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Changeset 0:fc2077c654fb (2023-01-13)

Next changeset 1:4b32f3b4a851 (2023-02-13)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209

added:
beta_diversity.xml
macros.xml
test-data/1.tabular
test-data/2.tabular
test-data/3.tabular
test-data/beta_bracken_1.tabular
test-data/beta_bracken_2.tabular
test-data/beta_bracken_3.tabular
test-data/beta_kreport_1.tabular
test-data/beta_kreport_2.tabular
test-data/beta_kreport_3.tabular
test-data/beta_krona_1.tabular
test-data/beta_krona_2.tabular
test-data/bracken_abundance.tabular
test-data/output.tabular
test-data/output_intermediate.tabular
test-data/sample.tabular

diff -r 000000000000 -r fc2077c654fb beta_diversity.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/beta_diversity.xml Fri Jan 13 13:21:51 2023 +0000

[

@@ -0,0 +1,95 @@
+<tool id="krakentools_beta_diversity" name="Krakentools: calculates beta diversity (Bray-Curtis dissimilarity)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from Kraken, Krona and Bracken files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+beta_diversity.py
+    --inputs
+    #for $input in $inputs
+        '$input'
+    #end for
+    --type '$sample.type'
+    #if $sample.type == 'kreport'
+        --level '$sample.level'
+    #else if $sample.type == 'krona'
+        --level '$sample.level'
+    #end if
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--inputs" type="data" multiple="true" format="tabular" label="Taxonomy file(s)" help="The files can be generated by Kraken, Bracken or Krona"/>
+        <conditional name="sample">
+            <param argument="--type" type="select" label="Specify type of input file(s)">
+                <option value="single" selected="true">Single tabular data file</option>
+                <option value="simple">Tabular data files</option>
+                <option value="bracken">Braken species abundance file</option>
+                <option value="kreport">Kraken report file</option>
+                <option value="krona">Krona file</option>
+            </param>
+            <when value="single"/>
+            <when value="simple"/>
+            <when value="bracken"/>
+            <when value="kreport">
+                <expand macro="param_level"/>
+            </when>
+            <when value="krona">
+                <expand macro="param_level"/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/>
+            <param name="type" value="bracken"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="0.629"/>
+                    <has_text text="0.993"/>
+                    <has_text text="0.995"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/>
+            <param name="type" value="kreport"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="0.584"/>
+                    <has_text text="0.996"/>
+                    <has_text text="0.995"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/>
+            <param name="type" value="krona"/>
+            <param name="level" value="G"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_text text="0.993"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This program calculates the beta diversity (Bray-Curtis dissimilarity) from kraken, krona and bracken files.
+
+Input
+------
+Bracken files, Kraken and Kracken2 report files and Krona files. Additionally, you can pass any tab-separated file and specify the columns with the taxonomical information and read counts (--cols).
+
+Output
+------
+Beta diversity of the input files
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

diff -r 000000000000 -r fc2077c654fb macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jan 13 13:21:51 2023 +0000

@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">krakentools</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">krakentools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command></version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41596-022-00738-y</citation>
+        </citations>
+    </xml>
+    <xml name="param_level">
+        <param argument="--level" type="select" label="Specify which level to measure at">
+            <option value="all" selected="true">All</option>
+            <option value="S">Species</option>
+            <option value="G">Genera</option>
+            <option value="F">Family</option>
+            <option value="O">Order</option>
+        </param>
+    </xml>
+</macros>

diff -r 000000000000 -r fc2077c654fb test-data/1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular Fri Jan 13 13:21:51 2023 +0000

