| Previous changeset 0:3ff4712dc111 (2022-09-03) Next changeset 2:b582a159bb10 (2024-03-11) |
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Commit message:
planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6 |
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modified:
kraken_biom.xml macros.xml |
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added:
test-data/MG_AIR20200707.tabular test-data/MG_AIR20200708.tabular test-data/MG_AIR20200709.tabular test-data/SamplesMetaDataTabular.csv |
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removed:
test-data/krakenReport1.tabular test-data/krakenReport2.tabular test-data/krakenReport3.tabular |
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| diff -r 3ff4712dc111 -r 65eb9962d272 kraken_biom.xml --- a/kraken_biom.xml Sat Sep 03 22:13:08 2022 +0000 +++ b/kraken_biom.xml Fri Sep 09 09:32:59 2022 +0000 |
| [ |
| @@ -11,6 +11,9 @@ ln -s '$s' './$i-kraken_report.tabular' && #end if #end for +#if $metadata + ln -s '$metadata' './metadata.tsv' && +#end if kraken-biom #for $i, $s in enumerate($kraken_reports) #if $s @@ -23,8 +26,11 @@ #if $min --min $min #end if +#if $metadata + --metadata 'metadata.tsv' +#end if #if $otu_fp - --otu_fp '$otu_fp' + --otu_fp 'OTU_FP' #end if #if $fmt --fmt $fmt @@ -40,6 +46,7 @@ <option value="F">F</option> <option value="G">G</option> <option value="S">S</option> + <option value="SS">SS</option> </param> <param argument="--min" type="select" optional="true" label="Min" help="Reads assigned at and below min rank will be recorded as being assigned to the min rank level. Default: S"> <option value="O">O</option> @@ -49,8 +56,10 @@ <option value="F">F</option> <option value="G">G</option> <option value="S" selected="true">S</option> + <option value="SS">SS</option> </param> - <param argument="--otu_fp" type="data" optional="true" format="tabular" label="OTU FP" help="Create a file containing just the (NCBI) OTU IDs for use with a service such as phyloT (http://phylot.biobyte.de/) to generate a phylogenetic tree for use in downstream analysis such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org)"/> + <param argument="--metadata" type="data" format="tabular" optional="true" label="Sample metadata file" help="This should be in TSV or CSV (Tabular) format. The first column should be the Sample ID (e.g. 0-kraken_report, 1-kraken_report, etc.). This is the same name as the input files. If no metadata is given, basic metadata is added to support importing the BIOM table into sites like phinch (http://phinch.org/index.html). Example for metadata files: http://qiime.org/documentation/ file_formats.html#mapping-file-overview"/> + <param name="otu_fp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Do you want to create an OTU IDs file" help="Create a file containing just the (NCBI) OTU IDs for use with a service such as phyloT (http://phylot.biobyte.de/) to generate a phylogenetic tree for use in downstream analysis such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org)"/> <param argument="--fmt" type="select" optional="true" label="Output Format" help="Set the output format of the BIOM table. Default is HDF5"> <option value="tsv">TSV</option> <option value="json">JSON</option> @@ -58,18 +67,21 @@ </param> </inputs> <outputs> - <data name="biomOutput" format="biom2" from_work_dir="./table.biom" label="Kraken biom output file"> + <data name="biomOutput" format="tabular" from_work_dir="./table.biom" label="Kraken-biom output file"> <change_format> - <when input="fmt" value="json" format="json" /> + <when input="fmt" value="json" format="biom1" /> + </change_format> + <change_format> + <when input="fmt" value="hdf5" format="biom2" /> </change_format> - <change_format> - <when input="fmt" value="tsv" format="tsv" /> - </change_format> - </data> + </data> + <data name="otuOutput" format="mothur.map" from_work_dir="./OTU_FP" label="OTU File"> + <filter>otu_fp is True</filter> + </data> </outputs> <tests> <test expect_num_outputs="1"> - <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/> + <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/> <param name="fmt" value="hdf5"/> <output name="biomOutput" ftype="biom2"> <assert_contents> @@ -78,9 +90,9 @@ </output> </test> <test expect_num_outputs="1"> - <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/> + <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/> <param name="fmt" value="tsv"/> - <output name="biomOutput" ftype="tsv"> + <output name="biomOutput" ftype="tabular"> <assert_contents> <has_n_lines n="8246"/> <has_text text="Constructed from biom file"/> @@ -88,14 +100,45 @@ </output> </test> <test expect_num_outputs="1"> - <param name="kraken_reports" value="krakenReport1.tabular,krakenReport2.tabular,krakenReport3.tabular"/> + <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/> <param name="fmt" value="json"/> - <output name="biomOutput" ftype="json"> + <output name="biomOutput" ftype="biom1"> + <assert_contents> + <has_text text="Biological Observation"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/> + <param name="otu_fp" value="true"/> + <param name="fmt" value="json"/> + <output name="biomOutput" ftype="biom1"> <assert_contents> <has_text text="Biological Observation"/> </assert_contents> </output> - </test> + <output name="otuOutput" ftype="mothur.map"> + <assert_contents> + <has_n_lines n="8244"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/> + <param name="metadata" value="SamplesMetaDataTabular.csv"/> + <param name="otu_fp" value="true"/> + <param name="fmt" value="json"/> + <output name="biomOutput" ftype="biom1"> + <assert_contents> + <has_text text="Biological Observation"/> + </assert_contents> + </output> + <output name="otuOutput" ftype="mothur.map"> + <assert_contents> + <has_n_lines n="8244"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Kraken-biom |
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| diff -r 3ff4712dc111 -r 65eb9962d272 macros.xml --- a/macros.xml Sat Sep 03 22:13:08 2022 +0000 +++ b/macros.xml Fri Sep 09 09:32:59 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.0.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> |
