| Previous changeset 7:91e554a9ced6 (2019-02-12) Next changeset 9:186972ed2a15 (2019-06-07) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty |
|
modified:
macros.xml |
|
added:
test-data/bgm-in1.fa test-data/bgm-in1.nhx test-data/bgm-out1.json test-data/fubar-in1.fa test-data/fubar-in1.nhx test-data/gard-in1.fa test-data/gard-out1.json test-data/gard-out1.nex test-data/meme-in1.fa test-data/meme-in1.nhx test-data/meme-out1.json test-data/params.json test-data/sm19-in1.nhx test-data/sm19-in2.nhx test-data/sm19-out1.json test-data/sm19-out2.json |
|
removed:
test-data/hyphy-in1.fa test-data/hyphy-in1.nhx test-data/messages.log |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 macros.xml --- a/macros.xml Tue Feb 12 09:47:54 2019 -0500 +++ b/macros.xml Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| @@ -1,53 +1,55 @@ <?xml version="1.0"?> <macros> - <xml name="inputs"> - <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> - <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> - </xml> - <xml name="gencode"> - <param name="gencodeid" type="select" label="Genetic code"> - <option value="1">Universal code</option> - <option value="2">Vertebrate mitochondrial DNA code</option> - <option value="3">Yeast mitochondrial DNA code</option> - <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> - <option value="5">Invertebrate mitochondrial DNA code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> - <option value="7">Echinoderm mitochondrial DNA code</option> - <option value="8">Euplotid Nuclear code</option> - <option value="9">Alternative Yeast Nuclear code</option> - <option value="10">Ascidian mitochondrial DNA code</option> - <option value="11">Flatworm mitochondrial DNA code</option> - <option value="12">Blepharisma Nuclear code</option> - </param> - </xml> - <xml name="branches"> - <param name="branches" type="select" label="Set of branches to test"> - <option value="1">All branches</option> - <option value="2">Internal branches</option> - <option value="3">Leaf branches</option> - <option value="4">Unlabeled branches</option> - </param> - </xml> - <xml name="version_command"> - <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> - </xml> - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/bti079</citation> - <yield /> - </citations> - </xml> - <token name="@VERSION@">2.3.14</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@VERSION@">hyphy</requirement> - <yield /> - </requirements> - </xml> - <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && + <xml name="inputs"> + <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> + <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> + </xml> + <xml name="gencode"> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="1">Universal code</option> + <option value="2">Vertebrate mitochondrial DNA code</option> + <option value="3">Yeast mitochondrial DNA code</option> + <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="5">Invertebrate mitochondrial DNA code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="7">Echinoderm mitochondrial DNA code</option> + <option value="8">Euplotid Nuclear code</option> + <option value="9">Alternative Yeast Nuclear code</option> + <option value="10">Ascidian mitochondrial DNA code</option> + <option value="11">Flatworm mitochondrial DNA code</option> + <option value="12">Blepharisma Nuclear code</option> + </param> + </xml> + <xml name="branches"> + <param name="branches" type="select" label="Set of branches to test"> + <option value="1">All branches</option> + <option value="2">Internal branches</option> + <option value="3">Leaf branches</option> + <option value="4">Unlabeled branches</option> + </param> + </xml> + <xml name="version_command"> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/bti079</citation> + <yield/> + </citations> + </xml> + <token name="@VERSION@">2.3.14</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">hyphy</requirement> + <yield/> + </requirements> + </xml> + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which HYPHYMP` && export HYPHY_PATH=`dirname \$HYPHY` && -export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]> - </token> - <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> - <token name="@HYPHYMPI_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]></token> +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]></token> + <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHYMPI=`which HYPHYMPI` && +export HYPHYMPI_PATH=`dirname \$HYPHYMPI` && +export HYPHYMPI_LIB=`readlink -f \$HYPHYMPI_PATH/../lib/hyphy` && +cat tool_params | mpirun -np \${GALAXY_SLOTS:-2} HYPHYMPI LIBPATH=\$HYPHYMPI_LIB ]]></token> </macros> |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/bgm-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.fa Mon Feb 18 15:16:35 2019 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>Human +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Chimp +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Baboon +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>RhMonkey +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>Cow +GCACGAATAAAGAAAGATATGCCACTTCAC +>Pig +GCAGAATTTAAAAAAAACAAAGAAACTCAC +>Horse +GCAAAATTCAAAAATGGCAGTATGACTTTC +>Cat +GCGAGGTTCCAAATTAGCAACAAGCCTAAG +>Mouse +GCAGAGTTTAAAAGGAAGAAGCCACCTTTT +>Rat +GCCGAGTTTAAAAGGAAGATGAAGCCTTTT |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/bgm-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.nhx Mon Feb 18 15:16:35 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/bgm-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,408 @@\n+{\n+ "analysis":{\n+ "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\\nmap substitution (non-synonymous only for coding data) events to branches in the\\nphylogeny and then analyzes the joint distribution of the\\nsubstitution map using a Bayesian graphical model (network).\\nNext, a Markov chain Monte Carlo analysis is used to generate\\na random sample of network structures from the posterior\\ndistribution given the data. Each node in the network\\nrepresents a codon site in the alignment, and links (edges)\\nbetween nodes indicate high posterior support for correlated\\nsubstitutions at the two sites over time, which implies coevolution.",\n+ "version":"1.0",\n+ "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",\n+ "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",\n+ "contact":"apoon42@uwo.ca",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "fits":{\n+ "models.DNA.GTR.ModelDescription":{\n+ "Log Likelihood":-210.2026740785434,\n+ "estimated parameters":24,\n+ "AIC-c":472.7689845207232,\n+ "Rate Distributions":null,\n+ "display order":0\n+ }\n+ },\n+ "timers":{\n+ "Overall":{\n+ "timer":5,\n+ "order":0\n+ },\n+ "Baseline fit":{\n+ "timer":0,\n+ "order":1\n+ },\n+ "Network inference":{\n+ "timer":5,\n+ "order":2\n+ }\n+ },\n+ "input":{\n+ "file name":"/home/sshank/galaxy/database/jobs_directory/000/169/working/bgm_input.fa",\n+ "number of sequences":10,\n+ "number of sites":30,\n+ "datatype":"nucleotide",\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "tested":0,\n+ "data partitions":{\n+ "0":{\n+ "name":"bgm.filter.default",\n+ "coverage":[\n+ [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]\n+ ]\n+ }\n+ },\n+ "branch attributes":{\n+ "0":{\n+ "Baboon":{\n+ "models.DNA.GTR.ModelDescription":0\n+ },\n+ "Cat":{\n+ "models.DNA.GTR.ModelDescription":0.7917287099579322\n+ },\n+ "Chimp":{\n+ "models.DNA.GTR.ModelDescription":0\n+ },\n+ "Cow":{\n+ "models.DNA.GTR.ModelDescription":0.8109626486128587\n+ },\n+ "Horse":{\n+ "models.DNA.GTR.ModelDescription":0.2774511857263992\n+ },\n+ "Human":{\n+ "models.DNA.GTR.ModelDescription":0\n+ },\n+ "Mouse":{\n+ "models.DNA.GTR.ModelDescription":0.109490513202464\n+ },\n+ "Node1":{\n+ "models.DNA.GTR.ModelDescription":0.4828249176632555\n+ },\n+ "Node12":{\n+ "models.DNA.GTR.ModelDescription":0\n+ },\n+ "Node2":{\n+ "models.DNA.GTR.ModelDescription":0.08314326398763638\n+ },\n+ "Node3":{\n+ "models.DNA.GTR.ModelDescription":0.2537759363872862\n+ },\n+ "Node8":{\n+ "models.DNA.GTR.ModelDescription":0.06505546117875916\n+ },\n+ "Node9":{\n+ "models.DNA.GTR.ModelDescription":0.0335844521856567\n+ },\n+ "Pig":{\n+ "models.DNA.GTR.ModelDescription":0\n+ },\n+ "Rat":{\n+ "models.DNA.GTR.ModelDescription":0.08888583909179715\n+ },\n+ "RhMonkey":{\n+ "models.DNA.GTR.ModelDescription":0\n+ }\n+ },\n+ "attributes":{\n+ "models.DNA.GTR.ModelDescription":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ }\n+ }\n+ },\n+ "MLE":{\n+ "headers":[\n+ ["Site 1", "Index of site 1"],\n+ ["Site 2", "Index of site 2"],\n+ ["P [Site 1 \xe2\x80\x93> Site 2]", "Probability that site 2 is conditionally dependent on site 1"],\n+ ["P [Site 2 \xe2\x80\x93> Site 1]", "Probability that site 1 is conditionally dependent on site 2"],\n+ '..b'328, 0.04296565384572757, 0.0516296755136259, 3, 5, 2],\n+ [20, 23, 0.05926063206263195, 0.1177077719070393, 0.1769684039696713, 3, 3, 2],\n+ [20, 24, 0.02190590375777864, 0.01515822253031395, 0.03706412628809259, 3, 2, 0],\n+ [20, 25, 0.002826480482922473, 0.0329959365130492, 0.03582241699597167, 3, 3, 1],\n+ [20, 26, 0.03500010153529706, 0.08814032622020453, 0.1231404277555016, 3, 1, 1],\n+ [20, 28, 0.006759314394401512, 0.0169587004744173, 0.02371801486881881, 3, 2, 0],\n+ [20, 29, 0.006300812922842021, 0.01879594226333304, 0.02509675518617506, 3, 2, 0],\n+ [20, 30, 0.00361631507657769, 0.02054834294198262, 0.02416465801856031, 3, 2, 0],\n+ [21, 22, 0.1088739705057051, 0.1524908201873962, 0.2613647906931013, 5, 5, 4],\n+ [21, 23, 0.03536746732698889, 0.009606902956295715, 0.04497437028328461, 5, 3, 2],\n+ [21, 24, 0.03311514728179001, 0.005221577298117681, 0.03833672457990769, 5, 2, 0],\n+ [21, 25, 0.05647236835132394, 0.1627253654083328, 0.2191977337596567, 5, 3, 3],\n+ [21, 26, 0.01649413791066693, 0.01572011785914604, 0.03221425576981297, 5, 1, 1],\n+ [21, 28, 0.009590580248001827, 0.008741569283172617, 0.01833214953117444, 5, 2, 1],\n+ [21, 29, 0.007112780028907996, 0.006470846102977449, 0.01358362613188544, 5, 2, 1],\n+ [21, 30, 0.02018466065938589, 0.05667854576989836, 0.07686320642928425, 5, 2, 2],\n+ [22, 23, 0.3092917280236416, 0.06929520886698605, 0.3785869368906277, 5, 3, 3],\n+ [22, 24, 0.0361676758346396, 0.007985230277029296, 0.0441529061116689, 5, 2, 1],\n+ [22, 25, 0.05518717435451984, 0.1977785735232886, 0.2529657478778085, 5, 3, 3],\n+ [22, 26, 0.01837112437292206, 0.01711296792742606, 0.03548409230034812, 5, 1, 1],\n+ [22, 28, 0.0148284194257516, 0.004366167632545609, 0.01919458705829721, 5, 2, 1],\n+ [22, 29, 0.01036174798845148, 0.004461411681642494, 0.01482315967009397, 5, 2, 1],\n+ [22, 30, 0.02949947252935224, 0.05713973075779002, 0.08663920328714227, 5, 2, 2],\n+ [23, 24, 0.04579305885319052, 0.01996088238362823, 0.06575394123681874, 3, 2, 1],\n+ [23, 25, 0.006859782044932026, 0.02095971907780951, 0.02781950112274154, 3, 3, 1],\n+ [23, 26, 0.0288195650546623, 0.06165987723123845, 0.09047944228590075, 3, 1, 1],\n+ [23, 28, 0.008038372463061548, 0.01096743313296602, 0.01900580559602757, 3, 2, 0],\n+ [23, 29, 0.005383376198140472, 0.01399260771599183, 0.0193759839141323, 3, 2, 0],\n+ [23, 30, 0.002586309731185126, 0.01879557060897289, 0.02138188034015802, 3, 2, 0],\n+ [24, 25, 0.002083732793642955, 0.0346577009558969, 0.03674143374953985, 2, 3, 0],\n+ [24, 26, 0.00900433314688253, 0.03145703054431225, 0.04046136369119478, 2, 1, 0],\n+ [24, 28, 0.02312755108106911, 0.07558297171919495, 0.09871052280026406, 2, 2, 1],\n+ [24, 29, 0.0239725583430664, 0.0667524203930851, 0.0907249787361515, 2, 2, 1],\n+ [24, 30, 0.001828578630548912, 0.04167655883831075, 0.04350513746885966, 2, 2, 0],\n+ [25, 26, 0.06030702783421876, 0.02397879790509632, 0.08428582573931508, 3, 1, 1],\n+ [25, 28, 0.02525394715650654, 0.01675694773843353, 0.04201089489494007, 3, 2, 1],\n+ [25, 29, 0.02294075564839412, 0.003437292134423187, 0.02637804778281731, 3, 2, 1],\n+ [25, 30, 0.1151692785938705, 0.1121068907379168, 0.2272761693317873, 3, 2, 2],\n+ [26, 28, 0.01426179745915288, 0.01122799193078968, 0.02548978938994256, 1, 2, 0],\n+ [26, 29, 0.009820850299733515, 0.00869481824885591, 0.01851566854858942, 1, 2, 0],\n+ [26, 30, 0.005678883362106206, 0.01573375185023243, 0.02141263521233863, 1, 2, 0],\n+ [28, 29, 0.3747904225279734, 0.3026924763162497, 0.6774828988442232, 2, 2, 2],\n+ [28, 30, 0.0137277446790239, 0.04595869328675781, 0.0596864379657817, 2, 2, 1],\n+ [29, 30, 0.01091586602165807, 0.03426775248485611, 0.04518361850651417, 2, 2, 1]\n+ ]\n+ },\n+ "settings":{\n+ "steps":100000,\n+ "burn-in":10000,\n+ "samples":100,\n+ "max-parents":1,\n+ "min-subs":1,\n+ "data-type":"nucleotide",\n+ "threshold":0.5\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/fubar-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.fa Mon Feb 18 15:16:35 2019 -0500 |
| b |
| b'@@ -0,0 +1,326 @@\n+>KF789585\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCCCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGACACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAATTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY025485\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCATCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAGTGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGGAATCTGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAATTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAGAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCAGCCTATATGCTCAAGCACCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCCGAGTAAGGGATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGACAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGCTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGACCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGACCTAACTGACTCAGAAATGAACAAATTGTTTGAAAGAACAAAAAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>KC535396\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGA'..b'GAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY012232\n+ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCCCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAGAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTACCAACGAAAACTTCAATTGGACTGGAGTCGCTCAGGATGGGAAAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATTAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGTGACCAAACCAGCCTATATGTCCGAGCATCAGGGAAAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGGATATCGGGTATAGACCATGGGTAAGGGGTCTTTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAACTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAGAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGACAAGCTGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAGTCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAATGCGGAGCTTCTTGTTGCTCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTATTTGAAAGAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTTGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>EU199367\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAGTCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/fubar-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.nhx Mon Feb 18 15:16:35 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/gard-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-in1.fa Mon Feb 18 15:16:35 2019 -0500 |
| b |
