Merge pull request #98 from compgenomicslab/dev-repo

Dev repo

examples/analytic_example/Anolis.tre

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+((((((((ahli:0.1308887296,allogus:0.1308887296):0.109078899,rubribarbus:0.2399676286):0.3477240729,imias:0.5876917015):0.1279779191,((((sagrei:0.2576204042,(bremeri:0.1097436524,quadriocellifer:0.1097436524):0.1478767518):0.06150599843,ophiolepis:0.3191264027):0.08721921759,mestrei:0.4063456203):0.1298140501,(((jubar:0.1188659524,homolechis:0.1188659524):0.09052271908,confusus:0.2093886715):0.04215577182,guafe:0.2515444433):0.2846152271):0.1795099503):0.1377237125,((((garmani:0.2000335809,opalinus:0.2000335809):0.01968719882,grahami:0.2197207797):0.2178099139,valencienni:0.4375306936):0.1226128606,(lineatopus:0.4713710622,reconditus:0.4713710622):0.08877249208):0.2932497789):0.06703519523,(((evermanni:0.2135202715,stratulus:0.2135202715):0.3521520586,(((krugi:0.3267560653,pulchellus:0.3267560653):0.1312930371,(gundlachi:0.3864660126,poncensis:0.3864660126):0.0715830898):0.03035078065,(cooki:0.395288192,cristatellus:0.395288192):0.09311169105):0.07727244709):0.1495575755,(((brevirostris:0.2757423466,(caudalis:0.1704974619,marron:0.1704974619):0.1052448847):0.02672749452,websteri:0.3024698411):0.09835748687,distichus:0.400827328):0.3144025776):0.2051986227):0.03488732303,(((barbouri:0.8021085018,(((alumina:0.2681076879,semilineatus:0.2681076879):0.219367178,olssoni:0.4874748658):0.2622236606,(etheridgei:0.5883072151,(fowleri:0.3770938401,insolitus:0.3770938401):0.211213375):0.1613913113):0.05240997539):0.0672038969,((((whitemani:0.3420271265,((haetianus:0.2669834072,breslini:0.2669834072):0.06962183477,((armouri:0.1483909526,cybotes:0.1483909526):0.04416718222,shrevei:0.1925581348):0.1440471072):0.005421884492):0.1066560095,(longitibialis:0.2521253346,strahmi:0.2521253346):0.1965578014):0.09143002532,marcanoi:0.5401131613):0.2505275207,((((((baleatus:0.04173045424,barahonae:0.04173045424):0.05263675531,ricordii:0.09436720956):0.2036021511,eugenegrahami:0.2979693606):0.0851110199,christophei:0.3830803805):0.09095334022,cuvieri:0.4740337207):0.1076385501,(barbatus:0.1467942669,(porcus:0.09310584235,(chamaeleonides:0.07630236186,guamuhaya:0.07630236186):0.01680348049):0.05368842459):0.4348780039):0.2089684112):0.07867171672):0.07597999248,((((((((altitudinalis:0.1748899419,oporinus:0.1748899419):0.09220318062,isolepis:0.2670931225):0.2538920892,(allisoni:0.29602293,porcatus:0.29602293):0.2249622817):0.03703491197,(((argillaceus:0.1142165228,centralis:0.1142165228):0.0249762444,pumilis:0.1391927672):0.2356256274,loysiana:0.3748183946):0.1832017291):0.08522862529,guazuma:0.6432487489):0.04644117492,((placidus:0.1869579579,sheplani:0.1869579579):0.3773659809,(alayoni:0.3793818065,(angusticeps:0.2172126961,paternus:0.2172126961):0.1621691104):0.1849421323):0.125365985):0.07887044542,((alutaceus:0.120861969,inexpectatus:0.120861969):0.4042515809,(((clivicola:0.3359598029,(cupeyalensis:0.08606303065,cyanopleurus:0.08606303065):0.2498967723):0.1189736423,(alfaroi:0.2802339379,macilentus:0.2802339379):0.1746995073):0.0092278683,vanidicus:0.4641613135):0.06095223642):0.2434468193):0.09435314761,(argenteolus:0.6564331946,lucius:0.6564331946):0.2064803223):0.08237887432):0.01002346021):0.04468414858,(((bartschi:0.5247253674,vermiculatus:0.5247253674):0.249459768,((((baracoae:0.05853977536,(noblei:0.02140617522,smallwoodi:0.02140617522):0.03713360014):0.02849164237,luteogularis:0.08703141773):0.017899207,equestris:0.1049306247):0.6297194497,(((monticola:0.6055537678,(bahorucoensis:0.3841100683,(dolichocephalus:0.1509270933,hendersoni:0.1509270933):0.2331829749):0.2214436996):0.03149201716,darlingtoni:0.637045785):0.03288736013,(((aliniger:0.1783542747,singularis:0.1783542747):0.1377057507,chlorocyanus:0.3160600254):0.2135626601,coelestinus:0.5296226856):0.1403104596):0.0647169293):0.0395350609):0.1207482386,occultus:0.8949333739):0.1050666261);