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| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/MG_AIR20200707.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MG_AIR20200707.tabular Fri Sep 09 09:32:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,12471 @@\n+ 91.15\t14195379\t14195379\tU\t0\tunclassified\n+ 8.85\t1379004\t401\tR\t1\troot\n+ 8.84\t1376958\t10737\tR1\t131567\t cellular organisms\n+ 7.20\t1121868\t43514\tD\t2\t Bacteria\n+ 3.57\t556613\t24838\tP\t1224\t Proteobacteria\n+ 1.47\t229058\t7482\tC\t28211\t Alphaproteobacteria\n+ 0.93\t144510\t6453\tO\t356\t Hyphomicrobiales\n+ 0.52\t80503\t1900\tF\t41294\t Bradyrhizobiaceae\n+ 0.44\t69011\t10554\tG\t374\t Bradyrhizobium\n+ 0.14\t22423\t4040\tG1\t2631580\t unclassified Bradyrhizobium\n+ 0.03\t5066\t5066\tS\t858422\t Bradyrhizobium sp. CCBAU 051011\n+ 0.01\t1865\t1865\tS\t1197460\t Bradyrhizobium sp. 6(2017)\n+ 0.01\t1549\t1549\tS\t1325100\t Bradyrhizobium sp. CCBAU 51753\n+ 0.01\t1005\t1005\tS\t376\t Bradyrhizobium sp.\n+ 0.01\t959\t959\tS\t2057741\t Bradyrhizobium sp. SK17\n+ 0.01\t947\t947\tS\t1325120\t Bradyrhizobium sp. CCBAU 53421\n+ 0.01\t895\t895\tS\t288000\t Bradyrhizobium sp. BTAi1\n+ 0.01\t858\t858\tS\t2715960\t Bradyrhizobium sp. PSBB068\n+ 0.00\t748\t748\tS\t115808\t Bradyrhizobium sp. ORS 285\n+ 0.00\t631\t631\tS\t114615\t Bradyrhizobium sp. ORS 278\n+ 0.00\t591\t591\tS\t1404888\t Bradyrhizobium sp. 1(2017)\n+ 0.00\t585\t585\tS\t1325102\t Bradyrhizobium sp. CCBAU 51765\n+ 0.00\t548\t548\tS\t1325112\t Bradyrhizobium sp. CCBAU 53340\n+ 0.00\t532\t532\tS\t1325111\t Bradyrhizobium sp. CCBAU 53338\n+ 0.00\t468\t468\tS\t1325114\t Bradyrhizobium sp. CCBAU 53351\n+ 0.00\t458\t458\tS\t1223566\t Bradyrhizobium sp. CCGE-LA001\n+ 0.00\t253\t253\tS\t319017\t Bradyrhizobium sp. WSM471\n+ 0.00\t205\t205\tS\t2493093\t Bradyrhizobium sp. LCT2\n+ 0.00\t82\t82\tS\t2599805\t Bradyrhizobium sp. SG09\n+ 0.00\t73\t73\tS\t1404649\t Bradyrhizobium sp. 323S2\n+ 0.00\t54\t54\tS\t2599819\t Bradyrhizobium sp. TM102\n+ 0.00\t10\t10\tS\t1325083\t Bradyrhizobium sp. CCBAU 21365\n+ 0.00\t1\t1\tS\t2578114\t Bradyrhizobium sp. KBS0727\n+ 0.07\t11646\t11646\tS\t1437360\t Bradyrhizobium erythrophlei\n+ 0.02\t3838\t3838\tS\t1274631\t Bradyrhizobium icense\n+ 0.02\t3704\t3704\tS\t722472\t Bradyrhizobium lablabi\n+ 0.02\t3445\t3445\tS\t190148\t Bradyrhizobium paxllaeri\n+ 0.02\t2527\t2525\tS\t1355477\t Bradyrhizobium diazoefficiens\n+ 0.00\t2\t2\tS1\t224911\t Bradyrhizobium diazoefficiens USDA 110\n+ 0.01\t2286\t2286\tS\t255045\t Bradyrhizobium canariense\n+ 0.01\t1081\t865\tS\t375\t Bradyrhizobium japonicum\n+ 0.00\t213\t213\tS1\t476282\t Bradyrhizobium japonicum SEMIA 5079\n+ 0.00\t3\t3\tS1\t1037409\t Bradyrhizobium japonicum USDA 6\n+ 0.01\t1054\t1054\tS\t83637\t Bradyrhizobium genosp. L\n+ 0.00\t694\t694\tS\t1325107\t Bradyrhizobium zhanjiangense\n+ 0.00\t661\t0\tS\t44255\t Bradyrhizobium oligotrophicum\n+ 0.00\t661\t661\tS1\t1245469\t Bradyrhizobium oligotrophicum S58\n+ 0.00\t576\t576\tS\t1549949\t Bradyrhizobium vignae\n+ 0.00\t562\t562\tS\t83627\t Bradyrhizobium genosp. B\n+ 0.00\t556\t556\tS\t1404367\t Bradyrhizobium symbiodeficiens\n+ 0.00\t547\t547\tS\t858423\t Bradyrhizobium arachidis\n+ 0.00\t480\t480\tS\t1404864\t Bradyrhizobium cosmicum\n+ 0.00\t459\t459\tS\t1325090\t Bradyrhizobium guangdongense\n+ 0.00\t450\t450\tS\t1325095\t Bradyrhizobium guangzhouense\n+ 0.00\t425\t425\tS\t931866\t Bradyrhizobium ottawaense\n+ 0.00\t362\t362\tS\t1325115\t Bradyrhizobium guangxiense\n+ 0.00\t320\t320\tS\t1404768\t Bradyrhizobium amphicarpaeae\n+ 0.00\t305\t305\tS\t244734\t Bradyrhizobium betae\n+ 0.00\t56\t0\tS\t29448\t Bradyrhizobium elkanii\n+ 0.00\t56\t56\tS1\t1275962\t '..b' Oxyplax ochracea nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1850906\t Catopsilia pomona nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1307956\t Leucania separata nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1642929\t Lambdina fiscellaria nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t74660\t Choristoneura fumiferana DEF multiple nucleopolyhedrovirus\n+ 0.00\t3\t0\tG\t558018\t Gammabaculovirus\n+ 0.00\t2\t2\tS\t111874\t Neodiprion sertifer nucleopolyhedrovirus\n+ 0.00\t1\t0\tG1\t1233523\t unclassified Gammabaculovirus\n+ 0.00\t1\t1\tS\t204507\t Neodiprion abietis NPV\n+ 0.00\t95\t0\tD1\t12429\t unclassified viruses\n+ 0.00\t88\t0\tD2\t2204151\t unclassified DNA viruses\n+ 0.00\t86\t0\tD3\t51368\t unclassified dsDNA viruses\n+ 0.00\t82\t7\tG\t2060084\t Pandoravirus\n+ 0.00\t30\t30\tS\t2107707\t Pandoravirus macleodensis\n+ 0.00\t11\t11\tS\t1349409\t Pandoravirus dulcis\n+ 0.00\t10\t10\tS\t1349410\t Pandoravirus salinus\n+ 0.00\t9\t9\tS\t1605721\t Pandoravirus inopinatum\n+ 0.00\t9\t9\tS\t2107708\t Pandoravirus neocaledonia\n+ 0.00\t6\t6\tS\t2107709\t Pandoravirus quercus\n+ 0.00\t2\t2\tS\t1100043\t Apis mellifera filamentous virus\n+ 0.00\t2\t0\tF\t2023203\t Pithoviridae\n+ 0.00\t1\t0\tG\t1805626\t Pithovirus\n+ 0.00\t1\t1\tS\t1450746\t Pithovirus sibericum\n+ 0.00\t1\t1\tS\t1903266\t Cedratvirus A11\n+ 0.00\t2\t0\tD3\t2136008\t unclassified archaeal dsDNA viruses\n+ 0.00\t2\t0\tD4\t128706\t Haloviruses\n+ 0.00\t2\t2\tS\t1262530\t Halovirus HSTV-1\n+ 0.00\t4\t4\tS\t1904876\t Human DNA virus\n+ 0.00\t3\t3\tS\t1678078\t Mollivirus sibericum\n+ 0.00\t11\t0\tD1\t2731342\t Monodnaviria\n+ 0.00\t11\t0\tK\t2732092\t Shotokuvirae\n+ 0.00\t8\t0\tP\t2732416\t Cressdnaviricota\n+ 0.00\t8\t0\tC\t2732424\t Repensiviricetes\n+ 0.00\t8\t0\tO\t2732539\t Geplafuvirales\n+ 0.00\t8\t0\tF\t10811\t Geminiviridae\n+ 0.00\t8\t0\tG\t10814\t Begomovirus\n+ 0.00\t4\t4\tS\t437063\t Ageratum yellow vein Hualian virus\n+ 0.00\t2\t2\tS\t1915203\t Common bean severe mosaic virus\n+ 0.00\t1\t1\tS\t1982675\t Jacquemontia yellow vein virus\n+ 0.00\t1\t1\tS\t85752\t Tomato yellow leaf curl Thailand virus\n+ 0.00\t3\t0\tP\t2732415\t Cossaviricota\n+ 0.00\t3\t0\tC\t2732421\t Papovaviricetes\n+ 0.00\t2\t0\tO\t2732532\t Sepolyvirales\n+ 0.00\t2\t0\tF\t151341\t Polyomaviridae\n+ 0.00\t2\t0\tG\t1891714\t Betapolyomavirus\n+ 0.00\t2\t2\tS\t1891762\t Human polyomavirus 1\n+ 0.00\t1\t0\tO\t2732533\t Zurhausenvirales\n+ 0.00\t1\t0\tF\t151340\t Papillomaviridae\n+ 0.00\t1\t0\tF1\t2169595\t Firstpapillomavirinae\n+ 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n+ 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n+ 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n+ 0.00\t5\t0\tF\t10482\t Polydnaviridae\n+ 0.00\t3\t0\tG\t10485\t Bracovirus\n+ 0.00\t3\t3\tS\t39640\t Cotesia congregata bracovirus\n+ 0.00\t2\t0\tG\t10483\t Ichnovirus\n+ 0.00\t2\t2\tS\t265522\t Hyposoter fugitivus ichnovirus\n+ 0.00\t3\t0\tF\t1511852\t Nudiviridae\n+ 0.00\t2\t0\tF1\t1110703\t unclassified Nudiviridae\n+ 0.00\t2\t2\tS\t1654582\t Kallithea virus\n+ 0.00\t1\t0\tG\t1511853\t Alphanudivirus\n+ 0.00\t1\t1\tS\t92521\t Oryctes rhinoceros nudivirus\n+ 0.00\t2\t0\tF\t1285590\t Hytrosaviridae\n+ 0.00\t1\t0\tG\t1285591\t Glossinavirus\n+ 0.00\t1\t0\tS\t2747309\t Glossina hytrosavirus\n+ 0.00\t1\t1\tS1\t379529\t Glossina pallidipes salivary gland hypertrophy virus\n+ 0.00\t1\t0\tG\t1285593\t Muscavirus\n+ 0.00\t1\t0\tS\t2747498\t Musca hytrosavirus\n+ 0.00\t1\t1\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n+ 0.00\t1\t0\tF\t196937\t Nimaviridae\n+ 0.00\t1\t0\tG\t249585\t Whispovirus\n+ 0.00\t1\t1\tS\t342409\t White spot syndrome virus\n+ 0.00\t1\t0\tR1\t2787854\t other entries\n+ 0.00\t1\t1\tR2\t28384\t other sequences\n' |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/MG_AIR20200708.