| b'@@ -0,0 +1,735 @@\n+>TREESPARROW_HENAN_1_2004\n+ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGA\n+TCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACA\n+CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\n+AAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\n+TTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\n+ACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\n+CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\n+GAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\n+CCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\n+TGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n+CAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\n+ACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\n+GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\n+AACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\n+AAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\n+CCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\n+ATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\n+AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\n+ATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\n+ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCA\n+GAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\n+GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\n+GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\n+AAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n+ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n+TAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\n+TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n+GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\n+GGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\n+TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\n+GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\n+GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\n+CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\n+GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n+>HUMAN_VIETNAM_CL105_2005\n+ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA\n+TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n+CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\n+AAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\n+TTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTG\n+ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAAT\n+CCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATT\n+GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\n+CCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTA\n+TGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n+CAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\n+ACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCG\n+GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\n+GACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\n+AAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAA\n+CCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\n+ATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\n+AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\n+ATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGA\n+ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\n+GAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\n+GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\n+GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\n+AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n+ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n+CAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\n+TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n+GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\n+GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\n+TCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\n+GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGA\n+GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\n+CAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCT\n+GGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------\n+>TREESPARROW_HENAN_4_2004\n+ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\n+TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n+CAATAATGCAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\n+AAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAAT\n+TTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\n+ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\n+CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\n+GAA'..b'GACGGAT\n+TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n+GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\n+GGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT\n+TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\n+GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\n+GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\n+CAATTTATTCAACAGTGGCGAGTTCCCTAGCGCTGGCAATCATGGTAGCT\n+GGTCTATCTTTATGGATGTGCTCC------------------------\n+>TREESPARROW_HENAN_2_2004\n+ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\n+TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n+CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\n+AAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\n+TTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\n+ACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\n+CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\n+GAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\n+CCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\n+TGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n+CAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\n+ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\n+GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\n+AACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\n+AAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA\n+CCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\n+ATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAGAGTG\n+AATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG\n+ATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\n+ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA\n+GAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA\n+GCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG\n+GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\n+AAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n+ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n+TAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\n+TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n+GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\n+GGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\n+TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\n+GGAACGTATGACTACCGGCTGGACTCAGAAGAAGCAAGACTAAACAGAGA\n+GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\n+CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\n+GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n+>HONGKONG_538_97\n+------------------------------------------------GA\n+TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n+CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA\n+AGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCAT\n+TTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTG\n+ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\n+CCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACT\n+GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\n+CCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA\n+TGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n+CAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA\n+ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\n+GCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG\n+AACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCA\n+AAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\n+CCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGA\n+ATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\n+AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\n+ATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGA\n+ATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCA\n+GAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\n+GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\n+GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACC\n+AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n+ATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n+TAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGAT\n+TCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAAT\n+GAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\n+GGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTT\n+TCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\n+GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\n+GGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT\n+CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\n+GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/gard-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,6644 @@\n+{\n+ "models": [\n+ {\n+ "aicc": "16552.0491801442",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 639\n+ ],\n+ [\n+ 640,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1101\n+ ],\n+ [\n+ 1102,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "28810.62671148782",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 513\n+ ],\n+ [\n+ 514,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 0\n+ ],\n+ [\n+ 1,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "8816.481065502234",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 584\n+ ],\n+ [\n+ 585,\n+ 682\n+ ],\n+ [\n+ 683,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "16523.88417120791",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 671\n+ ],\n+ [\n+ 672,\n+ 682\n+ ],\n+ [\n+ 683,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "16514.83689814388",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 671\n+ ],\n+ [\n+ 672,\n+ 1084\n+ ],\n+ [\n+ 1085,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "16638.99722457325",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 25\n+ ],\n+ [\n+ 26,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "9578.941517223964",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 639\n+ ],\n+ [\n+ 640,\n+ 682\n+ ],\n+ [\n+ 683,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "28970.16577255708",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 917\n+ ],\n+ [\n+ 918,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 0\n+ ],\n+ [\n+ 1,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "8754.825976078577",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 584\n+ ],\n+ [\n+ 585,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "16634.03353484062",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 29\n+ ],\n+ [\n+ 30,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "8737.342054102462",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 671\n+ ],\n+ [\n+ 672,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "36670.71757469786",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 639\n+ ],\n+ [\n+ 640,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1093\n+ ],\n+ [\n+ 1094,\n+ 0\n+ ],\n+ [\n+ 1,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "16553.97400340005",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 639\n+ ],\n+ [\n+ 640,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1093\n+ ],\n+ [\n+ 1094,\n+ 1697\n+ ]\n+ ]\n+ },\n+ {\n+ "aicc": "24323.58909304519",\n+ "breakpoints": [\n+ [\n+ 0,\n+ 542\n+ ],\n+ [\n+ 543,\n+ 1085\n+ ],\n+ [\n+ 1086,\n+ 1101\n+ ],\n+ '..b'4:0.0160599):0.00628993):0,TREESPARROW_HENAN_3_2004:0.007557):0.0168326,((DUCK_VIETNAM_376_2005:0.00753771,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00940355):0.00179475,VIETNAM_3062_2004:0):0.00185181):0,DUCK_VIETNAM_272_2005:0.00930519):0,HUMAN_VIETNAM_CL105_2005:0.00933176,MALLARD_VIETNAM_16_2003:0.00370987);",\n+ "bps": [\n+ 1,\n+ 543\n+ ]\n+ },\n+ {\n+ "tree": "(((((((TREESPARROW_HENAN_1_2004:0.00185578,TREESPARROW_HENAN_3_2004:0.00369517):0.00370687,TREESPARROW_HENAN_4_2004:0):0.00561562,((CHICKEN_HEBEI_326_2005:0.017067,(SWINE_ANHUI_2004:0.00372414,TREESPARROW_HENAN_2_2004:0.00182066):0.011243):0.0114326,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0):0.00184479):0.0018473,HONGKONG_97_98:0.00556112):0,HONGKONG_538_97:0):0.0227642):0.00556345):0.00553646,(((DUCK_GUANGZHOU_20_2005:0.0074364,GOOSE_SHANTOU_2216_2005:0.00559107):0.00182622,PEREGRINEFALCON_HK_D0028_2004:0.00556514):0.00185365,CK_HK_WF157_2003:0.00741717):0):0.00927913,DUCK_VIETNAM_272_2005:0.0131166):0,VIETNAM_3062_2004:0.001844):0,(HUMAN_VIETNAM_CL105_2005:0.00932392,DUCK_VIETNAM_376_2005:0.011203):0.00371409,(MALLARD_VIETNAM_16_2003:0.00556606,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00370617):0.0018452);",\n+ "bps": [\n+ 544,\n+ 1086\n+ ]\n+ },\n+ {\n+ "tree": "(((TREESPARROW_HENAN_1_2004:2.11182e-15,TREESPARROW_HENAN_2_2004:0.00658572):0.00163465,(CHICKEN_HEBEI_326_2005:0.00492123,(SWINE_ANHUI_2004:0.00656176,(((CHICKEN_HONGKONG_915_97:0.00163555,(HONGKONG_97_98:0.00163546,HONGKONG_538_97:0):0.00163576):0,GOOSE_HONGKONG_W355_97:0):0.0132195,((DUCK_HONGKONG_Y283_97:0.0304475,(((HUMAN_VIETNAM_CL105_2005:0.0016552,DUCK_VIETNAM_376_2005:0.00494069):0.00163812,(VIETNAM_3062_2004:0.00166859,MALLARD_VIETNAM_16_2003:0):0):0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.0032821,DUCK_VIETNAM_272_2005:0.00660576):0.00161845):0.0064711):0.00650152,(((DUCK_GUANGZHOU_20_2005:0.0032613,GOOSE_SHANTOU_2216_2005:0.00495087):0.00493945,PEREGRINEFALCON_HK_D0028_2004:0):0.00161808,CK_HK_WF157_2003:0.00498611):0.00488423):0.00193926):0.00325645):0.00330664):0.00163232):0.00163894,TREESPARROW_HENAN_3_2004:0.0065698,TREESPARROW_HENAN_4_2004:0);",\n+ "bps": [\n+ 1087,\n+ 1698\n+ ]\n+ }\n+ ],\n+ "improvements": [\n+ {\n+ "deltaAICc": 113.24755153045771,\n+ "breakpoints": [\n+ 692\n+ ]\n+ },\n+ {\n+ "deltaAICc": 46.4278011820079,\n+ "breakpoints": [\n+ 542,\n+ 1085\n+ ]\n+ },\n+ {\n+ "deltaAICc": -28.214182240875743,\n+ "breakpoints": [\n+ 338,\n+ 542,\n+ 1085\n+ ]\n+ }\n+ ],\n+ "rateMatrix": [\n+ [\n+ -0.9161393762464923,\n+ 0.07154161522280159,\n+ 0.7543775428800247,\n+ 0.09022021814366604\n+ ],\n+ [\n+ 0.1319183013671185,\n+ -0.9967069730466336,\n+ 0.08756864772330293,\n+ 0.7772200239562121\n+ ],\n+ [\n+ 1.13643646023497,\n+ 0.07154161522280159,\n+ -1.298198293601438,\n+ 0.09022021814366604\n+ ],\n+ [\n+ 0.1319183013671185,\n+ 0.6163094818590353,\n+ 0.08756864772330293,\n+ -0.8357964309494568\n+ ]\n+ ],\n+ "input": {\n+ "file name": "/home/sshank/galaxy/database/jobs_directory/000/50/working/gard_input.fa",\n+ "number of sequences": 21,\n+ "number of sites": 1698,\n+ "partition count": 4\n+ },\n+ "timeElapsed": 140,\n+ "rvChoice": 0,\n+ "rvRates": 0,\n+ "potentialBreakpoints": 838,\n+ "likelihoodScores": [\n+ [\n+ -1539.672903811515,\n+ -1596.546211280461,\n+ 0\n+ ],\n+ [\n+ -1571.370357202303,\n+ -1393.285043653173,\n+ -1608.489319024247\n+ ],\n+ [\n+ 0,\n+ -1340.327172390242,\n+ -1300.857269648867\n+ ]\n+ ],\n+ "pairwiseP": [\n+ [\n+ 0,\n+ 0.0005,\n+ 0\n+ ],\n+ [\n+ 0.0001,\n+ 0,\n+ 0.0001\n+ ],\n+ [\n+ 0,\n+ 0.0021,\n+ 0\n+ ]\n+ ],\n+ "singleTreeAICc": 8905.71401031873\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/gard-out1.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.nex Mon Feb 18 15:16:35 2019 -0500 |
| b |