examples/analytic_example/params.character_Country.method_MPPA.model_F81.tab

@@ -0,0 +1,23 @@
+parameter	value
+pastml_version	1.9.42
+character	Country
+log_likelihood	-118.96060539508915
+log_likelihood_restricted_JOINT	-123.1736321477836
+log_likelihood_restricted_MAP	-123.32443056599581
+log_likelihood_restricted_MPPA	-120.52779263128329
+num_scenarios	96
+num_states_per_node_avg	1.023102310231023
+num_unresolved_nodes	6
+percentage_of_unresolved_nodes	1.9801980198019802
+method	MPPA
+model	F81
+num_nodes	303
+num_tips	152
+scaling_factor	4.221092393997994
+state_changes_per_avg_branch	0.11724941037822946
+smoothing_factor	0
+Africa	0.07975434659308142
+Albania	0.05324662913604023
+EastEurope	0.07599888347875045
+Greece	0.3736973060165323
+WestEurope	0.4173028347755957

examples/analytic_example/show_tree_props.py

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+import sys
+from ete4 import Tree
+
+filename = sys.argv[1]
+
+t = Tree(open(filename), parser=1)
+
+print("Target tree internal node Root contains the following properties:  ")
+print(t.props)
+
+print(f"Target tree leaf node {next(t.leaves()).name}contains the following propertiies:  ")
+print(next(t.leaves()).props)

examples/analytic_example/svl.csv

@@ -0,0 +1,101 @@
+species,svl
+ahli,4.039125443
+alayoni,3.815704818
+alfaroi,3.526654599
+aliniger,4.036556538
+allisoni,4.375390078
+allogus,4.040138442
+altitudinalis,3.842994419
+alumina,3.588940722
+alutaceus,3.554890814
+angusticeps,3.788595498
+argenteolus,3.971307363
+argillaceus,3.757868992
+armouri,4.121684075
+bahorucoensis,3.827445029
+baleatus,5.05305601
+baracoae,5.042779747
+barahonae,5.076957937
+barbatus,5.003946306
+barbouri,3.663931948
+bartschi,4.280547466
+bremeri,4.113370744
+breslini,4.051110808
+brevirostris,3.874154977
+caudalis,3.911742966
+centralis,3.697941213
+chamaeleonides,5.04234927
+chlorocyanus,4.275448057
+christophei,3.884651809
+clivicola,3.758726128
+coelestinus,4.297965447
+confusus,3.938442349
+cooki,4.091535064
+cristatellus,4.189820018
+cupeyalensis,3.462013706
+cuvieri,4.875011919
+cyanopleurus,3.630161001
+cybotes,4.210982161
+darlingtoni,4.302036009
+distichus,3.928795837
+dolichocephalus,3.908550316
+equestris,5.113993807
+etheridgei,3.657990601
+eugenegrahami,4.128504414
+evermanni,4.165605231
+fowleri,4.288779949
+garmani,4.769473237
+grahami,4.154274265
+guafe,3.87745744
+guamuhaya,5.036952602
+guazuma,3.76388385
+gundlachi,4.18810472
+haetianus,4.316542212
+hendersoni,3.859834574
+homolechis,4.032805981
+imias,4.099687407
+inexpectatus,3.537438641
+insolitus,3.80047052
+isolepis,3.657087744
+jubar,3.952604971
+krugi,3.886500048
+lineatopus,4.128611788
+longitibialis,4.242103429
+loysiana,3.701240244
+lucius,4.198914766
+luteogularis,5.101085197
+macilentus,3.715764783
+marcanoi,4.079484699
+marron,3.831810283
+mestrei,3.987147344
+monticola,3.770613039
+noblei,5.083472618
+occultus,3.663048694
+olssoni,3.79389884
+opalinus,3.838376465
+ophiolepis,3.637962029
+oporinus,3.845669505
+paternus,3.802961204
+placidus,3.773967107
+poncensis,3.820377531
+porcatus,4.258990989
+porcus,5.038034268
+pulchellus,3.799022266
+pumilis,3.46686027
+quadriocellifer,3.901619072
+reconditus,4.482606994
+ricordii,5.013963084
+rubribarbus,4.078469213
+sagrei,4.067161768
+semilineatus,3.696630586
+sheplani,3.682924257
+shrevei,3.983003234
+singularis,4.057997494
+smallwoodi,5.035095592
+strahmi,4.274271278
+stratulus,3.869880695
+valencienni,4.321524401
+vanidicus,3.62620586
+vermiculatus,4.802849398
+websteri,3.916546094
+whitemani,4.097478535