[

b'@@ -0,0 +1,3033 @@\n+name\ttaxonomy_id\ttaxonomy_lvl\tkraken_assigned_reads\tadded_reads\tnew_est_reads\tfraction_total_reads\n+[Ruminococcus] gnavus\t33038\tS\t7691179\t616234\t8307413\t0.21418\n+[Ruminococcus] torques\t33039\tS\t252163\t27407\t279570\t0.00721\n+Anaerostipes hadrus\t649756\tS\t3603595\t156551\t3760146\t0.09695\n+Anaerostipes caccae\t105841\tS\t11765\t186\t11951\t0.00031\n+Anaerostipes rhamnosivorans\t1229621\tS\t10999\t247\t11246\t0.00029\n+Blautia obeum\t40520\tS\t738429\t54268\t792697\t0.02044\n+Blautia sp. SC05B48\t2479767\tS\t374191\t29634\t403825\t0.01041\n+Blautia sp. NBRC 113351\t2877527\tS\t102408\t0\t102408\t0.00264\n+Blautia argi\t1912897\tS\t439939\t17711\t457650\t0.01180\n+Blautia massiliensis\t1737424\tS\t285036\t0\t285036\t0.00735\n+Blautia hansenii\t1322\tS\t193377\t22845\t216222\t0.00557\n+Blautia producta\t33035\tS\t106549\t1632\t108181\t0.00279\n+Blautia pseudococcoides\t1796616\tS\t58164\t1079503\t1137667\t0.02933\n+Blautia liquoris\t2779518\tS\t17828\t85\t17913\t0.00046\n+Coprococcus comes\t410072\tS\t543570\t51308\t594878\t0.01534\n+Coprococcus catus\t116085\tS\t203082\t18305\t221387\t0.00571\n+Coprococcus sp. ART55/1\t751585\tS\t63068\t4154\t67222\t0.00173\n+Coprococcus eutactus\t33043\tS\t23305\t0\t23305\t0.00060\n+Anaerobutyricum hallii\t39488\tS\t838713\t83291\t922004\t0.02377\n+[Clostridium] scindens\t29347\tS\t222110\t10315\t232425\t0.00599\n+[Clostridium] hylemonae\t89153\tS\t77562\t46\t77608\t0.00200\n+Lachnoclostridium phocaeense\t1871021\tS\t38261\t1534\t39795\t0.00103\n+Lachnoclostridium sp. YL32\t1834196\tS\t36261\t18944\t55205\t0.00142\n+Lachnoclostridium phytofermentans\t66219\tS\t6578\t12\t6590\t0.00017\n+Dorea longicatena\t88431\tS\t329338\t0\t329338\t0.00849\n+Faecalicatena sp. Marseille-Q4148\t2823316\tS\t308410\t0\t308410\t0.00795\n+Roseburia intestinalis\t166486\tS\t163275\t32843\t196118\t0.00506\n+Roseburia hominis\t301301\tS\t76584\t12263\t88847\t0.00229\n+Roseburia sp. NSJ-69\t2763062\tS\t40206\t0\t40206\t0.00104\n+Enterocloster bolteae\t208479\tS\t70941\t4297\t75238\t0.00194\n+Enterocloster clostridioformis\t1531\tS\t20976\t17332\t38308\t0.00099\n+Sellimonas intestinalis\t1653434\tS\t76267\t0\t76267\t0.00197\n+Anaerocolumna sedimenticola\t2696063\tS\t10503\t662\t11165\t0.00029\n+Anaerocolumna cellulosilytica\t433286\tS\t10306\t618\t10924\t0.00028\n+Anaerocolumna chitinilytica\t1727145\tS\t9008\t0\t9008\t0.00023\n+Butyrivibrio fibrisolvens\t831\tS\t12755\t486\t13241\t0.00034\n+Butyrivibrio proteoclasticus\t43305\tS\t7048\t671\t7719\t0.00020\n+Butyrivibrio hungatei\t185008\tS\t6915\t790\t7705\t0.00020\n+Lacrimispora sphenoides\t29370\tS\t14521\t506\t15027\t0.00039\n+Lacrimispora saccharolytica\t84030\tS\t13000\t574\t13574\t0.00035\n+Novisyntrophococcus fermenticellae\t2068655\tS\t21594\t0\t21594\t0.00056\n+Lachnospira eligens\t39485\tS\t18953\t0\t18953\t0.00049\n+Pseudobutyrivibrio xylanivorans\t185007\tS\t11863\t220\t12083\t0.00031\n+Lachnoanaerobaculum umeaense\t617123\tS\t8308\t57\t8365\t0.00022\n+Herbinix luporum\t1679721\tS\t3282\t594\t3876\t0.00010\n+Anaerotignum propionicum\t28446\tS\t3227\t9\t3236\t0.00008\n+Cellulosilyticum sp. WCF-2\t2497860\tS\t357\t774\t1131\t0.00003\n+Cellulosilyticum lentocellum\t29360\tS\t349\t766\t1115\t0.00003\n+Faecalibacterium prausnitzii\t853\tS\t146424\t4697\t151121\t0.00390\n+Ruthenibacterium lactatiformans\t1550024\tS\t30179\t350\t30529\t0.00079\n+Vescimonas fastidiosa\t2714353\tS\t22258\t0\t22258\t0.00057\n+Vescimonas coprocola\t2714355\tS\t1553\t0\t1553\t0.00004\n+Flavonifractor plautii\t292800\tS\t23093\t242\t23335\t0.00060\n+Pusillibacter faecalis\t2714358\tS\t13607\t0\t13607\t0.00035\n+Ruminococcus bicirculans\t1160721\tS\t3717\t83\t3800\t0.00010\n+Ruminococcus albus\t1264\tS\t1129\t2\t1131\t0.00003\n+Ruminococcus bovis\t2564099\tS\t972\t2\t974\t0.00003\n+Ruminococcus champanellensis\t1161942\tS\t291\t3\t294\t0.00001\n+Anaerotruncus colihominis\t169435\tS\t5078\t0\t5078\t0.00013\n+Dysosmobacter welbionis\t2093857\tS\t4238\t7403\t11641\t0.00030\n+Dysosmobacter sp. Marseille-Q4140\t2830675\tS\t817\t0\t817\t0.00002\n+Monoglobus pectinilyticus\t1981510\tS\t3336\t98\t3434\t0.00009\n+Solibaculum mannosilyticum\t2780922\tS\t3184\t0\t3184\t0.00008\n+Acetivibrio clariflavus\t288965\tS\t1142\t266\t1408\t0.00004\n+Acetivibrio saccincola\t1677857\tS\t828\t164\t992\t0.00003\n+Acetivibrio thermocellus\t1515\tS\t644\t3\t647\t0.00002\n+Acutalibacter muris\t1796620\tS\t2575\t5\t2580\t0.00007\n+Ruminiclostr'..b'urispirillum indicum\t936456\tS\t110\t0\t110\t0.00000\n+Endomicrobium proavitum\t1408281\tS\t38\t0\t38\t0.00000\n+Candidatus Endomicrobium trichonymphae\t1408204\tS\t11\t0\t11\t0.00000\n+Elusimicrobium minutum\t423605\tS\t45\t0\t45\t0.00000\n+Dictyoglomus thermophilum\t14\tS\t33\t3\t36\t0.00000\n+Caldithrix abyssi\t187145\tS\t29\t0\t29\t0.00000\n+Caldisericum exile\t693075\tS\t12\t0\t12\t0.00000\n+Homo sapiens\t9606\tS\t3944\t126\t4070\t0.00010\n+Saccharomyces cerevisiae\t4932\tS\t2554\t0\t2554\t0.00007\n+Saccharomyces paradoxus\t27291\tS\t29\t0\t29\t0.00000\n+Saccharomyces eubayanus\t1080349\tS\t12\t0\t12\t0.00000\n+Torulaspora delbrueckii\t4950\tS\t280\t0\t280\t0.00001\n+Naumovozyma castellii\t27288\tS\t102\t0\t102\t0.00000\n+Kluyveromyces lactis\t28985\tS\t47\t0\t47\t0.00000\n+Zygotorulaspora mrakii\t42260\tS\t45\t0\t45\t0.00000\n+Tetrapisispora phaffii\t113608\tS\t12\t0\t12\t0.00000\n+Sugiyamaella lignohabitans\t796027\tS\t10\t0\t10\t0.00000\n+Fusarium fujikuroi\t5127\tS\t45\t0\t45\t0.00000\n+Fusarium verticillioides\t117187\tS\t14\t0\t14\t0.00000\n+Fusarium pseudograminearum\t101028\tS\t31\t0\t31\t0.00000\n+Drechmeria coniospora\t98403\tS\t22\t0\t22\t0.00000\n+Pyricularia oryzae\t318829\tS\t74\t0\t74\t0.00000\n+Talaromyces rugulosus\t121627\tS\t74\t0\t74\t0.00000\n+Aspergillus puulaauensis\t1220207\tS\t17\t0\t17\t0.00000\n+Schizosaccharomyces pombe\t4896\tS\t38\t0\t38\t0.00000\n+Rhizoctonia solani\t456999\tS\t133\t0\t133\t0.00000\n+Marasmius oreades\t181124\tS\t12\t0\t12\t0.00000\n+Plasmodium vinckei\t5860\tS\t62\t0\t62\t0.00000\n+Plasmodium relictum\t85471\tS\t53\t0\t53\t0.00000\n+Plasmodium malariae\t5858\tS\t31\t0\t31\t0.00000\n+Plasmodium reichenowi\t5854\tS\t15\t0\t15\t0.00000\n+Neospora caninum\t29176\tS\t34\t0\t34\t0.00000\n+Toxoplasma gondii\t5811\tS\t23\t0\t23\t0.00000\n+Besnoitia besnoiti\t94643\tS\t15\t0\t15\t0.00000\n+Phaeodactylum tricornutum\t2850\tS\t124\t0\t124\t0.00000\n+Dictyostelium discoideum\t44689\tS\t56\t0\t56\t0.00000\n+Methanosalsum zhilinae\t39669\tS\t409\t25\t434\t0.00001\n+Methanosarcina lacustris\t170861\tS\t237\t10\t247\t0.00001\n+Methanosarcina thermophila\t2210\tS\t10\t0\t10\t0.00000\n+Methanolobus zinderi\t536044\tS\t165\t6\t171\t0.00000\n+Methanococcoides sp. LMO-1\t2822137\tS\t112\t0\t112\t0.00000\n+Methanococcoides methylutens\t2226\tS\t36\t2\t38\t0.00000\n+Methanohalophilus mahii\t2176\tS\t19\t18\t37\t0.00000\n+Methanocorpusculum labreanum\t83984\tS\t144\t0\t144\t0.00000\n+Methanospirillum hungatei\t2203\tS\t13\t0\t13\t0.00000\n+Methanoplanus limicola\t2315\tS\t11\t0\t11\t0.00000\n+Methanofollis liminatans\t2201\tS\t11\t0\t11\t0.00000\n+Methanoregula formicica\t882104\tS\t20\t0\t20\t0.00000\n+Haladaptatus pallidirubidus\t1008152\tS\t46\t0\t46\t0.00000\n+Natranaeroarchaeum sulfidigenum\t2784880\tS\t16\t0\t16\t0.00000\n+Halomicrobium sp. LC1Hm\t2610902\tS\t27\t36\t63\t0.00000\n+Halosiccatus urmianus\t1586233\tS\t31\t0\t31\t0.00000\n+Haloterrigena longa\t370324\tS\t43\t48\t91\t0.00000\n+Methanobrevibacter millerae\t230361\tS\t31\t0\t31\t0.00000\n+Methanobrevibacter ruminantium\t83816\tS\t30\t13\t43\t0.00000\n+Methanobrevibacter arboriphilus\t39441\tS\t13\t0\t13\t0.00000\n+Methanobacterium paludis\t868131\tS\t27\t1\t28\t0.00000\n+Methanobacterium lacus\t877455\tS\t11\t0\t11\t0.00000\n+Methanocaldococcus sp. FS406-22\t644281\tS\t37\t12\t49\t0.00000\n+Methanococcus maripaludis\t39152\tS\t13\t5\t18\t0.00000\n+Archaeoglobus profundus\t84156\tS\t31\t0\t31\t0.00000\n+Sulfurisphaera ohwakuensis\t69656\tS\t56\t18\t74\t0.00000\n+Stygiolobus azoricus\t41675\tS\t14\t0\t14\t0.00000\n+Acidilobus sp. 7A\t1577685\tS\t10\t0\t10\t0.00000\n+Candidatus Nitrosotalea okcheonensis\t1903276\tS\t27\t0\t27\t0.00000\n+Picrophilus torridus\t82076\tS\t114\t0\t114\t0.00000\n+uncultured crAssphage\t1211417\tS\t402471\t0\t402471\t0.01038\n+CrAss-like virus sp.\t2831617\tS\t70247\t0\t70247\t0.00181\n+crAssphage cr110_1\t2772070\tS\t95\t0\t95\t0.00000\n+Lactococcus phage P335\t354260\tS\t533\t103\t636\t0.00002\n+Streptococcus phage PH15\t537874\tS\t34\t0\t34\t0.00000\n+Lactococcus phage TP901-1\t35345\tS\t19\t9\t28\t0.00000\n+Lactococcus phage 28201\t1871678\tS\t13\t4\t17\t0.00000\n+Lactococcus phage 63301\t1871687\tS\t10\t16\t26\t0.00000\n+Lactococcus phage ul36\t114416\tS\t10\t4\t14\t0.00000\n+Lentavirus PMBT5\t2734244\tS\t31\t0\t31\t0.00000\n+Sandinevirus BK5T\t2845191\tS\t17\t4\t21\t0.00000\n+Streptococcus phage EJ-1\t12402\tS\t39\t1\t40\t0.00000\n+Lettuce infectious yellows virus\t31713\tS\t31\t0\t31\t0.00000\n+Megavirus chiliensis\t1094892\tS\t21\t0\t21\t0.00000\n'

diff -r 000000000000 -r fc2077c654fb test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular Fri Jan 13 13:21:51 2023 +0000