| b"@@ -0,0 +1,53 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 21;\n+\tTAXLABELS\n+\t\t'TREESPARROW_HENAN_1_2004' 'HUMAN_VIETNAM_CL105_2005' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'CHICKEN_HONGKONG_915_97' 'VIETNAM_3062_2004' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'DUCK_VIETNAM_376_2005' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_GUANGZHOU_20_2005' 'CK_HK_WF157_2003' 'SWINE_ANHUI_2004' 'DUCK_VIETNAM_272_2005' 'HONGKONG_97_98' 'GOOSE_SHANTOU_2216_2005' 'TREESPARROW_HENAN_3_2004' 'PEREGRINEFALCON_HK_D0028_2004' 'TREESPARROW_HENAN_2_2004' 'HONGKONG_538_97' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1698;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t\tNOLABELS\n+\t;\n+\n+MATRIX\n+ ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n+ ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAATCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGAGGAAATA"..b'GTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACCAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT;\n+END;\n+BEGIN TREES;\n+\tTREE part_1 = ((((((((TREESPARROW_HENAN_1_2004:0.0168632,TREESPARROW_HENAN_2_2004:0):0.00750257,CHICKEN_HEBEI_326_2005:0.0365197):0.00550724,((DUCK_GUANGZHOU_20_2005:0.0093118,(GOOSE_SHANTOU_2216_2005:0.00742248,PEREGRINEFALCON_HK_D0028_2004:0.00557022):0):0.00746946,CK_HK_WF157_2003:0.00752337):0.00747832):0.00374343,((TREESPARROW_HENAN_4_2004:0.00522777,((CHICKEN_HONGKONG_915_97:0,(HONGKONG_97_98:0.0060893,HONGKONG_538_97:0):0):0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0):0.00185221):0.0271883):0.00169275,SWINE_ANHUI_2004:0.0160599):0.00628993):0,TREESPARROW_HENAN_3_2004:0.007557):0.0168326,((DUCK_VIETNAM_376_2005:0.00753771,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00940355):0.00179475,VIETNAM_3062_2004:0):0.00185181):0,DUCK_VIETNAM_272_2005:0.00930519):0,HUMAN_VIETNAM_CL105_2005:0.00933176,MALLARD_VIETNAM_16_2003:0.00370987);\n+\tTREE part_2 = (((((((TREESPARROW_HENAN_1_2004:0.00185578,TREESPARROW_HENAN_3_2004:0.00369517):0.00370687,TREESPARROW_HENAN_4_2004:0):0.00561562,((CHICKEN_HEBEI_326_2005:0.017067,(SWINE_ANHUI_2004:0.00372414,TREESPARROW_HENAN_2_2004:0.00182066):0.011243):0.0114326,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0):0.00184479):0.0018473,HONGKONG_97_98:0.00556112):0,HONGKONG_538_97:0):0.0227642):0.00556345):0.00553646,(((DUCK_GUANGZHOU_20_2005:0.0074364,GOOSE_SHANTOU_2216_2005:0.00559107):0.00182622,PEREGRINEFALCON_HK_D0028_2004:0.00556514):0.00185365,CK_HK_WF157_2003:0.00741717):0):0.00927913,DUCK_VIETNAM_272_2005:0.0131166):0,VIETNAM_3062_2004:0.001844):0,(HUMAN_VIETNAM_CL105_2005:0.00932392,DUCK_VIETNAM_376_2005:0.011203):0.00371409,(MALLARD_VIETNAM_16_2003:0.00556606,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00370617):0.0018452);\n+\tTREE part_3 = (((TREESPARROW_HENAN_1_2004:2.11182e-15,TREESPARROW_HENAN_2_2004:0.00658572):0.00163465,(CHICKEN_HEBEI_326_2005:0.00492123,(SWINE_ANHUI_2004:0.00656176,(((CHICKEN_HONGKONG_915_97:0.00163555,(HONGKONG_97_98:0.00163546,HONGKONG_538_97:0):0.00163576):0,GOOSE_HONGKONG_W355_97:0):0.0132195,((DUCK_HONGKONG_Y283_97:0.0304475,(((HUMAN_VIETNAM_CL105_2005:0.0016552,DUCK_VIETNAM_376_2005:0.00494069):0.00163812,(VIETNAM_3062_2004:0.00166859,MALLARD_VIETNAM_16_2003:0):0):0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.0032821,DUCK_VIETNAM_272_2005:0.00660576):0.00161845):0.0064711):0.00650152,(((DUCK_GUANGZHOU_20_2005:0.0032613,GOOSE_SHANTOU_2216_2005:0.00495087):0.00493945,PEREGRINEFALCON_HK_D0028_2004:0):0.00161808,CK_HK_WF157_2003:0.00498611):0.00488423):0.00193926):0.00325645):0.00330664):0.00163232):0.00163894,TREESPARROW_HENAN_3_2004:0.0065698,TREESPARROW_HENAN_4_2004:0);\n+\n+END;\n+\n+BEGIN ASSUMPTIONS;\n+\tCHARSET span_1 = 1-543;\n+\tCHARSET span_2 = 544-1086;\n+\tCHARSET span_3 = 1087-1698;\n+\n+END;\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/hyphy-in1.fa --- a/test-data/hyphy-in1.fa Tue Feb 12 09:47:54 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,326 +0,0 @@\n->KF789585\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCCCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGACACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAATTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n->CY025485\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCATCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAGTGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGGAATCTGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAATTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAGAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCAGCCTATATGCTCAAGCACCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCCGAGTAAGGGATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGACAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGCTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGACCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGACCTAACTGACTCAGAAATGAACAAATTGTTTGAAAGAACAAAAAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n->KC535396\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGA'..b'GAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n->CY012232\n-ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCCCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAGAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTACCAACGAAAACTTCAATTGGACTGGAGTCGCTCAGGATGGGAAAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATTAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGTGACCAAACCAGCCTATATGTCCGAGCATCAGGGAAAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGGATATCGGGTATAGACCATGGGTAAGGGGTCTTTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAACTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAGAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGACAAGCTGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAGTCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAATGCGGAGCTTCTTGTTGCTCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTATTTGAAAGAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTTGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n->EU199367\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAGTCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/hyphy-in1.nhx --- a/test-data/hyphy-in1.nhx Tue Feb 12 09:47:54 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/meme-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.fa Mon Feb 18 15:16:35 2019 -0500 |
| b |
| b'@@ -0,0 +1,1 @@\n+>TREESPARROW_HENAN_1_2004\rATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGA\rTCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\rACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>HUMAN_VIETNAM_CL105_2005\rATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAAT\rCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTA\rTGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCT\rGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------\r>TREESPARROW_HENAN_4_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGCAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAAT\rTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCA'..b'AA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCGCTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCC------------------------\r>TREESPARROW_HENAN_2_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAGAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG\rATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCGGCTGGACTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>HONGKONG_1_538_97\r------------------------------------------------GA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA\rAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCAT\rTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG\rAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCA\rAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCA\rGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACC\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGAT\rTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTT\rTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r\r\n\\ No newline at end of file\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Mon Feb 18 15:16:35 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((((TREESPARROW_HENAN_1_2004{FG}:0.0111333782927653,TREESPARROW_HENAN_3_2004{FG}:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.00906278098731238):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452) |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,9816 @@\n+{\n+ "analysis":{\n+ "info":"MEME (Mixed Effects Model of Evolution)\\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\\n uses a likelihood ratio test to determine if β+ > α at a site.