examples/automatic_query/color.config.collapsed

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+# TreeProfiler Conditional query Configuration
+# This file defines custom colors for properties of annotated tree nodes.
+# Columns: PROP, VALUE, COLOR, CONDITION
+
+# PROP: Property of the annotated tree node
+# VALUE: Value of the property to be colored
+# COLOR: Color to apply
+# CONDITION: operator
+
+PROP,VALUE,COLOR,CONDITION
+#random_type_counter:high,0.35,red,>
+sample1_avg,0.50,green,>
+

examples/automatic_query/color.config.query

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+# TreeProfiler Conditional query Configuration
+# This file defines custom colors for properties of annotated tree nodes.
+# Columns: PROP, VALUE, COLOR, CONDITION
+
+# PROP: Property of the annotated tree node
+# VALUE: Value of the property to be colored
+# COLOR: Color to apply
+# CONDITION: operator
+
+PROP,VALUE,COLOR,CONDITION
+random_type,low,red,=
+sample1,0.50,red,>

examples/automatic_query/color.config.template

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+# TreeProfiler Conditional query Configuration
+# This file defines custom colors for properties of annotated tree nodes.
+# Columns: PROP, VALUE, COLOR, CONDITION
+
+# PROP: Property of the annotated tree node
+# VALUE: Value of the property to be colored
+# COLOR: Color to apply
+# CONDITION: operator
+PROP,VALUE,COLOR,CONDITION

examples/basic_example0/categorical_ancestor.tsv

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+name,categorical1
+Taxa_0,A
+Taxa_1,B
+Taxa_2,B
+Taxa_3,C
+Taxa_4,C
+Taxa_0||Taxa_1,A
+Taxa_2||Taxa_4,C

examples/basic_example0/show_tree_props_ancestor.py

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+import sys
+from ete4 import Tree
+
+filename = sys.argv[1]
+
+t = Tree(open(filename), parser=1)
+
+print("Target tree internal node if Taxa_0 and Taxa_1 contains the following properties:  ")
+print(t.common_ancestor(['Taxa_0', 'Taxa_1']).props)

pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "treeprofiler"
+description = "A command line tool to annotate and visualize metadata in phylogenetic tree."
+version = "1.2.3"
+authors = [
+  { name="Ziqi Deng", email="dengziqi1234@gmail.com" },
+  { name="Jaime Huerta-Cepas", email="jhcepas@gmail.com" },
+]
+readme = "README.md"
+license = { file="LICENSE" }
+requires-python = ">=3.10"
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+  "Development Status :: 6 - Mature",
+  "Environment :: Console",
+  "Environment :: X11 Applications :: Qt",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Other Audience",
+  "Intended Audience :: Science/Research",
+  "Natural Language :: English",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX :: Linux",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Visualization",
+  "Topic :: Software Development :: Libraries :: Python Modules",
+]
+
+dependencies = [
+  "numpy>=1.22, <2.0",
+  "biopython>=1.8",
+  "selenium>=4.24.0",
+  "scipy>=1.8.0",
+  "matplotlib>=3.4.0",
+  "pymc>=5.0.0",
+  "aesara",
+  "ete4@git+https://github.com/etetoolkit/ete.git@ete4#egg=ete4",
+  "pastml@git+https://github.com/dengzq1234/pastml.git@pastml2ete4#egg=pastml"
+]
+
+[project.urls]
+"Homepage" = "http://dengzq1234.github.io/TreeProfiler/"
+
+[project.scripts]
+treeprofiler = "treeprofiler:main"
+