[

b'@@ -0,0 +1,3344 @@\n+name\ttaxonomy_id\ttaxonomy_lvl\tkraken_assigned_reads\tadded_reads\tnew_est_reads\tfraction_total_reads\n+[Ruminococcus] gnavus\t33038\tS\t1410218\t143928\t1554146\t0.09429\n+[Ruminococcus] torques\t33039\tS\t127057\t17039\t144096\t0.00874\n+Blautia obeum\t40520\tS\t323684\t30916\t354600\t0.02151\n+Blautia sp. SC05B48\t2479767\tS\t151592\t16026\t167618\t0.01017\n+Blautia sp. NBRC 113351\t2877527\tS\t91402\t0\t91402\t0.00555\n+Blautia argi\t1912897\tS\t160622\t9234\t169856\t0.01031\n+Blautia massiliensis\t1737424\tS\t127316\t0\t127316\t0.00772\n+Blautia producta\t33035\tS\t105084\t1718\t106802\t0.00648\n+Blautia hansenii\t1322\tS\t92090\t13165\t105255\t0.00639\n+Blautia pseudococcoides\t1796616\tS\t30463\t643054\t673517\t0.04086\n+Blautia liquoris\t2779518\tS\t9978\t59\t10037\t0.00061\n+Anaerostipes hadrus\t649756\tS\t951989\t60972\t1012961\t0.06146\n+Anaerostipes caccae\t105841\tS\t8136\t211\t8347\t0.00051\n+Anaerostipes rhamnosivorans\t1229621\tS\t6633\t233\t6866\t0.00042\n+Anaerobutyricum hallii\t39488\tS\t608192\t73003\t681195\t0.04133\n+Coprococcus comes\t410072\tS\t247369\t31158\t278527\t0.01690\n+Coprococcus catus\t116085\tS\t92108\t11960\t104068\t0.00631\n+Coprococcus sp. ART55/1\t751585\tS\t33589\t3450\t37039\t0.00225\n+Coprococcus eutactus\t33043\tS\t23528\t0\t23528\t0.00143\n+[Clostridium] scindens\t29347\tS\t189889\t11016\t200905\t0.01219\n+Lachnoclostridium sp. YL32\t1834196\tS\t51473\t30690\t82163\t0.00498\n+[Clostridium] hylemonae\t89153\tS\t39856\t15\t39871\t0.00242\n+Lachnoclostridium phocaeense\t1871021\tS\t20372\t994\t21366\t0.00130\n+Lachnoclostridium phytofermentans\t66219\tS\t4586\t12\t4598\t0.00028\n+Roseburia intestinalis\t166486\tS\t135631\t35157\t170788\t0.01036\n+Roseburia hominis\t301301\tS\t68703\t15444\t84147\t0.00511\n+Roseburia sp. NSJ-69\t2763062\tS\t40145\t0\t40145\t0.00244\n+Enterocloster bolteae\t208479\tS\t166113\t8914\t175027\t0.01062\n+Enterocloster clostridioformis\t1531\tS\t41584\t37044\t78628\t0.00477\n+Faecalicatena sp. Marseille-Q4148\t2823316\tS\t181956\t0\t181956\t0.01104\n+Dorea longicatena\t88431\tS\t143558\t0\t143558\t0.00871\n+Butyrivibrio fibrisolvens\t831\tS\t13711\t661\t14372\t0.00087\n+Butyrivibrio hungatei\t185008\tS\t10417\t1482\t11899\t0.00072\n+Butyrivibrio proteoclasticus\t43305\tS\t6336\t753\t7089\t0.00043\n+Lachnospira eligens\t39485\tS\t26772\t0\t26772\t0.00162\n+Sellimonas intestinalis\t1653434\tS\t24763\t0\t24763\t0.00150\n+Lacrimispora sphenoides\t29370\tS\t10916\t882\t11798\t0.00072\n+Lacrimispora saccharolytica\t84030\tS\t9173\t920\t10093\t0.00061\n+Anaerocolumna sedimenticola\t2696063\tS\t6025\t648\t6673\t0.00040\n+Anaerocolumna cellulosilytica\t433286\tS\t5819\t597\t6416\t0.00039\n+Anaerocolumna chitinilytica\t1727145\tS\t5721\t0\t5721\t0.00035\n+Pseudobutyrivibrio xylanivorans\t185007\tS\t18456\t412\t18868\t0.00114\n+Novisyntrophococcus fermenticellae\t2068655\tS\t13960\t0\t13960\t0.00085\n+Lachnoanaerobaculum umeaense\t617123\tS\t8494\t104\t8598\t0.00052\n+Anaerotignum propionicum\t28446\tS\t5020\t22\t5042\t0.00031\n+Herbinix luporum\t1679721\tS\t2533\t512\t3045\t0.00018\n+Cellulosilyticum sp. WCF-2\t2497860\tS\t553\t770\t1323\t0.00008\n+Cellulosilyticum lentocellum\t29360\tS\t363\t511\t874\t0.00005\n+Faecalibacterium prausnitzii\t853\tS\t161107\t7319\t168426\t0.01022\n+Faecalibacterium duncaniae\t411483\tS\t10\t250\t260\t0.00002\n+Ruthenibacterium lactatiformans\t1550024\tS\t183921\t2740\t186661\t0.01132\n+Ruminococcus bovis\t2564099\tS\t72769\t379\t73148\t0.00444\n+Ruminococcus bicirculans\t1160721\tS\t25818\t2437\t28255\t0.00171\n+Ruminococcus albus\t1264\tS\t7609\t85\t7694\t0.00047\n+Ruminococcus champanellensis\t1161942\tS\t4136\t312\t4448\t0.00027\n+Flavonifractor plautii\t292800\tS\t102511\t1208\t103719\t0.00629\n+Dysosmobacter welbionis\t2093857\tS\t29232\t38099\t67331\t0.00409\n+Dysosmobacter sp. Marseille-Q4140\t2830675\tS\t5055\t0\t5055\t0.00031\n+Monoglobus pectinilyticus\t1981510\tS\t25987\t1021\t27008\t0.00164\n+Vescimonas fastidiosa\t2714353\tS\t15740\t0\t15740\t0.00095\n+Vescimonas coprocola\t2714355\tS\t4262\t0\t4262\t0.00026\n+Solibaculum mannosilyticum\t2780922\tS\t14971\t0\t14971\t0.00091\n+Anaerotruncus colihominis\t169435\tS\t12007\t0\t12007\t0.00073\n+Pusillibacter faecalis\t2714358\tS\t11816\t0\t11816\t0.00072\n+Caproicibacterium lactatifermentans\t2666138\tS\t4213\t0\t4213\t0.00026\n+Caproicibacterium amylolyticum\t2766537\tS\t4013\t0\t4013\t0.00024\n+Acutalibacter muris\t'..b'\tS\t32\t0\t32\t0.00000\n+Thermosulfurimonas marina\t2047767\tS\t12\t0\t12\t0.00000\n+Thermosulfuriphilus ammonigenes\t1936021\tS\t12\t0\t12\t0.00000\n+Dictyoglomus thermophilum\t14\tS\t50\t0\t50\t0.00000\n+Desulfurispirillum indicum\t936456\tS\t44\t0\t44\t0.00000\n+Caldithrix abyssi\t187145\tS\t36\t0\t36\t0.00000\n+Saccharomyces cerevisiae\t4932\tS\t9010\t0\t9010\t0.00055\n+Saccharomyces paradoxus\t27291\tS\t42\t0\t42\t0.00000\n+Saccharomyces eubayanus\t1080349\tS\t10\t0\t10\t0.00000\n+Torulaspora delbrueckii\t4950\tS\t107\t0\t107\t0.00001\n+Naumovozyma castellii\t27288\tS\t24\t0\t24\t0.00000\n+Kluyveromyces lactis\t28985\tS\t22\t0\t22\t0.00000\n+Tetrapisispora blattae\t1071379\tS\t16\t0\t16\t0.00000\n+Zygotorulaspora mrakii\t42260\tS\t20\t0\t20\t0.00000\n+Sugiyamaella lignohabitans\t796027\tS\t10\t0\t10\t0.00000\n+Fusarium fujikuroi\t5127\tS\t80\t0\t80\t0.00000\n+Fusarium oxysporum\t5507\tS\t76\t0\t76\t0.00000\n+Drechmeria coniospora\t98403\tS\t21\t0\t21\t0.00000\n+Ustilaginoidea virens\t1159556\tS\t10\t0\t10\t0.00000\n+Pyricularia pennisetigena\t1578925\tS\t49\t0\t49\t0.00000\n+Pyricularia oryzae\t318829\tS\t26\t0\t26\t0.00000\n+Thermothelomyces thermophilus\t78579\tS\t12\t0\t12\t0.00000\n+Talaromyces rugulosus\t121627\tS\t43\t0\t43\t0.00000\n+Schizosaccharomyces pombe\t4896\tS\t18\t0\t18\t0.00000\n+Rhizoctonia solani\t456999\tS\t77\t0\t77\t0.00000\n+Homo sapiens\t9606\tS\t5336\t537\t5873\t0.00036\n+Plasmodium vinckei\t5860\tS\t19\t0\t19\t0.00000\n+Plasmodium malariae\t5858\tS\t17\t0\t17\t0.00000\n+Plasmodium relictum\t85471\tS\t11\t0\t11\t0.00000\n+Toxoplasma gondii\t5811\tS\t12\t0\t12\t0.00000\n+Besnoitia besnoiti\t94643\tS\t10\t0\t10\t0.00000\n+Phaeodactylum tricornutum\t2850\tS\t34\t0\t34\t0.00000\n+Methanosarcina barkeri\t2208\tS\t488\t97\t585\t0.00004\n+Methanosarcina sp. MTP4\t1434100\tS\t56\t14\t70\t0.00000\n+Methanosarcina sp. Kolksee\t1434099\tS\t42\t6\t48\t0.00000\n+Methanosarcina lacustris\t170861\tS\t87\t0\t87\t0.00001\n+Methanosarcina mazei\t2209\tS\t32\t0\t32\t0.00000\n+Methanosalsum zhilinae\t39669\tS\t340\t4\t344\t0.00002\n+Methanococcoides methylutens\t2226\tS\t128\t1\t129\t0.00001\n+Methanococcoides sp. LMO-1\t2822137\tS\t80\t0\t80\t0.00000\n+Methanolobus zinderi\t536044\tS\t73\t0\t73\t0.00000\n+Methanohalophilus portucalensis\t39664\tS\t11\t6\t17\t0.00000\n+Methanohalobium evestigatum\t2322\tS\t19\t0\t19\t0.00000\n+Methanoplanus limicola\t2315\tS\t518\t2\t520\t0.00003\n+Methanocorpusculum labreanum\t83984\tS\t106\t0\t106\t0.00001\n+Methanospirillum hungatei\t2203\tS\t35\t0\t35\t0.00000\n+Methanoregula formicica\t882104\tS\t24\t0\t24\t0.00000\n+Methanocella conradii\t1175444\tS\t11\t0\t11\t0.00000\n+Halosiccatus urmianus\t1586233\tS\t38\t0\t38\t0.00000\n+Halomicrobium sp. LC1Hm\t2610902\tS\t23\t19\t42\t0.00000\n+Haladaptatus pallidirubidus\t1008152\tS\t34\t0\t34\t0.00000\n+Halorubrum ezzemoulense\t337243\tS\t11\t8\t19\t0.00000\n+Methanobrevibacter arboriphilus\t39441\tS\t214\t0\t214\t0.00001\n+Methanobrevibacter millerae\t230361\tS\t29\t0\t29\t0.00000\n+Methanobrevibacter smithii\t2173\tS\t22\t0\t22\t0.00000\n+Methanobrevibacter ruminantium\t83816\tS\t11\t2\t13\t0.00000\n+Methanobacterium paludis\t868131\tS\t50\t1\t51\t0.00000\n+Methanobacterium formicicum\t2162\tS\t14\t0\t14\t0.00000\n+Methanococcus vannielii\t2187\tS\t70\t31\t101\t0.00001\n+Methanococcus maripaludis\t39152\tS\t20\t2\t22\t0.00000\n+Methanocaldococcus bathoardescens\t1301915\tS\t20\t2\t22\t0.00000\n+Methanocaldococcus sp. FS406-22\t644281\tS\t19\t1\t20\t0.00000\n+Sulfurisphaera ohwakuensis\t69656\tS\t12\t0\t12\t0.00000\n+Ignicoccus islandicus\t54259\tS\t12\t0\t12\t0.00000\n+Acidilobus sp. 7A\t1577685\tS\t13\t0\t13\t0.00000\n+Candidatus Nitrosotalea okcheonensis\t1903276\tS\t26\t0\t26\t0.00000\n+Picrophilus torridus\t82076\tS\t38\t0\t38\t0.00000\n+Candidatus Methanomethylophilus alvus\t1291540\tS\t10\t0\t10\t0.00000\n+Aciduliprofundum boonei\t379547\tS\t33\t0\t33\t0.00000\n+uncultured crAssphage\t1211417\tS\t85027\t0\t85027\t0.00516\n+CrAss-like virus sp.\t2831617\tS\t14543\t0\t14543\t0.00088\n+crAssphage cr110_1\t2772070\tS\t12\t0\t12\t0.00000\n+Oengusvirus oengus\t2734262\tS\t828\t0\t828\t0.00005\n+Moineauvirus DT1\t90410\tS\t18\t0\t18\t0.00000\n+Moineauvirus Abc2\t633135\tS\t10\t0\t10\t0.00000\n+Lentavirus PMBT5\t2734244\tS\t32\t0\t32\t0.00000\n+Streptococcus phage 5093\t646413\tS\t10\t8\t18\t0.00000\n+Parabacteroides phage YZ-2015b\t1655645\tS\t60\t0\t60\t0.00000\n+Pithovirus sibericum\t1450746\tS\t24\t0\t24\t0.00000\n+Lettuce infectious yellows virus\t31713\tS\t17\t0\t17\t0.00000\n'