\\n The estimates aggregate information over a proportion of branches at a site,\\n so the signal is derived from\\n episodic diversification, which is a combination of strength of selection [effect size] and\\n the proportion of the tree affected. A subset of branches can be selected\\n for testing as well, in which case an additional (nuisance) parameter will be\\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.0.1",\n+ "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",\n+ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-4394.17778442101,\n+ "estimated parameters":47,\n+ "AIC-c":8882.482274823486,\n+ "Equilibrium frequencies":[\n+ [0.3460163217230355],\n+ [0.1876507375623983],\n+ [0.2296889898480005],\n+ [0.2366439508665657]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,\n+ "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,\n+ "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,\n+ "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-4272.739394378317,\n+ "estimated parameters":54,\n+ "AIC-c":8653.980859587502,\n+ "Equilibrium frequencies":[\n+ [0.04794212053691846],\n+ [0.02918423386756777],\n+ [0.03061835466109362],\n+ [0.03395226455636327],\n+ [0.02063374857573568],\n+ [0.01256056547467788],\n+ [0.01317779490778274],\n+ [0.01461267216775245],\n+ [0.02309512129134449],\n+ [0.01405889880167917],\n+ [0.01474975672164567],\n+ [0.01635579860179934],\n+ [0.03032452824999034],\n+ [0.01845972006369387],\n+ [0.01936683547765817],\n+ [0.02147561255447049],\n+ [0.02137643485619778],\n+ [0.01301266750638816],\n+ [0.01365211335015547],\n+ [0.01513863724385318],\n+ [0.009200176740799796],\n+ [0.005600505497450756],\n+ [0.005875715784779066],\n+ [0.006515498921838312],\n+ [0.01029765371767897],\n+ [0.006268582428525358],\n+ [0.0065766221888793],\n+ [0.007292724214466442],\n+ [0.01352110201678854],\n+ [0.00823082081030041],\n+ [0.008635285471781717],\n+ [0.009575547089413102],\n+ [0.03891475766269277],\n+ [0.02368892689369449],\n+ [0.02485300688252417],\n+ [0.02755915117048418],\n+ [0.01674847329457107],\n+ [0.01019544726180969],\n+ [0.01069645417478218],\n+ [0.01186114818960848],\n+ [0.0187463766345312],\n+ [0.01141164874946168],\n+ [0.01197242011780667],\n+ [0.01327604894903844],\n+ [0.02461450713626915],\n+ [0.01498380807429274],\n+ [0.01572011627491417],\n+ [0.01743181671681681],\n+ [0.02096427272215724],\n+ [0.0243893513506083],\n+ [0.01482209656025475],\n+ [0.009022786801619234],\n+ [0.009466168876559794],\n+ [0.0104969020572672],\n+ [0.01009910316608133],\n+ [0.0105953757052942],\n+ [0.01174906369078435],\n+ [0.02178339453036125],\n+ [0.0132603996920412'..b'0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [3.814755404861853, 1.572851816866315, 0.1438716660523674, 0.9133509310228476, 0.8561283339476325, 0, 0.6666666666666666, 0, 0.7227144053850797],\n+ [1.632925368858752, 9.067515371869682e-14, 0.006624396040964042, 0, 0.993375603959036, 0, 0.6666666666666666, 0, 0.1893861876435577],\n+ [6.910467162191216e-17, 6.644009788709589e-17, 0.9530537860422115, 85.70098840469475, 0.04694621395778853, 1.225935500569101, 0.2790979511294799, 1, 1.118452011325364],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [11.1535743907125, 5.495472588337348e-15, 0.01781925113627541, 0, 0.9821807488637246, 0, 0.6666666666666666, 0, 1.293588165595197],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1.010942372745582e-08, 1.91494782694605, 0.9999999898905763, 0.2892532193905701, 0.4945031377423876, 2, 0.5323385189861313],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [1.4067965522307e-18, 1.29678984354774e-18, 1.168435917029792e-08, 1.208349982163844, 0.9999999883156409, 0.7347666355131786, 0.3713355934229282, 1, 0.335910581926816],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [6.368685611187767, 1.355989920668704e-13, 0.01759475909141055, 0, 0.9824052409085895, 0, 0.6666666666666666, 0, 0.7386382202183567],\n+ [2.971299687611712, 5.046872141495953e-14, 0.03213540026814934, 0, 0.9678645997318507, 0, 0.6666666666666666, 0, 0.3446104340803781],\n+ [5.225788799949489, 4.947569585464828e-14, 0.04033984096140914, 0, 0.9596601590385908, 0, 0.6666666666666666, 0, 0.6060853956507083],\n+ [2.274039764208154, 2.2709112751361, 0.3496099543716427, 2.266704309337646, 0.6503900456283573, 0, 0.6666666666666666, 0, 0.8942750177686055],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [2.911915266799392, 4.584056471766455e-14, 0.03076462226890157, 0, 0.9692353777310985, 0, 0.6666666666666666, 0, 0.3377230470156978],\n+ [1.26771203129804, 6.909493443060373e-14, 0.04025953489340931, 0, 0.9597404651065907, 0, 0.6666666666666666, 0, 0.1470288558289737],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [2.901922012595191, 2.621061526763822, 0.4839161180134702, 0.0006260070449028816, 0.5160838819865299, 0, 0.6666666666666666, 0, 0.6892505519758656],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [2.678942456400262, 5.858652373777976e-14, 0.03445131768569747, 0, 0.9655486823143026, 0, 0.6666666666666666, 0, 0.3107029313217802],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [8.844981831006641e-17, 8.153334315915164e-17, 0.6000047345675635, 3.553758402405184, 0.3999952654324365, 0.8531795900839363, 0.346031112193832, 1, 0.3951606587101648],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [5.922636877376851, 3.830380225985632e-14, 0.01771536752991297, 0, 0.982284632470087, 0, 0.6666666666666666, 0, 0.6869056237318886],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [3.778232489478013, 2.03776205152443e-13, 0.02561078725613944, 0, 0.9743892127438606, 0, 0.6666666666666666, 0, 0.4381982550209036],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/messages.log --- a/test-data/messages.log Tue Feb 12 09:47:54 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,633 +0,0 @@\n-\n-Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf\n-Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf\n-Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf\n-Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf\n-Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf\n-Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf\n-Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf\n-Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n-Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n-Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n-Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf\n-Overwritten previously defined function:'_sortStringsAux'\n-Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf\n-Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n-Already loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n-Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n-Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf\n-Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf\n-Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n-Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n-Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf\n-Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf\n-Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf\n-Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf\n-Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf\n-Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf\n-Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf\n-Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/Templa"..b"not initialized prior to being used\n-models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142\n-Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used\n-models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766\n-Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used\n-models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015\n-Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used\n-models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678\n-Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used\n-Set GUI update interval to every 26-th LF evaluation.