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MG_AIR20200708.tabular Fri Sep 09 09:32:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,11152 @@\n+ 92.06\t8810061\t8810061\tU\t0\tunclassified\n+ 7.94\t759690\t240\tR\t1\troot\n+ 7.93\t758772\t5483\tR1\t131567\t cellular organisms\n+ 6.64\t635165\t26878\tD\t2\t Bacteria\n+ 3.06\t293202\t14752\tP\t1224\t Proteobacteria\n+ 1.27\t121724\t4181\tC\t28211\t Alphaproteobacteria\n+ 0.72\t68949\t3483\tO\t356\t Hyphomicrobiales\n+ 0.35\t33460\t958\tF\t41294\t Bradyrhizobiaceae\n+ 0.29\t28150\t4256\tG\t374\t Bradyrhizobium\n+ 0.10\t9951\t1601\tG1\t2631580\t unclassified Bradyrhizobium\n+ 0.02\t2350\t2350\tS\t858422\t Bradyrhizobium sp. CCBAU 051011\n+ 0.01\t786\t786\tS\t1325100\t Bradyrhizobium sp. CCBAU 51753\n+ 0.01\t727\t727\tS\t1197460\t Bradyrhizobium sp. 6(2017)\n+ 0.01\t505\t505\tS\t376\t Bradyrhizobium sp.\n+ 0.00\t446\t446\tS\t2057741\t Bradyrhizobium sp. SK17\n+ 0.00\t396\t396\tS\t2715960\t Bradyrhizobium sp. PSBB068\n+ 0.00\t389\t389\tS\t288000\t Bradyrhizobium sp. BTAi1\n+ 0.00\t364\t364\tS\t1325120\t Bradyrhizobium sp. CCBAU 53421\n+ 0.00\t342\t342\tS\t115808\t Bradyrhizobium sp. ORS 285\n+ 0.00\t317\t317\tS\t114615\t Bradyrhizobium sp. ORS 278\n+ 0.00\t278\t278\tS\t1404888\t Bradyrhizobium sp. 1(2017)\n+ 0.00\t241\t241\tS\t1325112\t Bradyrhizobium sp. CCBAU 53340\n+ 0.00\t237\t237\tS\t1325102\t Bradyrhizobium sp. CCBAU 51765\n+ 0.00\t222\t222\tS\t1325111\t Bradyrhizobium sp. CCBAU 53338\n+ 0.00\t222\t222\tS\t1223566\t Bradyrhizobium sp. CCGE-LA001\n+ 0.00\t201\t201\tS\t1325114\t Bradyrhizobium sp. CCBAU 53351\n+ 0.00\t133\t133\tS\t319017\t Bradyrhizobium sp. WSM471\n+ 0.00\t104\t104\tS\t2493093\t Bradyrhizobium sp. LCT2\n+ 0.00\t49\t49\tS\t1404649\t Bradyrhizobium sp. 323S2\n+ 0.00\t16\t16\tS\t2599805\t Bradyrhizobium sp. SG09\n+ 0.00\t15\t15\tS\t1325083\t Bradyrhizobium sp. CCBAU 21365\n+ 0.00\t10\t10\tS\t2599819\t Bradyrhizobium sp. TM102\n+ 0.04\t3785\t3785\tS\t1437360\t Bradyrhizobium erythrophlei\n+ 0.02\t1883\t1883\tS\t1274631\t Bradyrhizobium icense\n+ 0.02\t1629\t1629\tS\t190148\t Bradyrhizobium paxllaeri\n+ 0.01\t1149\t1149\tS\t1355477\t Bradyrhizobium diazoefficiens\n+ 0.01\t1138\t1138\tS\t722472\t Bradyrhizobium lablabi\n+ 0.01\t819\t819\tS\t255045\t Bradyrhizobium canariense\n+ 0.01\t510\t397\tS\t375\t Bradyrhizobium japonicum\n+ 0.00\t113\t113\tS1\t476282\t Bradyrhizobium japonicum SEMIA 5079\n+ 0.00\t366\t366\tS\t83637\t Bradyrhizobium genosp. L\n+ 0.00\t295\t295\tS\t1325107\t Bradyrhizobium zhanjiangense\n+ 0.00\t294\t0\tS\t44255\t Bradyrhizobium oligotrophicum\n+ 0.00\t294\t294\tS1\t1245469\t Bradyrhizobium oligotrophicum S58\n+ 0.00\t260\t260\tS\t83627\t Bradyrhizobium genosp. B\n+ 0.00\t249\t249\tS\t858423\t Bradyrhizobium arachidis\n+ 0.00\t213\t213\tS\t1325095\t Bradyrhizobium guangzhouense\n+ 0.00\t206\t206\tS\t1404367\t Bradyrhizobium symbiodeficiens\n+ 0.00\t198\t198\tS\t1325115\t Bradyrhizobium guangxiense\n+ 0.00\t193\t193\tS\t1549949\t Bradyrhizobium vignae\n+ 0.00\t188\t188\tS\t1404864\t Bradyrhizobium cosmicum\n+ 0.00\t179\t179\tS\t931866\t Bradyrhizobium ottawaense\n+ 0.00\t133\t133\tS\t1404768\t Bradyrhizobium amphicarpaeae\n+ 0.00\t116\t116\tS\t1325090\t Bradyrhizobium guangdongense\n+ 0.00\t102\t102\tS\t244734\t Bradyrhizobium betae\n+ 0.00\t38\t0\tS\t29448\t Bradyrhizobium elkanii\n+ 0.00\t38\t38\tS1\t1275962\t Bradyrhizobium elkanii USDA 61\n+ 0.01\t1313\t44\tG\t85413\t Bosea\n+ 0.01\t1095\t83\tG1\t2653178\t unclassified Bosea\n+ 0.00\t221\t221\tS\t2599640\t Bosea sp. F3-2\n+ 0.00\t191\t191\tS\t1842539\t '..b'40\t1\tG\t558017\t Betabaculovirus\n+ 0.00\t23\t23\tS\t28289\t Cydia pomonella granulovirus\n+ 0.00\t11\t11\tS\t56947\t Choristoneura fumiferana granulovirus\n+ 0.00\t2\t2\tS\t192584\t Phthorimaea operculella granulovirus\n+ 0.00\t2\t2\tS\t489830\t Helicoverpa armigera granulovirus\n+ 0.00\t1\t1\tS\t51677\t Xestia c-nigrum granulovirus\n+ 0.00\t9\t0\tG\t558016\t Alphabaculovirus\n+ 0.00\t3\t3\tS\t224399\t Adoxophyes honmai nucleopolyhedrovirus\n+ 0.00\t2\t2\tS\t28288\t Hyphantria cunea nucleopolyhedrovirus\n+ 0.00\t2\t2\tS\t1987479\t Choristoneura murinana nucleopolyhedrovirus\n+ 0.00\t1\t0\tS\t2560642\t Perigonia lusca nucleopolyhedrovirus\n+ 0.00\t1\t1\tS1\t1675865\t Perigonia lusca single nucleopolyhedrovirus\n+ 0.00\t1\t0\tG1\t745176\t unclassified Alphabaculovirus\n+ 0.00\t1\t1\tS\t1346829\t Peridroma alphabaculovirus\n+ 0.00\t43\t0\tD1\t12429\t unclassified viruses\n+ 0.00\t41\t0\tD2\t2204151\t unclassified DNA viruses\n+ 0.00\t38\t0\tD3\t51368\t unclassified dsDNA viruses\n+ 0.00\t34\t1\tG\t2060084\t Pandoravirus\n+ 0.00\t10\t10\tS\t2107709\t Pandoravirus quercus\n+ 0.00\t9\t9\tS\t1349409\t Pandoravirus dulcis\n+ 0.00\t6\t6\tS\t1349410\t Pandoravirus salinus\n+ 0.00\t4\t4\tS\t1605721\t Pandoravirus inopinatum\n+ 0.00\t3\t3\tS\t2107708\t Pandoravirus neocaledonia\n+ 0.00\t1\t1\tS\t2107707\t Pandoravirus macleodensis\n+ 0.00\t3\t3\tS\t1100043\t Apis mellifera filamentous virus\n+ 0.00\t1\t0\tF\t2023203\t Pithoviridae\n+ 0.00\t1\t1\tS\t1903266\t Cedratvirus A11\n+ 0.00\t3\t0\tD3\t2136008\t unclassified archaeal dsDNA viruses\n+ 0.00\t3\t0\tD4\t128706\t Haloviruses\n+ 0.00\t3\t3\tS\t1273746\t Halovirus HCTV-1\n+ 0.00\t2\t2\tS\t1678078\t Mollivirus sibericum\n+ 0.00\t8\t0\tD1\t2731342\t Monodnaviria\n+ 0.00\t8\t0\tK\t2732092\t Shotokuvirae\n+ 0.00\t7\t0\tP\t2732415\t Cossaviricota\n+ 0.00\t7\t0\tC\t2732421\t Papovaviricetes\n+ 0.00\t7\t0\tO\t2732533\t Zurhausenvirales\n+ 0.00\t7\t0\tF\t151340\t Papillomaviridae\n+ 0.00\t7\t0\tF1\t2169595\t Firstpapillomavirinae\n+ 0.00\t4\t0\tG\t1513238\t Dyokappapapillomavirus\n+ 0.00\t4\t0\tS\t1513247\t