diff -r 000000000000 -r fc2077c654fb test-data/3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,345 @@\n+name\ttaxonomy_id\ttaxonomy_lvl\tkraken_assigned_reads\tadded_reads\tnew_est_reads\tfraction_total_reads\n+Enterococcus faecium\t1352\tS\t19117311\t5606915\t24724226\t0.91976\n+Enterococcus avium\t33945\tS\t185099\t8604\t193703\t0.00721\n+Enterococcus faecalis\t1351\tS\t23719\t2158\t25877\t0.00096\n+Enterococcus durans\t53345\tS\t21563\t1616\t23179\t0.00086\n+Enterococcus hirae\t1354\tS\t18570\t853\t19423\t0.00072\n+Enterococcus lactis\t357441\tS\t14452\t35311\t49763\t0.00185\n+Enterococcus mundtii\t53346\tS\t13586\t228\t13814\t0.00051\n+Enterococcus casseliflavus\t37734\tS\t11263\t3466\t14729\t0.00055\n+Enterococcus sp. FDAARGOS_375\t2060307\tS\t5363\t6531\t11894\t0.00044\n+Enterococcus sp. DA9\t2603296\tS\t3725\t15804\t19529\t0.00073\n+Enterococcus sp. FDAARGOS_553\t2420313\tS\t339\t1348\t1687\t0.00006\n+Enterococcus sp. M190262\t2582830\tS\t162\t175\t337\t0.00001\n+Enterococcus sp. CR-Ec1\t2057791\tS\t58\t52\t110\t0.00000\n+Enterococcus thailandicus\t417368\tS\t5457\t126\t5583\t0.00021\n+Enterococcus cecorum\t44008\tS\t2805\t68\t2873\t0.00011\n+Enterococcus saigonensis\t1805431\tS\t2378\t312\t2690\t0.00010\n+Enterococcus rotai\t118060\tS\t1300\t3\t1303\t0.00005\n+Enterococcus raffinosus\t71452\tS\t1102\t0\t1102\t0.00004\n+Enterococcus gilvus\t160453\tS\t246\t8\t254\t0.00001\n+Enterococcus gallinarum\t1353\tS\t190\t300\t490\t0.00002\n+Enterococcus wangshanyuanii\t2005703\tS\t147\t0\t147\t0.00001\n+Enterococcus innesii\t2839759\tS\t72\t0\t72\t0.00000\n+Vagococcus carniphilus\t218144\tS\t693\t52\t745\t0.00003\n+Vagococcus fluvialis\t2738\tS\t281\t0\t281\t0.00001\n+Vagococcus penaei\t633807\tS\t62\t1\t63\t0.00000\n+Vagococcus teuberi\t519472\tS\t52\t1\t53\t0.00000\n+Vagococcus lutrae\t81947\tS\t33\t0\t33\t0.00000\n+Vagococcus xieshaowenii\t2562451\tS\t25\t3\t28\t0.00000\n+Vagococcus zengguangii\t2571750\tS\t24\t2\t26\t0.00000\n+Vagococcus coleopterorum\t2714946\tS\t12\t0\t12\t0.00000\n+Tetragenococcus koreensis\t290335\tS\t423\t44\t467\t0.00002\n+Tetragenococcus halophilus\t51669\tS\t82\t10\t92\t0.00000\n+Tetragenococcus osmophilus\t526944\tS\t52\t14\t66\t0.00000\n+Melissococcus plutonius\t33970\tS\t13\t0\t13\t0.00000\n+Streptococcus thermophilus\t1308\tS\t91845\t3570\t95415\t0.00355\n+Streptococcus pyogenes\t1314\tS\t2298\t203\t2501\t0.00009\n+Streptococcus suis\t1307\tS\t1790\t39\t1829\t0.00007\n+Streptococcus agalactiae\t1311\tS\t1315\t1759\t3074\t0.00011\n+Streptococcus cristatus\t45634\tS\t772\t702\t1474\t0.00005\n+Streptococcus parauberis\t1348\tS\t174\t7\t181\t0.00001\n+Streptococcus pneumoniae\t1313\tS\t156\t159\t315\t0.00001\n+Streptococcus salivarius\t1304\tS\t96\t7\t103\t0.00000\n+Streptococcus infantis\t68892\tS\t93\t113\t206\t0.00001\n+Streptococcus sp. HSISS2\t1316411\tS\t16\t1\t17\t0.00000\n+Streptococcus sp. DAT741\t1940319\tS\t16\t2\t18\t0.00000\n+Streptococcus sp. HSISS3\t1316412\tS\t11\t1\t12\t0.00000\n+Streptococcus dysgalactiae\t1334\tS\t47\t17\t64\t0.00000\n+Streptococcus equi\t1336\tS\t12\t0\t12\t0.00000\n+Streptococcus gallolyticus\t315405\tS\t54\t7\t61\t0.00000\n+Streptococcus anginosus\t1328\tS\t25\t4\t29\t0.00000\n+Streptococcus constellatus\t76860\tS\t16\t103\t119\t0.00000\n+Streptococcus mitis\t28037\tS\t42\t1\t43\t0.00000\n+Streptococcus lutetiensis\t150055\tS\t39\t18\t57\t0.00000\n+Streptococcus pluranimalium\t82348\tS\t30\t0\t30\t0.00000\n+Streptococcus gordonii\t1302\tS\t24\t0\t24\t0.00000\n+Streptococcus vestibularis\t1343\tS\t22\t0\t22\t0.00000\n+Streptococcus pasteurianus\t197614\tS\t20\t18\t38\t0.00000\n+Streptococcus iniae\t1346\tS\t20\t0\t20\t0.00000\n+Streptococcus oralis\t1303\tS\t17\t0\t17\t0.00000\n+Streptococcus parasuis\t1501662\tS\t16\t0\t16\t0.00000\n+Streptococcus mutans\t1309\tS\t11\t0\t11\t0.00000\n+Streptococcus equinus\t1335\tS\t10\t0\t10\t0.00000\n+Lactococcus lactis\t1358\tS\t554\t571\t1125\t0.00004\n+Lactococcus raffinolactis\t1366\tS\t255\t9\t264\t0.00001\n+Lactococcus cremoris\t1359\tS\t253\t85\t338\t0.00001\n+Lactococcus garvieae\t1363\tS\t223\t40\t263\t0.00001\n+Lactococcus piscium\t1364\tS\t22\t18\t40\t0.00000\n+Lactococcus taiwanensis\t1151742\tS\t16\t0\t16\t0.00000\n+Lactococcus sp. LG606\t2816912\tS\t10\t9\t19\t0.00000\n+Jeotgalibaca sp. PTS2502\t1903686\tS\t3404\t392\t3796\t0.00014\n+Jeotgalibaca arthritidis\t1868794\tS\t59\t7\t66\t0.00000\n+Jeotgalibaca ciconiae\t2496265\tS\t27\t0\t27\t0.00000\n+Jeotgalibaca porci\t1868793\tS\t25\t1\t26\t0.00000\n+Granulicatella adiacens\t46124\tS\t1042\t0\t1042\t0.00004\n+Granulicatella