\n-Optimization settings:\n-\tOPTIMIZATION_METHOD = 4\n-\tOPTIMIZATION_PRECISION = 0.001\n-\tMAXIMUM_ITERATIONS_PER_VARIABLE = 5000\n-\n-Initial parameter values\n-\n-relax.test.theta_GT = 0.315401\n-relax.test.theta_CT = 0.98654\n-relax.test.theta_AC = 0.578523\n-relax.test.theta_CG = 0.469908\n-relax.test.theta_AT = 0.267066\n-relax.reference.bsrel_mixture_aux_1 = 0.818182\n-relax.reference.omega1 = 0.145496\n-relax.reference.omega2 = 0.4601\n-relax.reference.bsrel_mixture_aux_0 = 0.45\n-relax.reference.omega3 = 7.27482\n-relax.unclassified.omega3 = 1\n-relax.unclassified.bsrel_mixture_aux_1 = 0.5\n-relax.unclassified.omega2 = 1\n-relax.unclassified.omega1 = 1\n-relax.K = 1\n-relax.unclassified.bsrel_mixture_aux_0 = 0.5\n-RPGDJipv.tree_id_0.Pig.t = 1.37515\n-RPGDJipv.tree_id_0.Cow.t = 1.78195\n-RPGDJipv.tree_id_0.Node3.t = 0.71796\n-RPGDJipv.tree_id_0.Horse.t = 1.50107\n-RPGDJipv.tree_id_0.Cat.t = 1.97327\n-RPGDJipv.tree_id_0.Node2.t = 0.446186\n-RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585\n-RPGDJipv.tree_id_0.Baboon.t = 0.0125984\n-RPGDJipv.tree_id_0.Node9.t = 0.189189\n-RPGDJipv.tree_id_0.Human.t = 0\n-RPGDJipv.tree_id_0.Chimp.t = 0.0130215\n-RPGDJipv.tree_id_0.Node12.t = 0.123589\n-RPGDJipv.tree_id_0.Node8.t = 0.810855\n-RPGDJipv.tree_id_0.Node1.t = 2.05687\n-RPGDJipv.tree_id_0.Rat.t = 0.485173\n-RPGDJipv.tree_id_0.Mouse.t = 0.852285\n-Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch\n-Optimization finished in 156 loop passes.\n-19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made\n-\n-Variable 'MPI_NODE_COUNT' was not initialized prior to being used\n-Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used\n-Set GUI update interval to every 24-th LF evaluation.\n-Optimization settings:\n-\tOPTIMIZATION_METHOD = 4\n-\tOPTIMIZATION_PRECISION = 0.001\n-\tMAXIMUM_ITERATIONS_PER_VARIABLE = 5000\n-\n-Initial parameter values\n-\n-relax.test.theta_GT = 0.272534\n-relax.test.theta_CT = 0.989376\n-relax.test.theta_AC = 0.472659\n-relax.test.theta_CG = 0.409729\n-relax.test.theta_AT = 0.213063\n-relax.reference.omega2 = 0\n-relax.reference.omega3 = 1.81261\n-relax.reference.bsrel_mixture_aux_1 = 0.398417\n-relax.reference.bsrel_mixture_aux_0 = 0.26934\n-relax.reference.omega1 = 0\n-relax.unclassified.omega2 = 3.8108\n-relax.unclassified.bsrel_mixture_aux_1 = 0.965815\n-relax.unclassified.omega3 = 88.0589\n-relax.unclassified.omega1 = 0\n-relax.unclassified.bsrel_mixture_aux_0 = 0.488814\n-RPGDJipv.tree_id_0.Pig.t = 0.288673\n-RPGDJipv.tree_id_0.Cow.t = 0.415456\n-RPGDJipv.tree_id_0.Node3.t = 0.165342\n-RPGDJipv.tree_id_0.Horse.t = 0.373597\n-RPGDJipv.tree_id_0.Cat.t = 0.4862\n-RPGDJipv.tree_id_0.Node2.t = 0.071002\n-RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335\n-RPGDJipv.tree_id_0.Baboon.t = 0.00559127\n-RPGDJipv.tree_id_0.Node9.t = 0.0891892\n-RPGDJipv.tree_id_0.Human.t = 0\n-RPGDJipv.tree_id_0.Chimp.t = 0.0054891\n-RPGDJipv.tree_id_0.Node12.t = 0.0161348\n-RPGDJipv.tree_id_0.Node8.t = 0.405701\n-RPGDJipv.tree_id_0.Node1.t = 1.12055\n-RPGDJipv.tree_id_0.Rat.t = 0.217643\n-RPGDJipv.tree_id_0.Mouse.t = 0.392946\n-Optimization finished in 62 loop passes.\n-6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made\n-\n-Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used\n\\ No newline at end of file\n" |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,280 @@\n+{\n+ "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta",\n+ "msa": [\n+ {\n+ "rawsites": 1698,\n+ "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",\n+ "goodtree": 0,\n+ "sequences": 21,\n+ "sites": 566,\n+ "partitions": 1,\n+ "analysis_type": "1",\n+ "gencodeid": 0,\n+ "datatype": 0,\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "sequence_info": [\n+ {\n+ "seqindex": 0,\n+ "name": "TREESPARROW_HENAN_1_2004",\n+ "_id": "5446bc0d355080301f18a8c8"\n+ },\n+ {\n+ "seqindex": 1,\n+ "name": "HUMAN_VIETNAM_CL105_2005",\n+ "_id": "5446bc0d355080301f18a8c9"\n+ },\n+ {\n+ "seqindex": 2,\n+ "name": "TREESPARROW_HENAN_4_2004",\n+ "_id": "5446bc0d355080301f18a8ca"\n+ },\n+ {\n+ "seqindex": 3,\n+ "name": "CHICKEN_HEBEI_326_2005",\n+ "_id": "5446bc0d355080301f18a8cb"\n+ },\n+ {\n+ "seqindex": 4,\n+ "name": "CHICKEN_HONGKONG_915_97",\n+ "_id": "5446bc0d355080301f18a8cc"\n+ },\n+ {\n+ "seqindex": 5,\n+ "name": "HUMAN_VIETNAM_3062_2004",\n+ "_id": "5446bc0d355080301f18a8cd"\n+ },\n+ {\n+ "seqindex": 6,\n+ "name": "GOOSE_HONGKONG_W355_97",\n+ "_id": "5446bc0d355080301f18a8ce"\n+ },\n+ {\n+ "seqindex": 7,\n+ "name": "DUCK_HONGKONG_Y283_97",\n+ "_id": "5446bc0d355080301f18a8cf"\n+ },\n+ {\n+ "seqindex": 8,\n+ "name": "DUCK_VIETNAM_376_2005",\n+ "_id": "5446bc0d355080301f18a8d0"\n+ },\n+ {\n+ "seqindex": 9,\n+ "name": "MALLARD_VIETNAM_16_2003",\n+ "_id": "5446bc0d355080301f18a8d1"\n+ },\n+ {\n+ "seqindex": 10,\n+ "name": "CHICKEN_CK_160_2005",\n+ "_id": "5446bc0d355080301f18a8d2"\n+ },\n+ {\n+ "seqindex": 11,\n+ '..b'ex": 10\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d3",\n+ "name": "DUCK_GUANGZHOU_20_2005",\n+ "seqindex": 11\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d4",\n+ "name": "CK_HK_WF157_2003",\n+ "seqindex": 12\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d5",\n+ "name": "SWINE_ANHUI_1_2004",\n+ "seqindex": 13\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d6",\n+ "name": "DUCK_VIETNAM_272_2005",\n+ "seqindex": 14\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d7",\n+ "name": "HONGKONG_1_97_98",\n+ "seqindex": 15\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d8",\n+ "name": "GOOSE_SHANTOU_2216_2005",\n+ "seqindex": 16\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d9",\n+ "name": "TREESPARROW_HENAN_3_2004",\n+ "seqindex": 17\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8da",\n+ "name": "PEREGRINEFALCON_HK_D0028_2004",\n+ "seqindex": 18\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8db",\n+ "name": "TREESPARROW_HENAN_2_2004",\n+ "seqindex": 19\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8dc",\n+ "name": "HONGKONG_1_538_97",\n+ "seqindex": 20\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "datatype": 0,\n+ "gencodeid": 0,\n+ "partitions": 1,\n+ "sites": 566,\n+ "sequences": 21,\n+ "goodtree": 0,\n+ "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)",\n+ "rawsites": 1698\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.798Z"\n+ },\n+ "status_stack": [\n+ "In Queue",\n+ "Running",\n+ "Completed"\n+ ],\n+ "type": "relax"\n+}\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/sm19-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in1.nhx Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| @@ -0,0 +1,152 @@ +#NEXUS +begin taxa; + dimensions ntax=50; + taxlabels + C019-B2_10_1[&!color=#ff0000] + C019-B2_13_1[&!color=#ff0000] + C019-B2_16_1[&!color=#ff0000] + C019-B2_17_3[&!color=#ff0000] + C019-B2_18_1[&!color=#ff0000] + C019-B2_1_2[&!color=#ff0000] + C019-B2_24_1[&!color=#ff0000] + C019-B2_28_1[&!color=#ff0000] + C019-B2_29_1[&!color=#ff0000] + C019-B2_31_1[&!color=#ff0000] + C019-B2_32_1[&!color=#ff0000] + C019-B2_34_1[&!color=#ff0000] + C019-B2_35_1[&!color=#ff0000] + C019-B2_42_2[&!color=#ff0000] + C019-B2_43_2[&!color=#ff0000] + C019-B2_45_1[&!color=#ff0000] + C019-B2_46_2[&!color=#ff0000] + C019-B2_47_3[&!color=#ff0000] + C019-B2_4_1[&!color=#ff0000] + C019-B2_52_1[&!color=#ff0000] + C019-B2_53_1[&!color=#ff0000] + C019-B2_54_1[&!color=#ff0000] + C019-B2_5_1[&!color=#ff0000] + C019-B2_6_3[&!color=#ff0000] + C019-B2_9_1[&!color=#ff0000] + C019-S2_10_1[&!color=#0000ff] + C019-S2_11_1[&!color=#0000ff] + C019-S2_12_2[&!color=#0000ff] + C019-S2_13_1[&!color=#0000ff] + C019-S2_14_1[&!color=#0000ff] + C019-S2_15_4[&!color=#0000ff] + C019-S2_16_1[&!color=#0000ff] + C019-S2_17_1[&!color=#0000ff] + C019-S2_18_2[&!color=#0000ff] + C019-S2_19_1[&!color=#0000ff] + C019-S2_1_1[&!color=#0000ff] + C019-S2_20_2[&!color=#0000ff] + C019-S2_21_1[&!color=#0000ff] + C019-S2_22_1[&!color=#0000ff] + C019-S2_23_2[&!color=#0000ff] + C019-S2_24_1[&!color=#0000ff] + C019-S2_25_2[&!color=#0000ff] + C019-S2_2_1[&!color=#0000ff] + C019-S2_3_1[&!color=#0000ff] + C019-S2_4_1[&!color=#0000ff] + C019-S2_5_1[&!color=#0000ff] + C019-S2_6_1[&!color=#0000ff] + C019-S2_7_1[&!color=#0000ff] + C019-S2_8_1[&!color=#0000ff] + C019-S2_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] ((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):9.4E-4,((((((C019-B2_28_1:0.002896,C019-B2_29_1:9.09E-4):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):4.28E-4,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):5.94E-4,((((C019-B2_4_1:0.002924,C019-B2_6_3:8.81E-4):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):3.96E-4,((C019-S2_10_1:0.005429,C019-S2_12_2:3.52E-4):9.31E-4,C019-B2_42_2:9.87E-4):6.51E-4):5.28E-4,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):3.98E-4,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):1.58E-4,C019-S2_5_1:0.009998):2.67E-4,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):6.76E-4,C019-B2_16_1:0.003129):2.62E-4,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):3.0E-5,C019-S2_24_1:-3.0E-5):7.69E-4,C019-S2_23_2:0.003047):4.93E-4,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):8.52E-4,C019-S2_21_1:0.001446):8.3E-4,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):9.2E-4):0.003349):0.001411,C019-S2_13_1:-4.68E-4):0.001963):3.46E-4,(((C019-B2_45_1:8.37E-4,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:5.17E-4):3.77E-4,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):9.13E-4,C019-S2_11_1:0.002993):5.52E-4,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:8.77E-4):8.62E-4):7.32E-4):3.46E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/sm19-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in2.nhx Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| @@ -0,0 +1,166 @@ +#NEXUS +begin taxa; + dimensions ntax=64; + taxlabels + C019-B3_103_1[&!color=#ff0000] + C019-B3_10_1[&!color=#ff0000] + C019-B3_121_1[&!color=#ff0000] + C019-B3_122_4[&!color=#ff0000] + C019-B3_125_1[&!color=#ff0000] + C019-B3_132_1[&!color=#ff0000] + C019-B3_140_2[&!color=#ff0000] + C019-B3_144_1[&!color=#ff0000] + C019-B3_147_1[&!color=#ff0000] + C019-B3_154_1[&!color=#ff0000] + C019-B3_162_1[&!color=#ff0000] + C019-B3_164_1[&!color=#ff0000] + C019-B3_173_1[&!color=#ff0000] + C019-B3_179_1[&!color=#ff0000] + C019-B3_180_1[&!color=#ff0000] + C019-B3_18_1[&!color=#ff0000] + C019-B3_1_1[&!color=#ff0000] + C019-B3_201_1[&!color=#ff0000] + C019-B3_211_4[&!color=#ff0000] + C019-B3_26_6[&!color=#ff0000] + C019-B3_27_1[&!color=#ff0000] + C019-B3_32_1[&!color=#ff0000] + C019-B3_37_1[&!color=#ff0000] + C019-B3_3_2[&!color=#ff0000] + C019-B3_57_1[&!color=#ff0000] + C019-B3_59_1[&!color=#ff0000] + C019-B3_61_3[&!color=#ff0000] + C019-B3_63_1[&!color=#ff0000] + C019-B3_84_1[&!color=#ff0000] + C019-B3_87_1[&!color=#ff0000] + C019-B3_94_1[&!color=#ff0000] + C019-B3_98_1[&!color=#ff0000] + C019-S3_10_3[&!color=#0000ff] + C019-S3_11_1[&!color=#0000ff] + C019-S3_12_1[&!color=#0000ff] + C019-S3_13_1[&!color=#0000ff] + C019-S3_14_1[&!color=#0000ff] + C019-S3_15_1[&!color=#0000ff] + C019-S3_16_1[&!color=#0000ff] + C019-S3_17_1[&!color=#0000ff] + C019-S3_18_1[&!color=#0000ff] + C019-S3_19_2[&!color=#0000ff] + C019-S3_1_3[&!color=#0000ff] + C019-S3_20_1[&!color=#0000ff] + C019-S3_21_1[&!color=#0000ff] + C019-S3_22_2[&!color=#0000ff] + C019-S3_23_6[&!color=#0000ff] + C019-S3_24_1[&!color=#0000ff] + C019-S3_25_1[&!color=#0000ff] + C019-S3_26_1[&!color=#0000ff] + C019-S3_27_1[&!color=#0000ff] + C019-S3_28_1[&!color=#0000ff] + C019-S3_29_1[&!color=#0000ff] + C019-S3_2_1[&!color=#0000ff] + C019-S3_30_5[&!color=#0000ff] + C019-S3_31_1[&!color=#0000ff] + C019-S3_32_1[&!color=#0000ff] + C019-S3_3_1[&!color=#0000ff] + C019-S3_4_1[&!color=#0000ff] + C019-S3_5_1[&!color=#0000ff] + C019-S3_6_1[&!color=#0000ff] + C019-S3_7_44[&!color=#0000ff] + C019-S3_8_1[&!color=#0000ff] + C019-S3_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] (((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/sm19-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out1.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,2081 @@\n+{\n+ "compartments":2,\n+ "events":{\n+ "C019-B2_18_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_24_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_45_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_46_2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_47_3":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-S2_1_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_22_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_2_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_9_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node28":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node34":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node45":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node52":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node59":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node88":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ }\n+ },\n+ "migrations":16,\n+ "p-value":{\n+ "panmictic":0.3766233766233766,\n+ "structured":0.7812187812187812\n+ },\n+ "replicates":1000,\n+ "simulations":{\n+ "panmictic": [\n+[9],\n+ [11],\n+ [12],\n+ [12],\n+ [12],\n+ [12],\n+ [12],\n+ [12],\n+ [12],\n+ [12],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [13],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [14],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [15],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ '..b' [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [21],\n+ [21],\n+ [21],\n+ [21] \n+ ]\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 91e554a9ced6 -r 410942662a67 test-data/sm19-out2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out2.json Mon Feb 18 15:16:35 2019 -0500 |
| [ |
| b'@@ -0,0 +1,2089 @@\n+{\n+ "compartments":2,\n+ "events":{\n+ "C019-S3_12_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_15_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_18_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_1_3":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_24_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_27_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S3_28_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node106":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node110":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node114":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node14":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node44":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node47":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node6":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node61":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node64":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node77":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node98":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ }\n+ },\n+ "migrations":18,\n+ "p-value":{\n+ "panmictic":0.07192807192807193,\n+ "structured":0.6263736263736264\n+ },\n+ "replicates":1000,\n+ "simulations":{\n+ "panmictic": [\n+[14],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [16],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [17],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [18],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [19],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+ [20],\n+'..b' [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [21],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [22],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [23],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [24],\n+ [25],\n+ [25],\n+ [25],\n+ [25],\n+ [25],\n+ [25],\n+ [25],\n+ [26],\n+ [26],\n+ [26] \n+ ]\n+ }\n+}\n\\ No newline at end of file\n' |