Dyokappapapillomavirus 1\n+ 0.00\t4\t4\tS1\t634772\t Ovis aries papillomavirus 3\n+ 0.00\t2\t0\tG\t934803\t Dyozetapapillomavirus\n+ 0.00\t2\t0\tS\t1177766\t Dyozetapapillomavirus 1\n+ 0.00\t2\t2\tS1\t485241\t Caretta caretta papillomavirus 1\n+ 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n+ 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n+ 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n+ 0.00\t1\t0\tP\t2732416\t Cressdnaviricota\n+ 0.00\t1\t0\tC\t2732424\t Repensiviricetes\n+ 0.00\t1\t0\tO\t2732539\t Geplafuvirales\n+ 0.00\t1\t0\tF\t10811\t Geminiviridae\n+ 0.00\t1\t0\tG\t2022857\t Capulavirus\n+ 0.00\t1\t1\tS\t1830242\t Plantago lanceolata latent virus\n+ 0.00\t5\t0\tF\t1511852\t Nudiviridae\n+ 0.00\t3\t0\tG\t1511854\t Betanudivirus\n+ 0.00\t3\t0\tS\t29250\t Heliothis zea nudivirus\n+ 0.00\t3\t3\tS1\t1128424\t Helicoverpa zea nudivirus 2\n+ 0.00\t2\t0\tG\t1511853\t Alphanudivirus\n+ 0.00\t2\t2\tS\t432587\t Gryllus bimaculatus nudivirus\n+ 0.00\t3\t0\tF\t10482\t Polydnaviridae\n+ 0.00\t2\t0\tG\t10483\t Ichnovirus\n+ 0.00\t1\t1\tS\t10484\t Campoletis sonorensis ichnovirus\n+ 0.00\t1\t1\tS\t419435\t Glypta fumiferanae ichnovirus\n+ 0.00\t1\t0\tG\t10485\t Bracovirus\n+ 0.00\t1\t1\tS\t39640\t Cotesia congregata bracovirus\n+ 0.00\t1\t0\tF\t1285590\t Hytrosaviridae\n+ 0.00\t1\t0\tG\t1285593\t Muscavirus\n+ 0.00\t1\t0\tS\t2747498\t Musca hytrosavirus\n+ 0.00\t1\t1\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n+ 0.00\t1\t0\tF\t423358\t Bicaudaviridae\n+ 0.00\t1\t0\tF1\t1123963\t unclassified Bicaudaviridae\n+ 0.00\t1\t1\tS\t1732177\t Sulfolobus monocaudavirus SMV3\n' |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/MG_AIR20200709.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MG_AIR20200709.tabular Fri Sep 09 09:32:59 2022 +0000 |
| b |
| b"@@ -0,0 +1,12317 @@\n+ 91.75\t14211438\t14211438\tU\t0\tunclassified\n+ 8.25\t1277434\t386\tR\t1\troot\n+ 8.24\t1276166\t6094\tR1\t131567\t cellular organisms\n+ 7.70\t1192581\t48540\tD\t2\t Bacteria\n+ 3.62\t559951\t3486\tD1\t1783272\t Terrabacteria group\n+ 3.25\t503885\t2455\tP\t201174\t Actinobacteria\n+ 3.15\t487919\t42867\tC\t1760\t Actinomycetia\n+ 0.75\t116898\t5584\tO\t85006\t Micrococcales\n+ 0.34\t52165\t3276\tF\t85023\t Microbacteriaceae\n+ 0.10\t16078\t1589\tG\t33882\t Microbacterium\n+ 0.05\t7231\t591\tG1\t2609290\t unclassified Microbacterium\n+ 0.00\t641\t641\tS\t1906742\t Microbacterium sp. BH-3-3-3\n+ 0.00\t467\t467\tS\t2567934\t Microbacterium sp. 4R-513\n+ 0.00\t424\t424\tS\t2782168\t Microbacterium sp. WY121\n+ 0.00\t411\t411\tS\t2782169\t Microbacterium sp. NY27\n+ 0.00\t356\t356\tS\t1714373\t Microbacterium sp. No. 7\n+ 0.00\t314\t314\tS\t2483401\t Microbacterium sp. 10M-3C3\n+ 0.00\t305\t305\tS\t2763257\t Microbacterium sp. YJN-G\n+ 0.00\t286\t286\tS\t1906274\t Microbacterium sp. JZ31\n+ 0.00\t279\t279\tS\t912630\t Microbacterium sp. LKL04\n+ 0.00\t271\t271\tS\t2268461\t Microbacterium sp. ABRD_28\n+ 0.00\t260\t260\tS\t2782167\t Microbacterium sp. A18JL200\n+ 0.00\t255\t255\tS\t367477\t Microbacterium sp. XT11\n+ 0.00\t244\t244\tS\t2709304\t Microbacterium sp. Se63.02b\n+ 0.00\t243\t243\tS\t2048898\t Microbacterium sp. Y-01\n+ 0.00\t240\t240\tS\t2489212\t Microbacterium sp. RG1\n+ 0.00\t233\t233\tS\t2603598\t Microbacterium sp. CBA3102\n+ 0.00\t225\t225\tS\t2782166\t Microbacterium sp. A18JL241\n+ 0.00\t224\t224\tS\t2014534\t Microbacterium sp. PM5\n+ 0.00\t176\t176\tS\t2606451\t Microbacterium sp. 1S1\n+ 0.00\t171\t171\tS\t1938334\t Microbacterium sp. TPU 3598\n+ 0.00\t114\t114\tS\t2708079\t Microbacterium sp. HY82\n+ 0.00\t114\t114\tS\t2766784\t Microbacterium sp. Nx66\n+ 0.00\t104\t104\tS\t1795053\t Microbacterium sp. PAMC 28756\n+ 0.00\t87\t87\tS\t2769067\t Microbacterium sp. HY60\n+ 0.00\t75\t75\tS\t1696072\t Microbacterium sp. CGR1\n+ 0.00\t68\t68\tS\t1916917\t Microbacterium sp. 1.5R\n+ 0.00\t33\t33\tS\t2070348\t Microbacterium sp. SGAir0570\n+ 0.00\t20\t20\tS\t2103230\t Microbacterium sp. str. 'China'\n+ 0.01\t1187\t1187\tS\t1072463\t Microbacterium lemovicicum\n+ 0.01\t940\t940\tS\t104336\t Microbacterium foliorum\n+ 0.00\t770\t770\tS\t162426\t Microbacterium hominis\n+ 0.00\t527\t527\tS\t273677\t Microbacterium oleivorans\n+ 0.00\t443\t443\tS\t370764\t Microbacterium pygmaeum\n+ 0.00\t384\t384\tS\t82380\t Microbacterium oxydans\n+ 0.00\t290\t0\tS\t2033\t Microbacterium testaceum\n+ 0.00\t290\t290\tS1\t979556\t Microbacterium testaceum StLB037\n+ 0.00\t269\t269\tS\t36805\t Microbacterium aurum\n+ 0.00\t262\t262\tS\t2541726\t Microbacterium wangchenii\n+ 0.00\t262\t262\tS\t743009\t Microbacterium oryzae\n+ 0.00\t246\t246\tS\t904291\t Microbacterium sediminis\n+ 0.00\t240\t240\tS\t2614638\t Microbacterium caowuchunii\n+ 0.00\t235\t235\tS\t273678\t Microbacterium hydrocarbonoxydans\n+ 0.00\t229\t229\tS\t84292\t Microbacterium chocolatum\n+ 0.00\t216\t216\tS\t2614639\t Microbacterium lushaniae\n+ 0.00\t214\t214\tS\t57043\t Microbacterium esteraromaticum\n+ 0.00\t205\t205\tS\t2509458\t Microbacterium protaetiae\n+ 0.00\t134\t134\tS\t69362\t Microbacterium schleiferi\n+ 0.00\t77\t77\tS\t1526412\t Microbacterium endophyticum\n+ 0.00\t76\t76\tS\t936337\t "..b'ithovirus sibericum\n+ 0.00\t2\t2\tS\t1678078\t Mollivirus sibericum\n+ 0.00\t1\t1\tS\t1904876\t Human DNA virus\n+ 0.00\t47\t0\tF\t10442\t Baculoviridae\n+ 0.00\t25\t0\tG\t558017\t Betabaculovirus\n+ 0.00\t9\t9\tS\t28289\t Cydia pomonella granulovirus\n+ 0.00\t9\t9\tS\t56947\t Choristoneura fumiferana granulovirus\n+ 0.00\t4\t4\tS\t51677\t Xestia c-nigrum granulovirus\n+ 0.00\t2\t2\tS\t307454\t Spodoptera frugiperda granulovirus\n+ 0.00\t1\t1\tS\t2169746\t Mythimna unipuncta granulovirus B\n+ 0.00\t22\t0\tG\t558016\t Alphabaculovirus\n+ 0.00\t4\t4\tS\t1307956\t Leucania separata nucleopolyhedrovirus\n+ 0.00\t4\t0\tG1\t745176\t unclassified Alphabaculovirus\n+ 0.00\t3\t3\tS\t1346829\t Peridroma alphabaculovirus\n+ 0.00\t1\t1\tS\t38012\t Malacosoma neustria nucleopolyhedrovirus\n+ 0.00\t3\t3\tS\t10449\t Lymantria dispar multiple nucleopolyhedrovirus\n+ 0.00\t2\t2\tS\t447897\t Mythimna unipuncta nucleopolyhedrovirus\n+ 0.00\t2\t2\tS\t1850906\t Catopsilia pomona nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t262177\t Orgyia pseudotsugata multiple nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1675866\t Urbanus proteus nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1642929\t Lambdina fiscellaria nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1580580\t Agrotis