elegans\t137732\tS\t46\t0\t46\t0.00000\n+Carn'..b'00\n+Klebsiella sp. CTHL.F3a\t2873296\tS\t45\t0\t45\t0.00000\n+Klebsiella sp. A52\t2834819\tS\t43\t0\t43\t0.00000\n+Klebsiella sp. KPN54798\t2897413\tS\t30\t0\t30\t0.00000\n+Klebsiella sp. P1CD1\t2267618\tS\t21\t129\t150\t0.00001\n+Klebsiella aerogenes\t548\tS\t815\t92\t907\t0.00003\n+Klebsiella michiganensis\t1134687\tS\t547\t11082\t11629\t0.00043\n+Klebsiella oxytoca\t571\tS\t519\t180\t699\t0.00003\n+Klebsiella grimontii\t2058152\tS\t241\t1042\t1283\t0.00005\n+Klebsiella huaxiensis\t2153354\tS\t124\t13\t137\t0.00001\n+Raoultella ornithinolytica\t54291\tS\t316\t170\t486\t0.00002\n+Raoultella planticola\t575\tS\t56\t5\t61\t0.00000\n+Raoultella sp. XY-1\t2799495\tS\t10\t38\t48\t0.00000\n+Escherichia coli\t562\tS\t2179\t23338\t25517\t0.00095\n+Escherichia fergusonii\t564\tS\t17\t4\t21\t0.00000\n+Escherichia marmotae\t1499973\tS\t17\t1\t18\t0.00000\n+Escherichia albertii\t208962\tS\t13\t1\t14\t0.00000\n+Enterobacter cloacae complex sp. ECL411\t2912629\tS\t232\t0\t232\t0.00001\n+Enterobacter cloacae complex sp.\t2027919\tS\t51\t23\t74\t0.00000\n+Enterobacter hormaechei\t158836\tS\t267\t223\t490\t0.00002\n+Enterobacter cloacae\t550\tS\t224\t59\t283\t0.00001\n+Enterobacter roggenkampii\t1812935\tS\t201\t75\t276\t0.00001\n+Enterobacter asburiae\t61645\tS\t38\t12\t50\t0.00000\n+Enterobacter kobei\t208224\tS\t25\t14\t39\t0.00000\n+Enterobacter ludwigii\t299767\tS\t11\t2\t13\t0.00000\n+Enterobacter cancerogenus\t69218\tS\t10\t0\t10\t0.00000\n+Enterobacter sp. JBIWA005\t2831891\tS\t609\t0\t609\t0.00002\n+Enterobacter sp. DNB-S2\t2720029\tS\t14\t0\t14\t0.00000\n+Enterobacter mori\t539813\tS\t277\t81\t358\t0.00001\n+Salmonella enterica\t28901\tS\t368\t1315\t1683\t0.00006\n+Salmonella sp.\t599\tS\t43\t1737\t1780\t0.00007\n+Citrobacter freundii\t546\tS\t137\t88\t225\t0.00001\n+Citrobacter portucalensis\t1639133\tS\t33\t40\t73\t0.00000\n+Citrobacter arsenatis\t2546350\tS\t66\t9\t75\t0.00000\n+Citrobacter amalonaticus\t35703\tS\t14\t10\t24\t0.00000\n+Leclercia adecarboxylata\t83655\tS\t176\t35\t211\t0.00001\n+Leclercia sp. J807\t2681307\tS\t62\t2\t64\t0.00000\n+Shigella boydii\t621\tS\t84\t252\t336\t0.00001\n+Shigella flexneri\t623\tS\t64\t214\t278\t0.00001\n+Shigella dysenteriae\t622\tS\t12\t136\t148\t0.00001\n+Cronobacter sakazakii\t28141\tS\t35\t47\t82\t0.00000\n+Cronobacter universalis\t535744\tS\t13\t0\t13\t0.00000\n+Kosakonia radicincitans\t283686\tS\t16\t19\t35\t0.00000\n+Yokenella regensburgei\t158877\tS\t38\t1\t39\t0.00000\n+Jejubacter calystegiae\t2579935\tS\t29\t0\t29\t0.00000\n+Pluralibacter gergoviae\t61647\tS\t10\t0\t10\t0.00000\n+Lelliottia amnigena\t61646\tS\t14\t0\t14\t0.00000\n+Pectobacterium aquaticum\t2204145\tS\t1547\t0\t1547\t0.00006\n+Serratia fonticola\t47917\tS\t723\t13\t736\t0.00003\n+Serratia marcescens\t615\tS\t42\t6\t48\t0.00000\n+Serratia symbiotica\t138074\tS\t11\t0\t11\t0.00000\n+Yersinia ruckeri\t29486\tS\t246\t3\t249\t0.00001\n+Pantoea stewartii\t66269\tS\t333\t15\t348\t0.00001\n+Pantoea agglomerans\t549\tS\t14\t0\t14\t0.00000\n+Pantoea dispersa\t59814\tS\t11\t0\t11\t0.00000\n+Proteus mirabilis\t584\tS\t19\t2\t21\t0.00000\n+Arsenophonus endosymbiont of Aphis craccivora\t1231049\tS\t14\t0\t14\t0.00000\n+Morganella morganii\t582\tS\t11\t8\t19\t0.00000\n+Edwardsiella tarda\t636\tS\t10\t5\t15\t0.00000\n+Vibrio cholerae\t666\tS\t13\t1\t14\t0.00000\n+Photobacterium damselae\t38293\tS\t11\t1\t12\t0.00000\n+Gallibacterium anatis\t750\tS\t12\t0\t12\t0.00000\n+Acinetobacter baumannii\t470\tS\t17\t6\t23\t0.00000\n+Campylobacter coli\t195\tS\t398\t5\t403\t0.00001\n+Campylobacter jejuni\t197\tS\t58\t5\t63\t0.00000\n+Campylobacter sp. RM10537\t1032242\tS\t10\t0\t10\t0.00000\n+Helicobacter pylori\t210\tS\t12\t0\t12\t0.00000\n+Neisseria meningitidis\t487\tS\t12\t3\t15\t0.00000\n+Prevotella nigrescens\t28133\tS\t48\t0\t48\t0.00000\n+Prevotella enoeca\t76123\tS\t42\t11\t53\t0.00000\n+Prevotella intermedia\t28131\tS\t11\t4\t15\t0.00000\n+Phocaeicola vulgatus\t821\tS\t34\t22\t56\t0.00000\n+Tannerella forsythia\t28112\tS\t14\t1\t15\t0.00000\n+Porphyromonas endodontalis\t28124\tS\t20\t0\t20\t0.00000\n+Butyricimonas faecalis\t2093856\tS\t12\t11\t23\t0.00000\n+Polaribacter sp. HaHaR_3_91\t2745561\tS\t13\t0\t13\t0.00000\n+Treponema sp. Marseille-Q4132\t2766701\tS\t15\t2\t17\t0.00000\n+Treponema socranskii\t53419\tS\t15\t2\t17\t0.00000\n+Fusobacterium necrophorum\t859\tS\t24\t1\t25\t0.00000\n+Fusobacterium nucleatum\t851\tS\t18\t0\t18\t0.00000\n+Homo sapiens\t9606\tS\t363\t0\t363\t0.00001\n+Malassezia restricta\t76775\tS\t20\t0\t20\t0.00000\n+Sporisorium graminicola\t280036\tS\t10\t0\t10\t0.00000\n'

