| Previous changeset 5:e30bc6da7a36 (2024-09-08) Next changeset 7:2e7b727a0e05 (2025-02-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041 |
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added:
test-data/binid2taxid.tsv test-data/biobox_file.tsv test-data/kraken2.tsv test-data/modified_biobox_file_bin.tsv test-data/modified_biobox_file_contig.tsv |
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removed:
test-data/test_bat_file.tsv test-data/test_biobox_file.tsv test-data/test_biobox_file_add_taxid_bat.tsv test-data/test_biobox_file_add_taxid_gtdb.tsv test-data/test_gtdb_file.tsv test-data/test_gtdb_to_taxdump_file.tsv test-data/test_taxonkit_file_1.tsv test-data/test_taxonkit_file_2.tsv |
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| diff -r e30bc6da7a36 -r 319b8aac032d test-data/binid2taxid.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/binid2taxid.tsv Sat Feb 08 11:32:30 2025 +0000 |
| b |
| @@ -0,0 +1,39 @@ +#BinID NCBI_TaxID +SemiBin_SemiBin_234 12908 +SemiBin_SemiBin_78_sub 12908 +SemiBin_SemiBin_79 12908 +SemiBin_SemiBin_54 226 +SemiBin_SemiBin_56 226 +MetaBAT2_69 2234 +SemiBin_SemiBin_80 191412 +SemiBin_SemiBin_448 100716 +CONCOCT_117 1485 +CONCOCT_136_sub 897 +CONCOCT_73_sub 1263979 +SemiBin_SemiBin_1072 1263979 +CONCOCT_45_sub 39960 +CONCOCT_170 1188228 +MetaBAT2_13_sub 2745 +CONCOCT_60 54248 +MetaBAT2_42 12908 +CONCOCT_87 467094 +CONCOCT_2_sub 1124597 +CONCOCT_93 186192 +CONCOCT_8 936476 +SemiBin_SemiBin_50 2198 +CONCOCT_192 38027 +SemiBin_SemiBin_159 168695 +CONCOCT_62 133539 +CONCOCT_198 1229 +CONCOCT_17 971279 +SemiBin_SemiBin_93 497 +CONCOCT_166_sub 1335757 +MetaBAT2_7 1335746 +CONCOCT_27 1292 +CONCOCT_214 265570 +MetaBAT2_46 1129 +SemiBin_SemiBin_374 80679 +MetaBAT2_9_sub 171436 +SemiBin_SemiBin_19 662 +SemiBin_SemiBin_75 662 +MetaBAT2_24 29497 |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/biobox_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biobox_file.tsv Sat Feb 08 11:32:30 2025 +0000 |
| b |
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| diff -r e30bc6da7a36 -r 319b8aac032d test-data/kraken2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken2.tsv Sat Feb 08 11:32:30 2025 +0000 |
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| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/modified_biobox_file_bin.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/modified_biobox_file_bin.tsv Sat Feb 08 11:32:30 2025 +0000 |
| b |
| b'@@ -0,0 +1,321 @@\n+#CAMI Format for 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|
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/modified_biobox_file_contig.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/modified_biobox_file_contig.tsv Sat Feb 08 11:32:30 2025 +0000 |
| b |
| b'@@ -0,0 +1,321 @@\n+#CAMI Format for 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|
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_bat_file.tsv --- a/test-data/test_bat_file.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,39 +0,0 @@ -# bin classification reason lineage lineage scores -1.FASTA taxid assigned based on 4161/4187 ORFs 1;131567;2;1783272;201174;1760;85007;182102;85043;1736349 1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.99;0.31 -10.FASTA taxid assigned based on 1895/1915 ORFs 1;131567;2;1224;1236;135614;32033;2370;2371 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.94 -11.FASTA taxid assigned based on 4793/4923 ORFs 1;131567;2;1783272;1239;186801;186802;31979;1884934;191027* 1.00;1.00;1.00;0.99;0.99;0.98;0.98;0.83;0.81;0.81 -12.FASTA taxid assigned based on 4056/4136 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;398041;462367 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 -13.FASTA taxid assigned based on 3575/3644 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -14.FASTA taxid assigned based on 245/248 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736522 1.00;1.00;1.00;0.99;0.91;0.91;0.91;0.89;0.35 -15.FASTA taxid assigned based on 