segetum nucleopolyhedrovirus B\n+ 0.00\t1\t1\tS\t208013\t Agrotis ipsilon multiple nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t490711\t Orgyia leucostigma nucleopolyhedrovirus\n+ 0.00\t1\t1\tS\t1307954\t Maruca vitrata nucleopolyhedrovirus\n+ 0.00\t8\t0\tD1\t2731342\t Monodnaviria\n+ 0.00\t8\t0\tK\t2732092\t Shotokuvirae\n+ 0.00\t5\t0\tP\t2732416\t Cressdnaviricota\n+ 0.00\t3\t0\tC\t2732424\t Repensiviricetes\n+ 0.00\t3\t0\tO\t2732539\t Geplafuvirales\n+ 0.00\t3\t0\tF\t10811\t Geminiviridae\n+ 0.00\t2\t0\tG\t10814\t Begomovirus\n+ 0.00\t2\t2\tS\t1915203\t Common bean severe mosaic virus\n+ 0.00\t1\t0\tG\t2022857\t Capulavirus\n+ 0.00\t1\t1\tS\t1830242\t Plantago lanceolata latent virus\n+ 0.00\t2\t0\tC\t2732423\t Arfiviricetes\n+ 0.00\t2\t0\tO\t2732536\t Cirlivirales\n+ 0.00\t2\t0\tF\t39724\t Circoviridae\n+ 0.00\t2\t0\tG\t742914\t Cyclovirus\n+ 0.00\t2\t0\tS\t2038725\t Human associated cyclovirus 7\n+ 0.00\t2\t2\tS1\t742923\t Cyclovirus NG14\n+ 0.00\t3\t0\tP\t2732415\t Cossaviricota\n+ 0.00\t3\t0\tC\t2732421\t Papovaviricetes\n+ 0.00\t2\t0\tO\t2732532\t Sepolyvirales\n+ 0.00\t2\t0\tF\t151341\t Polyomaviridae\n+ 0.00\t2\t0\tG\t1891713\t Alphapolyomavirus\n+ 0.00\t2\t2\tS\t1236407\t Piliocolobus rufomitratus polyomavirus 1\n+ 0.00\t1\t0\tO\t2732533\t Zurhausenvirales\n+ 0.00\t1\t0\tF\t151340\t Papillomaviridae\n+ 0.00\t1\t0\tF1\t2169595\t Firstpapillomavirinae\n+ 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n+ 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n+ 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n+ 0.00\t4\t0\tF\t1285590\t Hytrosaviridae\n+ 0.00\t2\t0\tG\t1285591\t Glossinavirus\n+ 0.00\t2\t0\tS\t2747309\t Glossina hytrosavirus\n+ 0.00\t2\t2\tS1\t379529\t Glossina pallidipes salivary gland hypertrophy virus\n+ 0.00\t2\t0\tG\t1285593\t Muscavirus\n+ 0.00\t2\t0\tS\t2747498\t Musca hytrosavirus\n+ 0.00\t2\t2\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n+ 0.00\t3\t0\tF\t1511852\t Nudiviridae\n+ 0.00\t3\t0\tF1\t1110703\t unclassified Nudiviridae\n+ 0.00\t2\t2\tS\t2072209\t Esparto virus\n+ 0.00\t1\t1\tS\t2057187\t Drosophila innubila nudivirus\n+ 0.00\t2\t0\tF\t196937\t Nimaviridae\n+ 0.00\t2\t0\tG\t249585\t Whispovirus\n+ 0.00\t2\t2\tS\t342409\t White spot syndrome virus\n+ 0.00\t1\t0\tF\t423358\t Bicaudaviridae\n+ 0.00\t1\t0\tF1\t1123963\t unclassified Bicaudaviridae\n+ 0.00\t1\t1\tS\t1797140\t Acidianus tailed spindle virus\n+ 0.00\t1\t0\tR1\t2787854\t other entries\n+ 0.00\t1\t1\tR2\t28384\t other sequences\n' |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/SamplesMetaDataTabular.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SamplesMetaDataTabular.csv Fri Sep 09 09:32:59 2022 +0000 |
| [ |
| @@ -0,0 +1,4 @@ +ID_Samples Sample_Name Sampling Date Sampling start Sampling end Sampling Duration (h) Sampling Site EnvType Seasons Categoriy Renard et al. (2020) Boundary layer (min-max [average]) (m) LWC (g/m3) CPC Temp Humi Pres VentV VentD SonicV SonicD Cl(-) (µM) NO3(-) (µM) SO4(2-) (µM) Na(+) (µM) NH4(+) (µM) K(+) (µM) Mg(2+) (µM) Ca(2+) (µM) pH Cell/mL Cell/m3 ATP concentration (pmol/L) DNA concentration (ng/µl) +0-kraken_report MG_AIR20200707 07/07/20 07:00:00 UTC 13:30:00 UTC 6.5 PUY AIR Summer NA 1072-1638 [1430] 0 12.72 55.6 857.45 3.07 70.42 2.71 73.18 550.09 150.15 72.44 8.98 5.52 NA 1.89 0.58 NA NA 1620 3034 5.591 +1-kraken_report MG_AIR20200708 08/07/20 06:35:00 UTC 12:40:00 UTC 6.08 PUY AIR Summer NA 427-1479 [1057] 0 15.74 48.71 857.88 3.08 53.48 2.94 72.16 191.35 193.56 55.55 4.52 3.68 NA 1.36 0.07 NA NA 1720 1290 3.223 +2-kraken_report MG_AIR20200709 09/07/20 06:35:00 UTC 12:35:00 UTC 6 PUY AIR Summer NA 455-2181 [1291] 0 21.48 45.61 857.74 4.08 241.67 4.13 249.75 125.58 156.48 183.26 4.12 9.81 NA 2.33 0.08 NA NA 2620 3915 2.062 |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/krakenReport1.tabular --- a/test-data/krakenReport1.tabular Sat Sep 03 22:13:08 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,12471 +0,0 @@\n- 91.15\t14195379\t14195379\tU\t0\tunclassified\n- 8.85\t1379004\t401\tR\t1\troot\n- 8.84\t1376958\t10737\tR1\t131567\t cellular organisms\n- 7.20\t1121868\t43514\tD\t2\t Bacteria\n- 3.57\t556613\t24838\tP\t1224\t Proteobacteria\n- 1.47\t229058\t7482\tC\t28211\t Alphaproteobacteria\n- 0.93\t144510\t6453\tO\t356\t Hyphomicrobiales\n- 0.52\t80503\t1900\tF\t41294\t Bradyrhizobiaceae\n- 0.44\t69011\t10554\tG\t374\t Bradyrhizobium\n- 0.14\t22423\t4040\tG1\t2631580\t unclassified Bradyrhizobium\n- 0.03\t5066\t5066\tS\t858422\t Bradyrhizobium sp. CCBAU 051011\n- 0.01\t1865\t1865\tS\t1197460\t Bradyrhizobium sp. 6(2017)\n- 0.01\t1549\t1549\tS\t1325100\t Bradyrhizobium sp. CCBAU 51753\n- 0.01\t1005\t1005\tS\t376\t Bradyrhizobium sp.\n- 0.01\t959\t959\tS\t2057741\t Bradyrhizobium sp. SK17\n- 0.01\t947\t947\tS\t1325120\t Bradyrhizobium sp. CCBAU 53421\n- 0.01\t895\t895\tS\t288000\t Bradyrhizobium sp. BTAi1\n- 0.01\t858\t858\tS\t2715960\t Bradyrhizobium sp. PSBB068\n- 0.00\t748\t748\tS\t115808\t Bradyrhizobium sp. ORS 285\n- 0.00\t631\t631\tS\t114615\t Bradyrhizobium sp. ORS 278\n- 0.00\t591\t591\tS\t1404888\t Bradyrhizobium sp. 1(2017)\n- 0.00\t585\t585\tS\t1325102\t Bradyrhizobium sp. CCBAU 51765\n- 0.00\t548\t548\tS\t1325112\t Bradyrhizobium sp. CCBAU 53340\n- 0.00\t532\t532\tS\t1325111\t Bradyrhizobium sp. CCBAU 53338\n- 0.00\t468\t468\tS\t1325114\t Bradyrhizobium sp. CCBAU 53351\n- 0.00\t458\t458\tS\t1223566\t Bradyrhizobium sp. CCGE-LA001\n- 0.00\t253\t253\tS\t319017\t Bradyrhizobium sp. WSM471\n- 0.00\t205\t205\tS\t2493093\t Bradyrhizobium sp. LCT2\n- 0.00\t82\t82\tS\t2599805\t Bradyrhizobium sp. SG09\n- 0.00\t73\t73\tS\t1404649\t Bradyrhizobium sp. 323S2\n- 0.00\t54\t54\tS\t2599819\t Bradyrhizobium sp. TM102\n- 0.00\t10\t10\tS\t1325083\t Bradyrhizobium sp. CCBAU 21365\n- 0.00\t1\t1\tS\t2578114\t Bradyrhizobium sp. KBS0727\n- 0.07\t11646\t11646\tS\t1437360\t Bradyrhizobium erythrophlei\n- 0.02\t3838\t3838\tS\t1274631\t Bradyrhizobium icense\n- 0.02\t3704\t3704\tS\t722472\t Bradyrhizobium lablabi\n- 0.02\t3445\t3445\tS\t190148\t Bradyrhizobium paxllaeri\n- 0.02\t2527\t2525\tS\t1355477\t Bradyrhizobium diazoefficiens\n- 0.00\t2\t2\tS1\t224911\t Bradyrhizobium diazoefficiens USDA 110\n- 0.01\t2286\t2286\tS\t255045\t Bradyrhizobium canariense\n- 0.01\t1081\t865\tS\t375\t Bradyrhizobium japonicum\n- 0.00\t213\t213\tS1\t476282\t Bradyrhizobium japonicum SEMIA 5079\n- 0.00\t3\t3\tS1\t1037409\t Bradyrhizobium japonicum USDA 6\n- 0.01\t1054\t1054\tS\t83637\t