diff -r 000000000000 -r fc2077c654fb test-data/beta_bracken_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_1.tabular Fri Jan 13 13:21:51 2023 +0000

[

diff -r 000000000000 -r fc2077c654fb test-data/beta_bracken_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_2.tabular Fri Jan 13 13:21:51 2023 +0000

[

diff -r 000000000000 -r fc2077c654fb test-data/beta_bracken_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_3.tabular Fri Jan 13 13:21:51 2023 +0000

diff -r 000000000000 -r fc2077c654fb test-data/beta_kreport_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_1.tabular Fri Jan 13 13:21:51 2023 +0000

[

b'@@ -0,0 +1,10872 @@\n+ 35.71\t21579435\t21579435\t0\t0\tU\t0\tunclassified\n+ 64.29\t38851676\t12709\t1716815669\t30696760\tR\t1\troot\n+ 63.47\t38357104\t5793\t1696370519\t30611457\tR1\t131567\t cellular organisms\n+ 63.45\t38340776\t116876\t1693847758\t30366505\tD\t2\t Bacteria\n+ 62.76\t37924629\t48321\t1661909574\t26602294\tD1\t1783272\t Terrabacteria group\n+ 54.87\t33161332\t339823\t1417494340\t21021701\tP\t1239\t Firmicutes\n+ 33.38\t20169653\t3097\t739431937\t8766358\tC\t186801\t Clostridia\n+ 33.36\t20161613\t390917\t739085534\t8763259\tO\t186802\t Eubacteriales\n+ 30.91\t18677957\t1058423\t678136764\t6580300\tF\t186803\t Lachnospiraceae\n+ 13.17\t7960031\t16689\t328537108\t1052768\tG\t2316020\t Mediterraneibacter\n+ 12.73\t7691179\t6985759\t323718354\t1021673\tS\t33038\t [Ruminococcus] gnavus\n+ 1.17\t705420\t705420\t10495661\t48450\tS1\t411470\t [Ruminococcus] gnavus ATCC 29149\n+ 0.42\t252163\t0\t3683211\t28334\tS\t33039\t [Ruminococcus] torques\n+ 0.42\t252163\t252163\t3683211\t28334\tS1\t657313\t [Ruminococcus] torques L2-14\n+ 6.00\t3628569\t2210\t158096202\t838982\tG\t207244\t Anaerostipes\n+ 5.96\t3603595\t3603595\t157501729\t793268\tS\t649756\t Anaerostipes hadrus\n+ 0.02\t11765\t10345\t159102\t46139\tS\t105841\t Anaerostipes caccae\n+ 0.00\t1420\t1420\t13258\t514\tS1\t411490\t Anaerostipes caccae L1-92\n+ 0.02\t10999\t10999\t88424\t1459\tS\t1229621\t Anaerostipes rhamnosivorans\n+ 4.45\t2686194\t369464\t34675406\t1385919\tG\t572511\t Blautia\n+ 1.22\t738429\t0\t5918814\t28639\tS\t40520\t Blautia obeum\n+ 1.22\t738429\t738429\t5918814\t28639\tS1\t657314\t Blautia obeum A2-162\n+ 0.79\t477408\t809\t5214384\t600488\tG1\t2648079\t unclassified Blautia\n+ 0.62\t374191\t374191\t3453032\t17495\tS\t2479767\t Blautia sp. SC05B48\n+ 0.17\t102408\t102408\t1758000\t582917\tS\t2877527\t Blautia sp. NBRC 113351\n+ 0.73\t439939\t439939\t7552466\t533280\tS\t1912897\t Blautia argi\n+ 0.47\t285036\t285036\t2690078\t32777\tS\t1737424\t Blautia massiliensis\n+ 0.32\t193377\t0\t2149095\t19212\tS\t1322\t Blautia hansenii\n+ 0.32\t193377\t193377\t2149095\t19212\tS1\t537007\t Blautia hansenii DSM 20583\n+ 0.18\t106549\t106347\t959419\t27692\tS\t33035\t Blautia producta\n+ 0.00\t202\t202\t229\t7\tS1\t1121114\t Blautia producta ATCC 27340 = DSM 2950\n+ 0.10\t58164\t58164\t357362\t8823\tS\t1796616\t Blautia pseudococcoides\n+ 0.03\t17828\t17828\t100818\t1748\tS\t2779518\t Blautia liquoris\n+ 1.41\t850899\t17874\t16332523\t358373\tG\t33042\t Coprococcus\n+ 0.90\t543570\t543570\t10585830\t333422\tS\t410072\t Coprococcus comes\n+ 0.34\t203082\t203082\t3396391\t15605\tS\t116085\t Coprococcus catus\n+ 0.10\t63068\t0\t1451138\t4878\tG1\t2684943\t unclassified Coprococcus\n+ 0.10\t63068\t63068\t1451138\t4878\tS\t751585\t Coprococcus sp. ART55/1\n+ 0.04\t23305\t0\t297253\t2106\tS\t33043\t Coprococcus eutactus\n+ 0.04\t23305\t23305\t297253\t2106\tS1\t411474\t Coprococcus eutactus ATCC 27759\n+ 1.39\t838713\t0\t21976135\t605283\tG\t2569097\t Anaerobutyricum\n+ 1.39\t838713\t838713\t21976135\t605283\tS\t39488\t Anaerobutyricum hallii\n+ 0.64\t384616\t3844\t6337853\t912137\tG\t1506553\t Lachnoclostridium\n+ 0.37\t222110\t222107\t4837880\t889010\tS\t29347\t [Clostridium] scindens\n+ 0.00\t3\t3\t8\t6\tS1\t411468\t [Clostridium] scindens ATCC 35704\n+ 0.13\t77562\t72948\t699257\t5573\tS\t89153\t [Clostridium] hylemonae\n+ 0.01\t4614\t4614\t27023\t352\tS1\t553973\t [Clostridium] hylemonae DSM 15053\n+ 0.06\t38261\t38261\t368303\t5901\tS\t1871021\t Lachnoclostridium phocaeense\n+ 0.06\t36261\t0\t310554\t6399\tG1\t2608895\t unclassified Lachnoclostridium\n+ 0.06\t36261\t362'..b"phage fHe-Yen9-04\n+ 0.00\t1\t0\t285\t47\tF\t2560065\t Herelleviridae\n+ 0.00\t1\t0\t42\t3\tG\t2843105\t Tybeckvirus\n+ 0.00\t1\t0\t41\t2\tS\t2845127\t Tybeckvirus tv521B\n+ 0.00\t1\t1\t41\t2\tS1\t2510942\t Lactobacillus phage 521B\n+ 0.00\t1\t0\t90\t24\tP\t2731361\t Peploviricota\n+ 0.00\t1\t0\t90\t24\tC\t2731363\t Herviviricetes\n+ 0.00\t1\t0\t90\t24\tO\t548681\t Herpesvirales\n+ 0.00\t1\t0\t40\t4\tF\t548682\t Alloherpesviridae\n+ 0.00\t1\t0\t34\t1\tG\t692605\t Batrachovirus\n+ 0.00\t1\t1\t34\t1\tS\t1987509\t Ranid herpesvirus 3\n+ 0.00\t34\t0\t2203\t71\tD1\t2559587\t Riboviria\n+ 0.00\t32\t0\t2137\t59\tK\t2732396\t Orthornavirae\n+ 0.00\t31\t0\t1336\t12\tP\t2732406\t Kitrinoviricota\n+ 0.00\t31\t0\t1308\t10\tC\t2732461\t Alsuviricetes\n+ 0.00\t31\t0\t1302\t6\tO\t2732544\t Martellivirales\n+ 0.00\t31\t0\t1297\t3\tF\t69973\t Closteroviridae\n+ 0.00\t31\t0\t757\t1\tG\t67753\t Crinivirus\n+ 0.00\t31\t31\t757\t1\tS\t31713\t Lettuce infectious yellows virus\n+ 0.00\t1\t0\t108\t20\tP\t2732408\t Pisuviricota\n+ 0.00\t1\t0\t77\t14\tC\t2732506\t Pisoniviricetes\n+ 0.00\t1\t0\t39\t6\tO\t76804\t Nidovirales\n+ 0.00\t1\t0\t37\t4\tO1\t2499399\t Cornidovirineae\n+ 0.00\t1\t0\t37\t4\tF\t11118\t Coronaviridae\n+ 0.00\t1\t0\t37\t4\tF1\t2501931\t Orthocoronavirinae\n+ 0.00\t1\t0\t33\t2\tG\t693996\t Alphacoronavirus\n+ 0.00\t1\t0\t32\t1\tG1\t2509509\t Rhinacovirus\n+ 0.00\t1\t1\t32\t1\tS\t693998\t Rhinolophus bat coronavirus HKU2\n+ 0.00\t2\t0\t46\t9\tD2\t2585030\t unclassified Riboviria\n+ 0.00\t2\t0\t45\t8\tD3\t1922348\t unclassified RNA viruses ShiM-2016\n+ 0.00\t2\t2\t37\t1\tS\t1922687\t Beihai sobemo-like virus 16\n+ 0.00\t25\t0\t3910\t124\tD1\t2732004\t Varidnaviria\n+ 0.00\t25\t0\t3910\t124\tK\t2732005\t Bamfordvirae\n+ 0.00\t25\t0\t3892\t116\tP\t2732007\t Nucleocytoviricota\n+ 0.00\t23\t0\t2996\t65\tC\t2732523\t Megaviricetes\n+ 0.00\t21\t0\t2288\t26\tO\t2732554\t Imitervirales\n+ 0.00\t21\t0\t2288\t26\tF\t549779\t Mimiviridae\n+ 0.00\t21\t0\t2086\t14\tG\t315393\t Mimivirus\n+ 0.00\t21\t0\t1850\t13\tG1\t2501774\t unclassified Mimivirus\n+ 0.00\t21\t21\t833\t7\tS\t1094892\t Megavirus chiliensis\n+ 0.00\t1\t0\t401\t24\tO\t2732524\t Algavirales\n+ 0.00\t1\t0\t401\t24\tF\t10501\t Phycodnaviridae\n+ 0.00\t1\t0\t61\t10\tF1\t455363\t unclassified Phycodnaviridae\n+ 0.00\t1\t1\t11\t3\tS\t455364\t Chrysochromulina ericina virus\n+ 0.00\t1\t0\t307\t15\tO\t2732555\t Pimascovirales\n+ 0.00\t1\t0\t187\t6\tF\t10486\t Iridoviridae\n+ 0.00\t1\t0\t135\t2\tF1\t2017757\t Betairidovirinae\n+ 0.00\t1\t1\t135\t2\tG\t10491\t Chloriridovirus\n+ 0.00\t2\t0\t896\t51\tC\t2732525\t Pokkesviricetes\n+ 0.00\t2\t0\t896\t51\tO\t2732527\t Chitovirales\n+ 0.00\t2\t0\t896\t51\tF\t10240\t Poxviridae\n+ 0.00\t1\t0\t656\t36\tF1\t10241\t Chordopoxvirinae\n+ 0.00\t1\t0\t7\t4\tG\t10282\t Yatapoxvirus\n+ 0.00\t1\t1\t4\t2\tS\t99000\t Tanapox virus\n+ 0.00\t1\t0\t240\t15\tF1\t10284\t Entomopoxvirinae\n+ 0.00\t1\t0\t218\t12\tG\t10286\t Betaentomopoxvirus\n+ 0.00\t1\t0\t39\t3\tS\t1993631\t Choristoneura rosaceana entomopoxvirus\n+ 0.00\t1\t1\t39\t3\tS1\t1293539\t Choristoneura rosaceana entomopoxvirus 'L'\n+ 0.00\t2\t0\t140\t96\tD1\t2731342\t Monodnaviria\n+ 0.00\t2\t0\t98\t84\tK\t2732091\t Sangervirae\n+ 0.00\t2\t0\t98\t84\tP\t2732412\t Phixviricota\n+ 0.00\t2\t0\t98\t84\tC\t2732413\t Malgrandaviricetes\n+ 0.00\t2\t0\t98\t84\tO\t2732414\t Petitvirales\n+ 0.00\t2\t0\t98\t84\tF\t10841\t Microviridae\n+ 0.00\t2\t0\t98\t84\tF1\t117574\t unclassified Microviridae\n+ 0.00\t2\t2\t97\t83\tS\t1655645\t Parabacteroides phage YZ-2015b\n+ 0.00\t22\t0\t922\t300\tR1\t2787854\t other entries\n+ 0.00\t22\t22\t922\t300\tR2\t28384\t other sequences\n"

diff -r 000000000000 -r fc2077c654fb test-data/beta_kreport_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_2.tabular Fri Jan 13 13:21:51 2023 +0000