3834/3853 ORFs 1;131567;2;1224;28211;204455;31989;1097466;404881 1.00;1.00;1.00;1.00;1.00;0.99;0.97;0.96;0.96 -16.FASTA taxid assigned based on 2824/2869 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -17.FASTA taxid assigned based on 2646/2678 ORFs 1;131567;2;1783272;1239;186801;186802;186804;214904;227138 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.90 -18.FASTA taxid assigned based on 6183/6302 ORFs 1;131567;2;1783272;200795;388447;388448;768649;768650* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -19.FASTA taxid assigned based on 8855/8930 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -2.FASTA taxid assigned based on 3440/3461 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -20.FASTA taxid assigned based on 4264/4287 ORFs 1;131567;2;1224;28216;206351;1499392;397275;1121000 1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.97 -21.FASTA taxid assigned based on 5835/5867 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736522 1.00;1.00;1.00;1.00;0.98;0.98;0.98;0.97;0.59 -22.FASTA taxid assigned based on 2576/2598 ORFs 1;131567;2;1783270;68336;976;117743;200644;49546;363408;328515 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.97;0.97;0.96;0.89 -23.FASTA taxid assigned based on 5759/5763 ORFs 1;131567;2 1.00;0.74;0.73 -24.FASTA taxid assigned based on 6458/6478 ORFs 1;131567;2;1224;28211;204455;31989;265;266 1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.95;0.46 -25.FASTA taxid assigned based on 4145/4341 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;398041;462367 1.00;1.00;1.00;0.99;0.99;0.99;0.93;0.93;0.93;0.89;0.88 -26.FASTA taxid assigned based on 2208/2231 ORFs 1;131567;2;1783272;1239;186801;186802;1491775;42447;182411 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.97;0.97;0.72 -27.FASTA taxid assigned based on 4557/4633 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.88 -28.FASTA taxid assigned based on 1856/1860 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -29.FASTA taxid assigned based on 3780/3817 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -3.FASTA taxid assigned based on 205/207 ORFs 1;131567;2;1783272;1239;909932;909929;1843491;55506;55507* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 -30.FASTA taxid assigned based on 6218/6259 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736532 1.00;1.00;1.00;1.00;0.98;0.98;0.98;0.97;0.57 -31.FASTA taxid assigned based on 2720/2744 ORFs 1;131567;2;1224;28216;80840;80864;198705;198706 1.00;1.00;1.00;1.00;0.99;0.99;0.98;0.97;0.97 -32.FASTA taxid assigned based on 3222/3245 ORFs 1;131567;2;1783272;201174;1760;85006;85021;99479;1736399 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.96;0.53 -33.FASTA taxid assigned based on 292/297 ORFs 1;131567;2;1224;28211;204455;31989 1.00;1.00;0.99;0.89;0.84;0.50;0.49 -34.FASTA taxid assigned based on 3557/3604 ORFs 1;131567;2;1783272;1239;186801;186802;186803;653683;264463* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.99 -35.FASTA taxid assigned based on 2175/2205 ORFs 1;131567;2;1783272;1239;909932;909929;1843491;55506;55507* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 -36.FASTA taxid assigned based on 3370/3422 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.87 -37.FASTA taxid assigned based on 4212/4264 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.92;0.92;0.92;0.92;0.91 -38.FASTA taxid assigned based on 8008/8038 ORFs 1;131567;2;1224;28211;204455;31989;265;266 1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.98;0.40 -4.FASTA taxid assigned based on 8568/8682 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.92;0.92;0.92;0.92;0.90 -5.FASTA taxid assigned based on 2948/2952 ORFs 1;131567;2;1224;28211;204455;31989;205889;990712 1.00;1.00;1.00;1.00;1.00;0.87;0.87;0.86;0.86 -6.FASTA taxid assigned based on 2846/2901 ORFs 1;131567;2;1224;1236;135614;32033;68;1736549 1.00;1.00;1.00;0.96;0.94;0.92;0.85;0.65;0.52 -7.FASTA taxid assigned based on 5030/5081 ORFs 1;131567;2;1224;68525;28221;213118;213119;218207;259354 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.38 -8.FASTA taxid assigned based on 2537/2579 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 -9.FASTA taxid assigned based on 1648/1673 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 \ No newline at end of file |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_biobox_file.tsv --- a/test-data/test_biobox_file.