Bradyrhizobium genosp. L\n- 0.00\t694\t694\tS\t1325107\t Bradyrhizobium zhanjiangense\n- 0.00\t661\t0\tS\t44255\t Bradyrhizobium oligotrophicum\n- 0.00\t661\t661\tS1\t1245469\t Bradyrhizobium oligotrophicum S58\n- 0.00\t576\t576\tS\t1549949\t Bradyrhizobium vignae\n- 0.00\t562\t562\tS\t83627\t Bradyrhizobium genosp. B\n- 0.00\t556\t556\tS\t1404367\t Bradyrhizobium symbiodeficiens\n- 0.00\t547\t547\tS\t858423\t Bradyrhizobium arachidis\n- 0.00\t480\t480\tS\t1404864\t Bradyrhizobium cosmicum\n- 0.00\t459\t459\tS\t1325090\t Bradyrhizobium guangdongense\n- 0.00\t450\t450\tS\t1325095\t Bradyrhizobium guangzhouense\n- 0.00\t425\t425\tS\t931866\t Bradyrhizobium ottawaense\n- 0.00\t362\t362\tS\t1325115\t Bradyrhizobium guangxiense\n- 0.00\t320\t320\tS\t1404768\t Bradyrhizobium amphicarpaeae\n- 0.00\t305\t305\tS\t244734\t Bradyrhizobium betae\n- 0.00\t56\t0\tS\t29448\t Bradyrhizobium elkanii\n- 0.00\t56\t56\tS1\t1275962\t '..b' Oxyplax ochracea nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1850906\t Catopsilia pomona nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1307956\t Leucania separata nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1642929\t Lambdina fiscellaria nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t74660\t Choristoneura fumiferana DEF multiple nucleopolyhedrovirus\n- 0.00\t3\t0\tG\t558018\t Gammabaculovirus\n- 0.00\t2\t2\tS\t111874\t Neodiprion sertifer nucleopolyhedrovirus\n- 0.00\t1\t0\tG1\t1233523\t unclassified Gammabaculovirus\n- 0.00\t1\t1\tS\t204507\t Neodiprion abietis NPV\n- 0.00\t95\t0\tD1\t12429\t unclassified viruses\n- 0.00\t88\t0\tD2\t2204151\t unclassified DNA viruses\n- 0.00\t86\t0\tD3\t51368\t unclassified dsDNA viruses\n- 0.00\t82\t7\tG\t2060084\t Pandoravirus\n- 0.00\t30\t30\tS\t2107707\t Pandoravirus macleodensis\n- 0.00\t11\t11\tS\t1349409\t Pandoravirus dulcis\n- 0.00\t10\t10\tS\t1349410\t Pandoravirus salinus\n- 0.00\t9\t9\tS\t1605721\t Pandoravirus inopinatum\n- 0.00\t9\t9\tS\t2107708\t Pandoravirus neocaledonia\n- 0.00\t6\t6\tS\t2107709\t Pandoravirus quercus\n- 0.00\t2\t2\tS\t1100043\t Apis mellifera filamentous virus\n- 0.00\t2\t0\tF\t2023203\t Pithoviridae\n- 0.00\t1\t0\tG\t1805626\t Pithovirus\n- 0.00\t1\t1\tS\t1450746\t Pithovirus sibericum\n- 0.00\t1\t1\tS\t1903266\t Cedratvirus A11\n- 0.00\t2\t0\tD3\t2136008\t unclassified archaeal dsDNA viruses\n- 0.00\t2\t0\tD4\t128706\t Haloviruses\n- 0.00\t2\t2\tS\t1262530\t Halovirus HSTV-1\n- 0.00\t4\t4\tS\t1904876\t Human DNA virus\n- 0.00\t3\t3\tS\t1678078\t Mollivirus sibericum\n- 0.00\t11\t0\tD1\t2731342\t Monodnaviria\n- 0.00\t11\t0\tK\t2732092\t Shotokuvirae\n- 0.00\t8\t0\tP\t2732416\t Cressdnaviricota\n- 0.00\t8\t0\tC\t2732424\t Repensiviricetes\n- 0.00\t8\t0\tO\t2732539\t Geplafuvirales\n- 0.00\t8\t0\tF\t10811\t Geminiviridae\n- 0.00\t8\t0\tG\t10814\t Begomovirus\n- 0.00\t4\t4\tS\t437063\t Ageratum yellow vein Hualian virus\n- 0.00\t2\t2\tS\t1915203\t Common bean severe mosaic virus\n- 0.00\t1\t1\tS\t1982675\t Jacquemontia yellow vein virus\n- 0.00\t1\t1\tS\t85752\t Tomato yellow leaf curl Thailand virus\n- 0.00\t3\t0\tP\t2732415\t Cossaviricota\n- 0.00\t3\t0\tC\t2732421\t Papovaviricetes\n- 0.00\t2\t0\tO\t2732532\t Sepolyvirales\n- 0.00\t2\t0\tF\t151341\t Polyomaviridae\n- 0.00\t2\t0\tG\t1891714\t Betapolyomavirus\n- 0.00\t2\t2\tS\t1891762\t Human polyomavirus 1\n- 0.00\t1\t0\tO\t2732533\t Zurhausenvirales\n- 0.00\t1\t0\tF\t151340\t Papillomaviridae\n- 0.00\t1\t0\tF1\t2169595\t Firstpapillomavirinae\n- 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n- 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n- 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n- 0.00\t5\t0\tF\t10482\t Polydnaviridae\n- 0.00\t3\t0\tG\t10485\t Bracovirus\n- 0.00\t3\t3\tS\t39640\t Cotesia congregata bracovirus\n- 0.00\t2\t0\tG\t10483\t Ichnovirus\n- 0.00\t2\t2\tS\t265522\t Hyposoter fugitivus ichnovirus\n- 0.00\t3\t0\tF\t1511852\t Nudiviridae\n- 0.00\t2\t0\tF1\t1110703\t unclassified Nudiviridae\n- 0.00\t2\t2\tS\t1654582\t Kallithea virus\n- 0.00\t1\t0\tG\t1511853\t Alphanudivirus\n- 0.00\t1\t1\tS\t92521\t Oryctes rhinoceros nudivirus\n- 0.00\t2\t0\tF\t1285590\t Hytrosaviridae\n- 0.00\t1\t0\tG\t1285591\t Glossinavirus\n- 0.00\t1\t0\tS\t2747309\t Glossina hytrosavirus\n- 0.00\t1\t1\tS1\t379529\t Glossina pallidipes salivary gland hypertrophy virus\n- 0.00\t1\t0\tG\t1285593\t Muscavirus\n- 0.00\t1\t0\tS\t2747498\t Musca hytrosavirus\n- 0.00\t1\t1\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n- 0.00\t1\t0\tF\t196937\t Nimaviridae\n- 0.00\t1\t0\tG\t249585\t Whispovirus\n- 0.00\t1\t1\tS\t342409\t White spot syndrome virus\n- 0.00\t1\t0\tR1\t2787854\t other entries\n- 0.00\t1\t1\tR2\t28384\t other sequences\n' |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/krakenReport2.tabular --- a/test-data/krakenReport2.tabular Sat Sep 03 22:13:08 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,11152 +0,0 @@\n- 92.06\t8810061\t8810061\tU\t0\tunclassified\n- 7.94\t759690\t240\tR\t1\troot\n- 7.93\t758772\t5483\tR1\t131567\t cellular organisms\n- 6.64\t635165\t26878\tD\t2\t Bacteria\n- 3.06\t293202\t14752\tP\t1224\t Proteobacteria\n- 1.27\t121724\t4181\tC\t28211\t Alphaproteobacteria\n- 0.72\t68949\t3483\tO\t356\t Hyphomicrobiales\n- 0.35\t33460\t958\tF\t41294\t Bradyrhizobiaceae\n- 0.29\t28150\t4256\tG\t374\t Bradyrhizobium\n- 0.10\t9951\t1601\tG1\t2631580\t unclassified Bradyrhizobium\n- 0.02\t2350\t2350\tS\t858422\t Bradyrhizobium sp. CCBAU 051011\n- 0.01\t786\t786\tS\t1325100\t Bradyrhizobium sp. CCBAU 51753\n- 0.01\t727\t727\tS\t1197460\t Bradyrhizobium sp. 6(2017)\n- 0.01\t505\t505\tS\t376\t Bradyrhizobium sp.