[

b'@@ -0,0 +1,11579 @@\n+ 54.60\t19935306\t19935306\t0\t0\tU\t0\tunclassified\n+ 45.40\t16575444\t5298\t716473275\t41687701\tR\t1\troot\n+ 45.10\t16467797\t6201\t712027351\t41661424\tR1\t131567\t cellular organisms\n+ 45.04\t16442783\t110800\t710319459\t41133682\tD\t2\t Bacteria\n+ 31.32\t11436812\t41002\t440988605\t25679261\tD1\t1783272\t Terrabacteria group\n+ 27.13\t9906153\t184803\t357526919\t21207671\tP\t1239\t Firmicutes\n+ 22.14\t8082642\t3087\t264342317\t14671292\tC\t186801\t Clostridia\n+ 22.11\t8072139\t234413\t264115921\t14671292\tO\t186802\t Eubacteriales\n+ 18.06\t6592731\t516767\t210495649\t9328354\tF\t186803\t Lachnospiraceae\n+ 4.23\t1544417\t7142\t56067199\t1018405\tG\t2316020\t Mediterraneibacter\n+ 3.86\t1410218\t1280670\t53961039\t976293\tS\t33038\t [Ruminococcus] gnavus\n+ 0.35\t129548\t129548\t1939948\t42652\tS1\t411470\t [Ruminococcus] gnavus ATCC 29149\n+ 0.35\t127057\t0\t1865249\t38786\tS\t33039\t [Ruminococcus] torques\n+ 0.35\t127057\t127057\t1865249\t38786\tS1\t657313\t [Ruminococcus] torques L2-14\n+ 3.43\t1252438\t159800\t17518586\t1642232\tG\t572511\t Blautia\n+ 0.89\t323684\t0\t2573641\t33366\tS\t40520\t Blautia obeum\n+ 0.89\t323684\t323684\t2573641\t33366\tS1\t657314\t Blautia obeum A2-162\n+ 0.67\t243401\t407\t4127599\t1063434\tG1\t2648079\t unclassified Blautia\n+ 0.42\t151592\t151592\t1379677\t19727\tS\t2479767\t Blautia sp. SC05B48\n+ 0.25\t91402\t91402\t2746022\t1038938\tS\t2877527\t Blautia sp. NBRC 113351\n+ 0.44\t160622\t160622\t2777275\t246515\tS\t1912897\t Blautia argi\n+ 0.35\t127316\t127316\t1322904\t36914\tS\t1737424\t Blautia massiliensis\n+ 0.29\t105084\t104967\t1104473\t41368\tS\t33035\t Blautia producta\n+ 0.00\t117\t117\t135\t10\tS1\t1121114\t Blautia producta ATCC 27340 = DSM 2950\n+ 0.25\t92090\t0\t1017446\t20902\tS\t1322\t Blautia hansenii\n+ 0.25\t92090\t92090\t1017446\t20902\tS1\t537007\t Blautia hansenii DSM 20583\n+ 0.08\t30463\t30463\t189676\t14959\tS\t1796616\t Blautia pseudococcoides\n+ 0.03\t9978\t9978\t55640\t2631\tS\t2779518\t Blautia liquoris\n+ 2.65\t968022\t1264\t42285614\t870510\tG\t207244\t Anaerostipes\n+ 2.61\t951989\t951989\t41982652\t787059\tS\t649756\t Anaerostipes hadrus\n+ 0.02\t8136\t7193\t153385\t83319\tS\t105841\t Anaerostipes caccae\n+ 0.00\t943\t943\t12120\t3929\tS1\t411490\t Anaerostipes caccae L1-92\n+ 0.02\t6633\t6633\t51543\t2041\tS\t1229621\t Anaerostipes rhamnosivorans\n+ 1.67\t608192\t0\t18164831\t610405\tG\t2569097\t Anaerobutyricum\n+ 1.67\t608192\t608192\t18164831\t610405\tS\t39488\t Anaerobutyricum hallii\n+ 1.12\t410481\t13887\t7406627\t363701\tG\t33042\t Coprococcus\n+ 0.68\t247369\t247369\t4596443\t333953\tS\t410072\t Coprococcus comes\n+ 0.25\t92108\t92108\t1448485\t19556\tS\t116085\t Coprococcus catus\n+ 0.09\t33589\t0\t598944\t5593\tG1\t2684943\t unclassified Coprococcus\n+ 0.09\t33589\t33589\t598944\t5593\tS\t751585\t Coprococcus sp. ART55/1\n+ 0.06\t23528\t0\t217029\t2748\tS\t33043\t Coprococcus eutactus\n+ 0.06\t23528\t23528\t217029\t2748\tS1\t411474\t Coprococcus eutactus ATCC 27759\n+ 0.84\t307984\t1808\t8122491\t1320201\tG\t1506553\t Lachnoclostridium\n+ 0.52\t189889\t189869\t6929632\t1222612\tS\t29347\t [Clostridium] scindens\n+ 0.00\t20\t20\t43\t12\tS1\t411468\t [Clostridium] scindens ATCC 35704\n+ 0.14\t51473\t0\t585690\t74217\tG1\t2608895\t unclassified Lachnoclostridium\n+ 0.14\t51473\t51473\t585690\t74217\tS\t1834196\t Lachnoclostridium sp. YL32\n+ 0.11\t39856\t37460\t363069\t6764\tS\t89153\t [Clostridium] hylemonae\n+ 0.01\t2396\t2396\t14191\t504\tS1\t553973\t [Clostridium] hylemonae DSM 15053\n+ 0.06\t20372\t20372\t157322\t7790\tS\t1871021\t'..b'ichia phage ID52\n+ 0.00\t24\t0\t499\t32\tD1\t12429\t unclassified viruses\n+ 0.00\t24\t0\t488\t28\tD2\t2204151\t unclassified DNA viruses\n+ 0.00\t24\t0\t484\t26\tD3\t51368\t unclassified dsDNA viruses\n+ 0.00\t24\t0\t361\t5\tF\t2023203\t Pithoviridae\n+ 0.00\t24\t0\t357\t4\tG\t1805626\t Pithovirus\n+ 0.00\t24\t24\t357\t4\tS\t1450746\t Pithovirus sibericum\n+ 0.00\t20\t0\t1312\t58\tD1\t2559587\t Riboviria\n+ 0.00\t18\t0\t1272\t46\tK\t2732396\t Orthornavirae\n+ 0.00\t17\t0\t490\t11\tP\t2732406\t Kitrinoviricota\n+ 0.00\t17\t0\t490\t11\tC\t2732461\t Alsuviricetes\n+ 0.00\t17\t0\t486\t7\tO\t2732544\t Martellivirales\n+ 0.00\t17\t0\t481\t4\tF\t69973\t Closteroviridae\n+ 0.00\t17\t0\t297\t2\tG\t67753\t Crinivirus\n+ 0.00\t17\t17\t296\t1\tS\t31713\t Lettuce infectious yellows virus\n+ 0.00\t1\t0\t91\t15\tP\t2732408\t Pisuviricota\n+ 0.00\t1\t0\t60\t10\tC\t2732506\t Pisoniviricetes\n+ 0.00\t1\t0\t28\t9\tO\t76804\t Nidovirales\n+ 0.00\t1\t0\t25\t7\tO1\t2499399\t Cornidovirineae\n+ 0.00\t1\t0\t25\t7\tF\t11118\t Coronaviridae\n+ 0.00\t1\t0\t24\t6\tF1\t2501931\t Orthocoronavirinae\n+ 0.00\t1\t0\t22\t5\tG\t693996\t Alphacoronavirus\n+ 0.00\t1\t0\t15\t1\tG1\t2509509\t Rhinacovirus\n+ 0.00\t1\t1\t15\t1\tS\t693998\t Rhinolophus bat coronavirus HKU2\n+ 0.00\t2\t0\t32\t8\tD2\t2585030\t unclassified Riboviria\n+ 0.00\t2\t0\t32\t8\tD3\t1922348\t unclassified RNA viruses ShiM-2016\n+ 0.00\t2\t2\t2\t1\tS\t1922550\t Beihai picorna-like virus 121\n+ 0.00\t17\t0\t2173\t106\tD1\t2732004\t Varidnaviria\n+ 0.00\t17\t0\t2173\t106\tK\t2732005\t Bamfordvirae\n+ 0.00\t14\t0\t2161\t101\tP\t2732007\t Nucleocytoviricota\n+ 0.00\t10\t0\t1752\t72\tC\t2732523\t Megaviricetes\n+ 0.00\t9\t0\t831\t27\tO\t2732554\t Imitervirales\n+ 0.00\t9\t0\t831\t27\tF\t549779\t Mimiviridae\n+ 0.00\t9\t1\t733\t19\tG\t315393\t Mimivirus\n+ 0.00\t8\t0\t660\t13\tG1\t2501774\t unclassified Mimivirus\n+ 0.00\t8\t8\t276\t8\tS\t1094892\t Megavirus chiliensis\n+ 0.00\t1\t0\t397\t28\tO\t2732524\t Algavirales\n+ 0.00\t1\t0\t397\t28\tF\t10501\t Phycodnaviridae\n+ 0.00\t1\t0\t307\t13\tF1\t455363\t unclassified Phycodnaviridae\n+ 0.00\t1\t1\t229\t4\tS\t1474867\t Aureococcus anophagefferens virus\n+ 0.00\t4\t0\t409\t29\tC\t2732525\t Pokkesviricetes\n+ 0.00\t4\t0\t408\t28\tO\t2732527\t Chitovirales\n+ 0.00\t4\t0\t408\t28\tF\t10240\t Poxviridae\n+ 0.00\t4\t0\t362\t18\tF1\t10241\t Chordopoxvirinae\n+ 0.00\t2\t0\t27\t2\tG\t2005509\t Centapoxvirus\n+ 0.00\t2\t0\t26\t1\tS\t2734570\t Murmansk microtuspox virus\n+ 0.00\t2\t2\t26\t1\tS1\t2025359\t Murmansk poxvirus\n+ 0.00\t1\t0\t1\t1\tG\t2733301\t Vespertilionpoxvirus\n+ 0.00\t1\t1\t1\t1\tS\t1329402\t Eptesipox virus\n+ 0.00\t1\t0\t243\t2\tG\t10265\t Capripoxvirus\n+ 0.00\t1\t0\t242\t1\tS\t186805\t Goatpox virus\n+ 0.00\t1\t1\t242\t1\tS1\t376852\t Goatpox virus Pellor\n+ 0.00\t3\t0\t12\t5\tP\t2732008\t Preplasmiviricota\n+ 0.00\t3\t0\t9\t4\tC\t2732529\t Tectiliviricetes\n+ 0.00\t3\t0\t8\t3\tO\t2732559\t Rowavirales\n+ 0.00\t3\t0\t8\t3\tF\t10508\t Adenoviridae\n+ 0.00\t3\t0\t6\t1\tG\t10552\t Aviadenovirus\n+ 0.00\t3\t3\t6\t1\tS\t190064\t Fowl aviadenovirus D\n+ 0.00\t8\t0\t76\t5\tD1\t2840022\t Adnaviria\n+ 0.00\t8\t0\t76\t5\tK\t2840023\t Zilligvirae\n+ 0.00\t8\t0\t76\t5\tP\t2840024\t Taleaviricota\n+ 0.00\t8\t0\t76\t5\tC\t2841637\t Tokiviricetes\n+ 0.00\t8\t0\t76\t5\tO\t1511857\t Ligamenvirales\n+ 0.00\t8\t0\t76\t5\tF\t157897\t Rudiviridae\n+ 0.00\t8\t0\t75\t4\tG\t2843109\t Usarudivirus\n+ 0.00\t8\t0\t49\t1\tS\t2846588\t Usarudivirus SIRV10\n+ 0.00\t8\t8\t49\t1\tS1\t1983545\t Sulfolobus islandicus rod-shaped virus 10\n+ 0.00\t36\t0\t612\t85\tR1\t2787854\t other entries\n+ 0.00\t36\t36\t612\t85\tR2\t28384\t other sequences\n'