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -#CAMI Format for Binning -@Version:0.9.0 -@SampleID:gsa -@@SEQUENCEID BINID -RL|S1|C1198 1 -RL|S1|C3912 1 -RL|S1|C131 10 -RL|S1|C1410 10 -RL|S1|C2929 10 -RL|S1|C3754 10 -RL|S1|C1335 11 -RL|S1|C1344 11 -RL|S1|C1352 11 \ No newline at end of file |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_biobox_file_add_taxid_bat.tsv --- a/test-data/test_biobox_file_add_taxid_bat.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -#CAMI Format for Binning -@Version:0.9.0 -@SampleID:_SAMPLEID_ -@@SEQUENCEID BINID TAXID -RL|S1|C1198 1 1736349 -RL|S1|C3912 1 1736349 -RL|S1|C131 10 2371 -RL|S1|C1410 10 2371 -RL|S1|C2929 10 2371 -RL|S1|C3754 10 2371 -RL|S1|C1335 11 191027 -RL|S1|C1344 11 191027 -RL|S1|C1352 11 191027 |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_biobox_file_add_taxid_gtdb.tsv --- a/test-data/test_biobox_file_add_taxid_gtdb.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,13 +0,0 @@ -#CAMI Format for Binning -@Version:0.9.0 -@SampleID:_SAMPLEID_ -@@SEQUENCEID BINID TAXID -RL|S1|C1198 1 12908 -RL|S1|C3912 1 12908 -RL|S1|C131 10 2371 -RL|S1|C1410 10 2371 -RL|S1|C2929 10 2371 -RL|S1|C3754 10 2371 -RL|S1|C1335 11 191027 -RL|S1|C1344 11 191027 -RL|S1|C1352 11 191027 |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_gtdb_file.tsv --- a/test-data/test_gtdb_file.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,39 +0,0 @@\n-user_genome\tclassification\tfastani_reference\tfastani_reference_radius\tfastani_taxonomy\tfastani_ani\tfastani_af\tclosest_placement_reference\tclosest_placement_radius\tclosest_placement_taxonomy\tclosest_placement_ani\tclosest_placement_af\tpplacer_taxonomy\tclassification_method\tnote\tother_related_references(genome_id,species_name,radius,ANI,AF)\tmsa_percent\ttranslation_table\tred_value\twarnings\n-1\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\tGCF_000964005.1\t95.0\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\t95.01\t0.891\tGCF_000964005.1\t95.0\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\t95.01\t0.891\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCF_014635305.1, s__Williamsia_A phyllosphaerae, 95.0, 82.43, 0.702; GCA_016462415.1, s__Williamsia_A sp016462415, 95.0, 82.15, 0.649; GCF_018474015.1, s__Williamsia_A sp018474015, 95.0, 80.23, 0.523\t96.49\t11\tN/A\tN/A\n-10\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\tGCF_011801475.1\t95.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\t99.99\t1.0\tGCF_011801475.1\t95.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\t99.99\t1.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCF_013177435.1, s__Xylella taiwanensis, 95.0, 82.85, 0.849\t85.13\t11\tN/A\tN/A\n-11\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\tGCF_900142245.1\t95.0\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\t99.97\t0.872\tGCF_900142245.1\t95.0\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\t99.97\t0.872\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tN/A\t78.49\t11\tN/A\tGenome has more than 10.0% of markers with multiple hits\n-12\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\tGCF_900129295.1\t95.0\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\t100.0\t0.999\tGCF_900129295.1\t95.0\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\t100.0\t0.999\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017745135.1, s__Flavisolibacter sp017745135, 95.0, 77.32, 0.1; GCA_013327885.1, s__Flavisolibacter sp013327885, 95.0, 77.25, 0.081; GCF_007970805.1, s__Flavisolibacter ginsenosidimutans, 95.0, 76.92, 