\n- 0.00\t446\t446\tS\t2057741\t Bradyrhizobium sp. SK17\n- 0.00\t396\t396\tS\t2715960\t Bradyrhizobium sp. PSBB068\n- 0.00\t389\t389\tS\t288000\t Bradyrhizobium sp. BTAi1\n- 0.00\t364\t364\tS\t1325120\t Bradyrhizobium sp. CCBAU 53421\n- 0.00\t342\t342\tS\t115808\t Bradyrhizobium sp. ORS 285\n- 0.00\t317\t317\tS\t114615\t Bradyrhizobium sp. ORS 278\n- 0.00\t278\t278\tS\t1404888\t Bradyrhizobium sp. 1(2017)\n- 0.00\t241\t241\tS\t1325112\t Bradyrhizobium sp. CCBAU 53340\n- 0.00\t237\t237\tS\t1325102\t Bradyrhizobium sp. CCBAU 51765\n- 0.00\t222\t222\tS\t1325111\t Bradyrhizobium sp. CCBAU 53338\n- 0.00\t222\t222\tS\t1223566\t Bradyrhizobium sp. CCGE-LA001\n- 0.00\t201\t201\tS\t1325114\t Bradyrhizobium sp. CCBAU 53351\n- 0.00\t133\t133\tS\t319017\t Bradyrhizobium sp. WSM471\n- 0.00\t104\t104\tS\t2493093\t Bradyrhizobium sp. LCT2\n- 0.00\t49\t49\tS\t1404649\t Bradyrhizobium sp. 323S2\n- 0.00\t16\t16\tS\t2599805\t Bradyrhizobium sp. SG09\n- 0.00\t15\t15\tS\t1325083\t Bradyrhizobium sp. CCBAU 21365\n- 0.00\t10\t10\tS\t2599819\t Bradyrhizobium sp. TM102\n- 0.04\t3785\t3785\tS\t1437360\t Bradyrhizobium erythrophlei\n- 0.02\t1883\t1883\tS\t1274631\t Bradyrhizobium icense\n- 0.02\t1629\t1629\tS\t190148\t Bradyrhizobium paxllaeri\n- 0.01\t1149\t1149\tS\t1355477\t Bradyrhizobium diazoefficiens\n- 0.01\t1138\t1138\tS\t722472\t Bradyrhizobium lablabi\n- 0.01\t819\t819\tS\t255045\t Bradyrhizobium canariense\n- 0.01\t510\t397\tS\t375\t Bradyrhizobium japonicum\n- 0.00\t113\t113\tS1\t476282\t Bradyrhizobium japonicum SEMIA 5079\n- 0.00\t366\t366\tS\t83637\t Bradyrhizobium genosp. L\n- 0.00\t295\t295\tS\t1325107\t Bradyrhizobium zhanjiangense\n- 0.00\t294\t0\tS\t44255\t Bradyrhizobium oligotrophicum\n- 0.00\t294\t294\tS1\t1245469\t Bradyrhizobium oligotrophicum S58\n- 0.00\t260\t260\tS\t83627\t Bradyrhizobium genosp. B\n- 0.00\t249\t249\tS\t858423\t Bradyrhizobium arachidis\n- 0.00\t213\t213\tS\t1325095\t Bradyrhizobium guangzhouense\n- 0.00\t206\t206\tS\t1404367\t Bradyrhizobium symbiodeficiens\n- 0.00\t198\t198\tS\t1325115\t Bradyrhizobium guangxiense\n- 0.00\t193\t193\tS\t1549949\t Bradyrhizobium vignae\n- 0.00\t188\t188\tS\t1404864\t Bradyrhizobium cosmicum\n- 0.00\t179\t179\tS\t931866\t Bradyrhizobium ottawaense\n- 0.00\t133\t133\tS\t1404768\t Bradyrhizobium amphicarpaeae\n- 0.00\t116\t116\tS\t1325090\t Bradyrhizobium guangdongense\n- 0.00\t102\t102\tS\t244734\t Bradyrhizobium betae\n- 0.00\t38\t0\tS\t29448\t Bradyrhizobium elkanii\n- 0.00\t38\t38\tS1\t1275962\t Bradyrhizobium elkanii USDA 61\n- 0.01\t1313\t44\tG\t85413\t Bosea\n- 0.01\t1095\t83\tG1\t2653178\t unclassified Bosea\n- 0.00\t221\t221\tS\t2599640\t Bosea sp. F3-2\n- 0.00\t191\t191\tS\t1842539\t '..b'40\t1\tG\t558017\t Betabaculovirus\n- 0.00\t23\t23\tS\t28289\t Cydia pomonella granulovirus\n- 0.00\t11\t11\tS\t56947\t Choristoneura fumiferana granulovirus\n- 0.00\t2\t2\tS\t192584\t Phthorimaea operculella granulovirus\n- 0.00\t2\t2\tS\t489830\t Helicoverpa armigera granulovirus\n- 0.00\t1\t1\tS\t51677\t Xestia c-nigrum granulovirus\n- 0.00\t9\t0\tG\t558016\t Alphabaculovirus\n- 0.00\t3\t3\tS\t224399\t Adoxophyes honmai nucleopolyhedrovirus\n- 0.00\t2\t2\tS\t28288\t Hyphantria cunea nucleopolyhedrovirus\n- 0.00\t2\t2\tS\t1987479\t Choristoneura murinana nucleopolyhedrovirus\n- 0.00\t1\t0\tS\t2560642\t Perigonia lusca nucleopolyhedrovirus\n- 0.00\t1\t1\tS1\t1675865\t Perigonia lusca single nucleopolyhedrovirus\n- 0.00\t1\t0\tG1\t745176\t unclassified Alphabaculovirus\n- 0.00\t1\t1\tS\t1346829\t Peridroma alphabaculovirus\n- 0.00\t43\t0\tD1\t12429\t unclassified viruses\n- 0.00\t41\t0\tD2\t2204151\t unclassified DNA viruses\n- 0.00\t38\t0\tD3\t51368\t unclassified dsDNA viruses\n- 0.00\t34\t1\tG\t2060084\t Pandoravirus\n- 0.00\t10\t10\tS\t2107709\t Pandoravirus quercus\n- 0.00\t9\t9\tS\t1349409\t Pandoravirus dulcis\n- 0.00\t6\t6\tS\t1349410\t Pandoravirus salinus\n- 0.00\t4\t4\tS\t1605721\t Pandoravirus inopinatum\n- 0.00\t3\t3\tS\t2107708\t Pandoravirus neocaledonia\n- 0.00\t1\t1\tS\t2107707\t Pandoravirus macleodensis\n- 0.00\t3\t3\tS\t1100043\t Apis mellifera filamentous virus\n- 0.00\t1\t0\tF\t2023203\t Pithoviridae\n- 0.00\t1\t1\tS\t1903266\t Cedratvirus A11\n- 0.00\t3\t0\tD3\t2136008\t unclassified archaeal dsDNA viruses\n- 0.00\t3\t0\tD4\t128706\t Haloviruses\n- 0.00\t3\t3\tS\t1273746\t Halovirus HCTV-1\n- 0.00\t2\t2\tS\t1678078\t Mollivirus sibericum\n- 0.00\t8\t0\tD1\t2731342\t Monodnaviria\n- 0.00\t8\t0\tK\t2732092\t Shotokuvirae\n- 0.00\t7\t0\tP\t2732415\t Cossaviricota\n- 0.00\t7\t0\tC\t2732421\t Papovaviricetes\n- 0.00\t7\t0\tO\t2732533\t Zurhausenvirales\n- 0.00\t7\t0\tF\t151340\t Papillomaviridae\n- 0.00\t7\t0\tF1\t2169595\t Firstpapillomavirinae\n- 0.00\t4\t0\tG\t1513238\t Dyokappapapillomavirus\n- 0.00\t4\t0\tS\t1513247\t Dyokappapapillomavirus 1\n- 0.00\t4\t4\tS1\t634772\t Ovis aries papillomavirus 3\n- 0.00\t2\t0\tG\t934803\t Dyozetapapillomavirus\n- 0.00\t2\t0\tS\t1177766\t Dyozetapapillomavirus 1\n- 0.00\t2\t2\tS1\t485241\t Caretta caretta papillomavirus 1\n- 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n- 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n- 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n- 0.00\t1\t0\tP\t2732416\t Cressdnaviricota\n- 0.00\t1\t0\tC\t2732424\t Repensiviricetes\n- 0.00\t1\t0\tO\t2732539\t Geplafuvirales\n- 0.00\t1\t0\tF\t10811\t Geminiviridae\n- 0.00\t1\t0\tG\t2022857\t Capulavirus\n- 0.00\t1\t1\tS\t1830242\t Plantago lanceolata latent virus\n- 0.00\t5\t0\tF\t1511852\t Nudiviridae\n- 0.00\t3\t0\tG\t1511854\t Betanudivirus\n- 0.00\t3\t0\tS\t29250\t Heliothis zea nudivirus\n- 0.00\t3\t3\tS1\t1128424\t Helicoverpa zea nudivirus 2\n- 0.00\t2\t0\tG\t1511853\t Alphanudivirus\n- 0.00\t2\t2\tS\t432587\t Gryllus bimaculatus nudivirus\n- 0.00\t3\t0\tF\t10482\t Polydnaviridae\n- 0.00\t2\t0\tG\t10483\t Ichnovirus\n- 0.00\t1\t1\tS\t10484\t Campoletis sonorensis ichnovirus\n- 0.00\t1\t1\tS\t419435\t Glypta fumiferanae ichnovirus\n- 0.00\t1\t0\tG\t10485\t Bracovirus\n- 0.00\t1\t1\tS\t39640\t Cotesia congregata bracovirus\n- 0.00\t1\t0\tF\t1285590\t Hytrosaviridae\n- 0.00\t1\t0\tG\t1285593\t Muscavirus\n- 0.00\t1\t0\tS\t2747498\t Musca hytrosavirus\n- 0.00\t1\t1\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n- 0.00\t1\t0\tF\t423358\t Bicaudaviridae\n- 0.00\t1\t0\tF1\t1123963\t unclassified Bicaudaviridae\n- 0.00\t1\t1\tS\t1732177\t Sulfolobus monocaudavirus SMV3\n' |
| b |
