.3361114626):0.0283502279,Idori:0.2219599092):0.0292904394):0.0361875746,((Bertkauia_sp:0.3832621946,Ptycta_johnsoni:0.3643924335):0.0771794895,Heterocaecilius_solocipennis:0.3672314209):0.0630369267):0.1789144285,((Anama:0.0534345579,AnspLA:0.0551688796):0.1626658476,(GRA1sp1LA:0.0801877236,Grint:0.1161832572):0.0987008193):0.0251440606):0.0538297391,Wajar:0.1936296251):0.0843190159,(GRA2sp1LA:0.0058000833,GRAspLA:0.0056482550):0.0752862083):0.0140802391,(Anpal:0.0544385358,PrspLA:0.0971035402):0.0246760636):0.0651149887,(Daanc:0.0256311204,Dacal:0.0342578557):0.0249309009);

Thanks for the help,

Best,

Os.

phylogenomics detection outlier • 91 views
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Entering edit mode
6 days ago
Mensur Dlakic ★ 20k
split -l 1 -d -a 4 locus.treefile gene_

Your files will be named gene_???? where those question marks stand for numbers from 0000-2059.

There may be a better way to rename them so they all end up with .tree, but here is my suggestion:

for i in gene_???? ; do mv $i $i.tree ; done
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