0.056; GCF_003628535.1, s__Flavisolibacter nicotianae, 95.0, 76.88, 0.08; GCA_014163555.1, s__Flavisolibacter sp014163555, 95.0, 76.86, 0.077; GCA_002050435.1, s__Flavisolibacter sp002050435, 95.0, 76.62, 0.139\t97.8\t11\tN/A\tN/A\n-13\td__Bacteria;p__Fir'..b'eae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t99.22\t0.892\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t99.22\t0.892\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017388605.1, s__Anaeroplasma sp017388605, 95.0, 83.89, 0.71; GCA_017449215.1, s__Anaeroplasma sp017449215, 95.0, 78.37, 0.262; GCA_017441525.1, s__Anaeroplasma sp017441525, 95.0, 78.17, 0.272; GCA_002449755.1, s__Anaeroplasma sp002449755, 95.0, 78.14, 0.275; GCA_017462645.1, s__Anaeroplasma sp017462645, 95.0, 78.0, 0.236; GCA_017524905.1, s__Anaeroplasma sp017524905, 95.0, 77.92, 0.242; GCA_016280975.1, s__Anaeroplasma sp016280975, 95.0, 77.86, 0.273; GCA_017444645.1, s__Anaeroplasma sp017444645, 95.0, 77.57, 0.26; GCA_900770055.1, s__Anaeroplasma sp900770055, 95.0, 77.54, 0.192; GCA_902783745.1, s__Anaeroplasma sp902783745, 95.0, 77.5, 0.231; GCA_016282815.1, s__Anaeroplasma sp016282815, 95.0, 77.44, 0.216; GCA_017542485.1, s__Anaeroplasma sp017542485, 95.0, 77.43, 0.189; GCA_016288855.1, s__Anaeroplasma sp016288855, 95.0, 77.42, 0.212; GCA_015059145.1, s__Anaeroplasma sp015059145, 95.0, 77.4, 0.199; GCA_900767915.1, s__Anaeroplasma sp900767915, 95.0, 77.38, 0.187; GCA_017454375.1, s__Anaeroplasma sp017454375, 95.0, 77.11, 0.128; GCA_902796895.1, s__Anaeroplasma sp902796895, 95.0, 76.99, 0.242; GCA_018715825.1, s__Anaeroplasma faecigallinarum, 95.0, 76.73, 0.118; GCA_905236965.1, s__Anaeroplasma sp905236965, 95.0, 76.07, 0.2; GCA_905236105.1, s__Anaeroplasma sp905236105, 95.0, 76.05, 0.133\t57.15\t11\tN/A\tGenome has more than 10.0% of markers with multiple hits\n-9\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t100.0\t1.0\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t100.0\t1.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017388605.1, s__Anaeroplasma sp017388605, 95.0, 84.15, 0.658; GCA_002449755.1, s__Anaeroplasma sp002449755, 95.0, 78.65, 0.256; GCA_017441525.1, s__Anaeroplasma sp017441525, 95.0, 78.34, 0.265; GCA_017449215.1, s__Anaeroplasma sp017449215, 95.0, 78.33, 0.263; GCA_017524905.1, s__Anaeroplasma sp017524905, 95.0, 78.01, 0.244; GCA_017462645.1, s__Anaeroplasma sp017462645, 95.0, 78.0, 0.23; GCA_016280975.1, s__Anaeroplasma sp016280975, 95.0, 77.96, 0.23; GCA_017542485.1, s__Anaeroplasma sp017542485, 95.0, 77.74, 0.195; GCA_017444645.1, s__Anaeroplasma sp017444645, 95.0, 77.7, 0.258; GCA_900767915.1, s__Anaeroplasma sp900767915, 95.0, 77.52, 0.172; GCA_016288855.1, s__Anaeroplasma sp016288855, 95.0, 77.51, 0.196; GCA_902783745.1, s__Anaeroplasma sp902783745, 95.0, 77.5, 0.209; GCA_016282815.1, s__Anaeroplasma sp016282815, 95.0, 77.5, 0.201; GCA_900770055.1, s__Anaeroplasma sp900770055, 95.0, 77.43, 0.184; GCA_015059145.1, s__Anaeroplasma sp015059145, 95.0, 77.28, 0.183; GCA_902796895.1, s__Anaeroplasma sp902796895, 95.0, 77.2, 0.221; GCA_017454375.1, s__Anaeroplasma sp017454375, 95.0, 77.19, 0.129; GCA_018715825.1, s__Anaeroplasma faecigallinarum, 95.0, 76.79, 0.111; GCA_905236965.1, s__Anaeroplasma sp905236965, 95.0, 76.42, 0.19; GCA_905236105.1, s__Anaeroplasma sp905236105, 95.0, 76.12, 0.118\t66.58\t11\tN/A\tN/A\n\\ No newline at end of file\n' |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_gtdb_to_taxdump_file.tsv --- a/test-data/test_gtdb_to_taxdump_file.