| diff -r 3ff4712dc111 -r 65eb9962d272 test-data/krakenReport3.tabular --- a/test-data/krakenReport3.tabular Sat Sep 03 22:13:08 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,12317 +0,0 @@\n- 91.75\t14211438\t14211438\tU\t0\tunclassified\n- 8.25\t1277434\t386\tR\t1\troot\n- 8.24\t1276166\t6094\tR1\t131567\t cellular organisms\n- 7.70\t1192581\t48540\tD\t2\t Bacteria\n- 3.62\t559951\t3486\tD1\t1783272\t Terrabacteria group\n- 3.25\t503885\t2455\tP\t201174\t Actinobacteria\n- 3.15\t487919\t42867\tC\t1760\t Actinomycetia\n- 0.75\t116898\t5584\tO\t85006\t Micrococcales\n- 0.34\t52165\t3276\tF\t85023\t Microbacteriaceae\n- 0.10\t16078\t1589\tG\t33882\t Microbacterium\n- 0.05\t7231\t591\tG1\t2609290\t unclassified Microbacterium\n- 0.00\t641\t641\tS\t1906742\t Microbacterium sp. BH-3-3-3\n- 0.00\t467\t467\tS\t2567934\t Microbacterium sp. 4R-513\n- 0.00\t424\t424\tS\t2782168\t Microbacterium sp. WY121\n- 0.00\t411\t411\tS\t2782169\t Microbacterium sp. NY27\n- 0.00\t356\t356\tS\t1714373\t Microbacterium sp. No. 7\n- 0.00\t314\t314\tS\t2483401\t Microbacterium sp. 10M-3C3\n- 0.00\t305\t305\tS\t2763257\t Microbacterium sp. YJN-G\n- 0.00\t286\t286\tS\t1906274\t Microbacterium sp. JZ31\n- 0.00\t279\t279\tS\t912630\t Microbacterium sp. LKL04\n- 0.00\t271\t271\tS\t2268461\t Microbacterium sp. ABRD_28\n- 0.00\t260\t260\tS\t2782167\t Microbacterium sp. A18JL200\n- 0.00\t255\t255\tS\t367477\t Microbacterium sp. XT11\n- 0.00\t244\t244\tS\t2709304\t Microbacterium sp. Se63.02b\n- 0.00\t243\t243\tS\t2048898\t Microbacterium sp. Y-01\n- 0.00\t240\t240\tS\t2489212\t Microbacterium sp. RG1\n- 0.00\t233\t233\tS\t2603598\t Microbacterium sp. CBA3102\n- 0.00\t225\t225\tS\t2782166\t Microbacterium sp. A18JL241\n- 0.00\t224\t224\tS\t2014534\t Microbacterium sp. PM5\n- 0.00\t176\t176\tS\t2606451\t Microbacterium sp. 1S1\n- 0.00\t171\t171\tS\t1938334\t Microbacterium sp. TPU 3598\n- 0.00\t114\t114\tS\t2708079\t Microbacterium sp. HY82\n- 0.00\t114\t114\tS\t2766784\t Microbacterium sp. Nx66\n- 0.00\t104\t104\tS\t1795053\t Microbacterium sp. PAMC 28756\n- 0.00\t87\t87\tS\t2769067\t Microbacterium sp. HY60\n- 0.00\t75\t75\tS\t1696072\t Microbacterium sp. CGR1\n- 0.00\t68\t68\tS\t1916917\t Microbacterium sp. 1.5R\n- 0.00\t33\t33\tS\t2070348\t Microbacterium sp. SGAir0570\n- 0.00\t20\t20\tS\t2103230\t Microbacterium sp. str. 'China'\n- 0.01\t1187\t1187\tS\t1072463\t Microbacterium lemovicicum\n- 0.01\t940\t940\tS\t104336\t Microbacterium foliorum\n- 0.00\t770\t770\tS\t162426\t Microbacterium hominis\n- 0.00\t527\t527\tS\t273677\t Microbacterium oleivorans\n- 0.00\t443\t443\tS\t370764\t Microbacterium pygmaeum\n- 0.00\t384\t384\tS\t82380\t Microbacterium oxydans\n- 0.00\t290\t0\tS\t2033\t Microbacterium testaceum\n- 0.00\t290\t290\tS1\t979556\t Microbacterium testaceum StLB037\n- 0.00\t269\t269\tS\t36805\t Microbacterium aurum\n- 0.00\t262\t262\tS\t2541726\t Microbacterium wangchenii\n- 0.00\t262\t262\tS\t743009\t Microbacterium oryzae\n- 0.00\t246\t246\tS\t904291\t Microbacterium sediminis\n- 0.00\t240\t240\tS\t2614638\t Microbacterium caowuchunii\n- 0.00\t235\t235\tS\t273678\t Microbacterium hydrocarbonoxydans\n- 0.00\t229\t229\tS\t84292\t Microbacterium chocolatum\n- 0.00\t216\t216\tS\t2614639\t Microbacterium lushaniae\n- 0.00\t214\t214\tS\t57043\t Microbacterium esteraromaticum\n- 0.00\t205\t205\tS\t2509458\t Microbacterium protaetiae\n- 0.00\t134\t134\tS\t69362\t Microbacterium schleiferi\n- 0.00\t77\t77\tS\t1526412\t Microbacterium endophyticum\n- 0.00\t76\t76\tS\t936337\t "..b'ithovirus sibericum\n- 0.00\t2\t2\tS\t1678078\t Mollivirus sibericum\n- 0.00\t1\t1\tS\t1904876\t Human DNA virus\n- 0.00\t47\t0\tF\t10442\t Baculoviridae\n- 0.00\t25\t0\tG\t558017\t Betabaculovirus\n- 0.00\t9\t9\tS\t28289\t Cydia pomonella granulovirus\n- 0.00\t9\t9\tS\t56947\t Choristoneura fumiferana granulovirus\n- 0.00\t4\t4\tS\t51677\t Xestia c-nigrum granulovirus\n- 0.00\t2\t2\tS\t307454\t Spodoptera frugiperda granulovirus\n- 0.00\t1\t1\tS\t2169746\t Mythimna unipuncta granulovirus B\n- 0.00\t22\t0\tG\t558016\t Alphabaculovirus\n- 0.00\t4\t4\tS\t1307956\t Leucania separata nucleopolyhedrovirus\n- 0.00\t4\t0\tG1\t745176\t unclassified Alphabaculovirus\n- 0.00\t3\t3\tS\t1346829\t Peridroma alphabaculovirus\n- 0.00\t1\t1\tS\t38012\t Malacosoma neustria nucleopolyhedrovirus\n- 0.00\t3\t3\tS\t10449\t Lymantria dispar multiple nucleopolyhedrovirus\n- 0.00\t2\t2\tS\t447897\t Mythimna unipuncta nucleopolyhedrovirus\n- 0.00\t2\t2\tS\t1850906\t Catopsilia pomona nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t262177\t Orgyia pseudotsugata multiple nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1675866\t Urbanus proteus nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1642929\t Lambdina fiscellaria nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1580580\t Agrotis segetum nucleopolyhedrovirus B\n- 0.00\t1\t1\tS\t208013\t Agrotis ipsilon multiple nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t490711\t Orgyia leucostigma nucleopolyhedrovirus\n- 0.00\t1\t1\tS\t1307954\t Maruca vitrata nucleopolyhedrovirus\n- 0.00\t8\t0\tD1\t2731342\t Monodnaviria\n- 0.00\t8\t0\tK\t2732092\t Shotokuvirae\n- 0.00\t5\t0\tP\t2732416\t Cressdnaviricota\n- 0.00\t3\t0\tC\t2732424\t Repensiviricetes\n- 0.00\t3\t0\tO\t2732539\t Geplafuvirales\n- 0.00\t3\t0\tF\t10811\t Geminiviridae\n- 0.00\t2\t0\tG\t10814\t Begomovirus\n- 0.00\t2\t2\tS\t1915203\t Common bean severe mosaic virus\n- 0.00\t1\t0\tG\t2022857\t Capulavirus\n- 0.00\t1\t1\tS\t1830242\t Plantago lanceolata latent virus\n- 0.00\t2\t0\tC\t2732423\t Arfiviricetes\n- 0.00\t2\t0\tO\t2732536\t Cirlivirales\n- 0.00\t2\t0\tF\t39724\t Circoviridae\n- 0.00\t2\t0\tG\t742914\t Cyclovirus\n- 0.00\t2\t0\tS\t2038725\t Human associated cyclovirus 7\n- 0.00\t2\t2\tS1\t742923\t Cyclovirus NG14\n- 0.00\t3\t0\tP\t2732415\t Cossaviricota\n- 0.00\t3\t0\tC\t2732421\t Papovaviricetes\n- 0.00\t2\t0\tO\t2732532\t Sepolyvirales\n- 0.00\t2\t0\tF\t151341\t Polyomaviridae\n- 0.00\t2\t0\tG\t1891713\t Alphapolyomavirus\n- 0.00\t2\t2\tS\t1236407\t Piliocolobus rufomitratus polyomavirus 1\n- 0.00\t1\t0\tO\t2732533\t Zurhausenvirales\n- 0.00\t1\t0\tF\t151340\t Papillomaviridae\n- 0.00\t1\t0\tF1\t2169595\t Firstpapillomavirinae\n- 0.00\t1\t0\tG\t325455\t Gammapapillomavirus\n- 0.00\t1\t0\tG1\t735504\t unclassified Gammapapillomavirus\n- 0.00\t1\t1\tS\t2049444\t Gammapapillomavirus sp.\n- 0.00\t4\t0\tF\t1285590\t Hytrosaviridae\n- 0.00\t2\t0\tG\t1285591\t Glossinavirus\n- 0.00\t2\t0\tS\t2747309\t Glossina hytrosavirus\n- 0.00\t2\t2\tS1\t379529\t Glossina pallidipes salivary gland hypertrophy virus\n- 0.00\t2\t0\tG\t1285593\t Muscavirus\n- 0.00\t2\t0\tS\t2747498\t Musca hytrosavirus\n- 0.00\t2\t2\tS1\t523909\t Musca domestica salivary gland hypertrophy virus\n- 0.00\t3\t0\tF\t1511852\t Nudiviridae\n- 0.00\t3\t0\tF1\t1110703\t unclassified Nudiviridae\n- 0.00\t2\t2\tS\t2072209\t Esparto virus\n- 0.00\t1\t1\tS\t2057187\t Drosophila innubila nudivirus\n- 0.00\t2\t0\tF\t196937\t Nimaviridae\n- 0.00\t2\t0\tG\t249585\t Whispovirus\n- 0.00\t2\t2\tS\t342409\t White spot syndrome virus\n- 0.00\t1\t0\tF\t423358\t Bicaudaviridae\n- 0.00\t1\t0\tF1\t1123963\t unclassified Bicaudaviridae\n- 0.00\t1\t1\tS\t1797140\t Acidianus tailed spindle virus\n- 0.00\t1\t0\tR1\t2787854\t other entries\n- 0.00\t1\t1\tR2\t28384\t other sequences\n' |