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -ncbi_taxonomy gtdb_taxonomy lca_frac target_tax_level lineage -s__Williamsia_A herbipolensis unclassified NA NA NA -s__Xylella fastidiosa s__Xylella fastidiosa 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__xanthomonadales;f__xanthomonadaceae;g__xylella;s__xylella fastidiosa -s__Paramaledivibacter caminithermalis s__Paramaledivibacter caminithermalis 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__peptostreptococcales;f__caminicellaceae;g__paramaledivibacter;s__paramaledivibacter caminithermalis -s__Flavisolibacter ginsengisoli s__Flavisolibacter ginsengisoli 1.0 species d__bacteria;p__bacteroidota;c__bacteroidia;o__chitinophagales;f__chitinophagaceae;g__flavisolibacter;s__flavisolibacter ginsengisoli -s__Anaeroplasma bactoclasticum c__Bacilli 1.0 class d__bacteria;p__bacillota;c__bacilli -s__Pseudoduganella sp001425045 unclassified NA NA NA -s__Albidovulum denitrificans unclassified NA NA NA -s__Tepidibacter formicigenes s__Tepidibacter formicigenes 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__peptostreptococcales;f__peptostreptococcaceae;g__tepidibacter;s__tepidibacter formicigenes -s__Thermosporothrix hazakensis unclassified NA NA NA -s__Exiguobacterium_A sp001423965 unclassified NA NA NA -s__Andreprevotia lacus s__Andreprevotia lacus 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__burkholderiales;f__chitinibacteraceae;g__andreprevotia;s__andreprevotia lacus -s__Nonlabens dokdonensis g__Nonlabens 1.0 genus d__bacteria;p__bacteroidota;c__bacteroidia;o__flavobacteriales;f__flavobacteriaceae;g__nonlabens -s__Pseudomonas aeruginosa s__Pseudomonas aeruginosa 0.99 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__pseudomonadales;f__pseudomonadaceae;g__pseudomonas;s__pseudomonas aeruginosa -s__Paracoccus denitrificans g__Paracoccus 1.0 genus d__bacteria;p__pseudomonadota;c__alphaproteobacteria;o__rhodobacterales;f__rhodobacteraceae;g__paracoccus -N/A unclassified NA NA NA -s__Anaerobranca californiensis s__Anaerobranca californiensis 1.0 species d__bacteria;p__bacillota_d;c__proteinivoracia;o__proteinivoracales;f__proteinivoraceae;g__anaerobranca;s__anaerobranca californiensis -s__Hydrotalea sandarakina s__Hydrotalea sandarakina 1.0 species d__bacteria;p__bacteroidota;c__bacteroidia;o__chitinophagales;f__chitinophagaceae;g__hydrotalea;s__hydrotalea sandarakina -s__Schwartzia succinivorans f__Selenomonadaceae 1.0 family d__bacteria;p__bacillota_c;c__negativicutes;o__selenomonadales;f__selenomonadaceae -s__Pseudoduganella sp001425265 unclassified NA NA NA -s__Lampropedia hyalina s__Lampropedia hyalina 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__burkholderiales;f__burkholderiaceae_b;g__lampropedia;s__lampropedia hyalina -s__Phycicoccus sp001428065 unclassified NA NA NA -s__Anaerosporobacter mobilis s__Anaerosporobacter mobilis 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__lachnospirales;f__lachnospiraceae;g__anaerosporobacter;s__anaerosporobacter mobilis -s__Meinhardsimonia xiamenensis s__Meinhardsimonia xiamenensis 1.0 species d__bacteria;p__pseudomonadota;c__alphaproteobacteria;o__rhodobacterales;f__rhodobacteraceae;g__meinhardsimonia;s__meinhardsimonia xiamenensis -s__Desulfatibacillum alkenivorans s__Desulfatibacillum alkenivorans 1.0 species d__bacteria;p__desulfobacterota;c__desulfobacteria;o__desulfobacterales;f__desulfatibacillaceae;g__desulfatibacillum;s__desulfatibacillum alkenivorans |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_taxonkit_file_1.tsv --- a/test-data/test_taxonkit_file_1.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -unclassified 12908 -Xylella fastidiosa 2371 -Paramaledivibacter caminithermalis 191027 -Flavisolibacter ginsengisoli 462367 -Bacilli 91061 -unclassified 12908 -unclassified 12908 -Tepidibacter formicigenes 227138 -unclassified 12908 -unclassified 12908 -Andreprevotia lacus 1121000 |
| b |
| diff -r e30bc6da7a36 -r 319b8aac032d test-data/test_taxonkit_file_2.tsv --- a/test-data/test_taxonkit_file_2.tsv Sun Sep 08 14:37:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -Nonlabens 363408 -Pseudomonas aeruginosa 287 -Paracoccus 265 -Paracoccus 249411 -unclassified 12908 -Anaerobranca californiensis 182411 -Hydrotalea sandarakina 1004304 -Selenomonadaceae 1843491 -unclassified 12908 -Lampropedia hyalina 198706 -unclassified 12908 -Anaerosporobacter mobilis 264463 -Meinhardsimonia xiamenensis 990712 -Desulfatibacillum alkenivorans 259354 |