diff -r 000000000000 -r fc2077c654fb test-data/beta_kreport_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_3.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,3695 @@\n+ 0.39\t106031\t106031\t0\t0\tU\t0\tunclassified\n+ 99.61\t26893437\t64507\t1477437790\t4229124\tR\t1\troot\n+ 99.37\t26828910\t53\t1467438279\t4198954\tR1\t131567\t cellular organisms\n+ 99.37\t26828361\t441146\t1466288112\t4174203\tD\t2\t Bacteria\n+ 91.96\t24827889\t44318\t1283698682\t2079098\tD1\t1783272\t Terrabacteria group\n+ 91.79\t24782417\t164270\t1279926117\t2060362\tP\t1239\t Firmicutes\n+ 91.15\t24610130\t1009510\t1265588084\t1930928\tC\t91061\t Bacilli\n+ 87.24\t23554641\t134265\t1180431285\t1861547\tO\t186826\t Lactobacillales\n+ 86.31\t23304329\t22318\t1160119573\t1189906\tF\t81852\t Enterococcaceae\n+ 86.22\t23280142\t3851230\t1156884148\t1183146\tG\t1350\t Enterococcus\n+ 70.81\t19117311\t19022067\t552598355\t611676\tS\t1352\t Enterococcus faecium\n+ 0.20\t54986\t54986\t168674\t888\tS1\t1305849\t Enterococcus faecium Aus0085\n+ 0.07\t17755\t17755\t47482\t907\tS1\t333849\t Enterococcus faecium DO\n+ 0.05\t13797\t13797\t39152\t754\tS1\t565663\t Enterococcus faecium Com15\n+ 0.01\t3869\t3869\t13778\t835\tS1\t1158600\t Enterococcus faecium ATCC 8459 = NRRL B-2354\n+ 0.01\t3314\t3314\t5506\t773\tS1\t1328870\t Enterococcus faecium UC7251\n+ 0.01\t1523\t1523\t1642\t88\tS1\t1344042\t Enterococcus faecium T110\n+ 0.69\t185099\t185099\t3581240\t7489\tS\t33945\t Enterococcus avium\n+ 0.09\t23719\t23466\t99801\t5428\tS\t1351\t Enterococcus faecalis\n+ 0.00\t63\t63\t248\t77\tS1\t936153\t Enterococcus faecalis 62\n+ 0.00\t56\t56\t115\t35\tS1\t699186\t Enterococcus faecalis R712\n+ 0.00\t42\t42\t181\t90\tS1\t1201292\t Enterococcus faecalis ATCC 29212\n+ 0.00\t40\t40\t145\t27\tS1\t565651\t Enterococcus faecalis ARO1/DG\n+ 0.00\t24\t24\t80\t44\tS1\t1287066\t Enterococcus faecalis DENG1\n+ 0.00\t17\t17\t70\t28\tS1\t1206105\t Enterococcus faecalis D32\n+ 0.00\t6\t6\t11\t4\tS1\t226185\t Enterococcus faecalis V583\n+ 0.00\t5\t5\t9\t7\tS1\t1157365\t Enterococcus faecalis EnGen0107\n+ 0.08\t21563\t21563\t113346\t7852\tS\t53345\t Enterococcus durans\n+ 0.07\t18570\t18332\t152372\t8271\tS\t1354\t Enterococcus hirae\n+ 0.00\t238\t238\t2150\t8\tS1\t768486\t Enterococcus hirae ATCC 9790\n+ 0.05\t14452\t14452\t102519\t5331\tS\t357441\t Enterococcus lactis\n+ 0.05\t13586\t13304\t77960\t6050\tS\t53346\t Enterococcus mundtii\n+ 0.00\t282\t282\t3118\t777\tS1\t1300150\t Enterococcus mundtii QU 25\n+ 0.04\t11263\t11223\t45393\t2277\tS\t37734\t Enterococcus casseliflavus\n+ 0.00\t40\t40\t140\t79\tS1\t565655\t Enterococcus casseliflavus EC20\n+ 0.04\t9647\t0\t66305\t1898\tG1\t2608891\t unclassified Enterococcus\n+ 0.02\t5363\t5363\t16331\t176\tS\t2060307\t Enterococcus sp. FDAARGOS_375\n+ 0.01\t3725\t3725\t46685\t1150\tS\t2603296\t Enterococcus sp. DA9\n+ 0.00\t339\t339\t1190\t162\tS\t2420313\t Enterococcus sp. FDAARGOS_553\n+ 0.00\t162\t162\t1841\t326\tS\t2582830\t Enterococcus sp. M190262\n+ 0.00\t58\t58\t258\t84\tS\t2057791\t Enterococcus sp. CR-Ec1\n+ 0.02\t5457\t5457\t34051\t3053\tS\t417368\t Enterococcus thailandicus\n+ 0.01\t2805\t2805\t8614\t1208\tS\t44008\t Enterococcus cecorum\n+ 0.01\t2378\t2378\t19583\t1010\tS\t1805431\t Enterococcus saigonensis\n+ 0.00\t1300\t1300\t2092\t593\tS\t118060\t Enterococcus rotai\n+ 0.00\t1102\t1102\t10853\t899\tS\t71452\t Enterococcus raffinosus\n+ 0.00\t246\t246\t4180\t875\tS\t160453\t Enterococcus gilvus\n+ 0.00\t190\t190\t783\t326\tS\t1353\t Enterococcus gallinarum\n+ 0.00\t147\t147\t4830\t730\tS\t2005703\t Enterococcus wangshanyuanii\n+ 0.00\t72\t72\t190\t72\tS\t2839759\t Enterococcus innesii\n+ 0.00\t5\t5\t10\t4\tS\t246144\t Enterococcus italicus\n+ '..b'+ 0.00\t2\t0\t11\t9\tO\t38748\t Naviculales\n+ 0.00\t2\t0\t11\t9\tF\t38749\t Phaeodactylaceae\n+ 0.00\t2\t0\t11\t9\tG\t2849\t Phaeodactylum\n+ 0.00\t2\t0\t11\t9\tS\t2850\t Phaeodactylum tricornutum\n+ 0.00\t2\t2\t11\t9\tS1\t556484\t Phaeodactylum tricornutum CCAP 1055/1\n+ 0.00\t1\t0\t63\t43\tD1\t554915\t Amoebozoa\n+ 0.00\t1\t0\t63\t43\tP\t2605435\t Evosea\n+ 0.00\t1\t0\t63\t43\tC\t142796\t Eumycetozoa\n+ 0.00\t1\t0\t63\t43\tC1\t33083\t Dictyostelia\n+ 0.00\t1\t0\t63\t43\tO\t2058949\t Dictyosteliales\n+ 0.00\t1\t0\t63\t43\tF\t2058185\t Dictyosteliaceae\n+ 0.00\t1\t0\t63\t43\tG\t5782\t Dictyostelium\n+ 0.00\t1\t0\t63\t43\tS\t44689\t Dictyostelium discoideum\n+ 0.00\t1\t1\t63\t43\tS1\t352472\t Dictyostelium discoideum AX4\n+ 0.00\t1\t0\t1197\t43\tD1\t2611352\t Discoba\n+ 0.00\t1\t0\t1197\t43\tP\t33682\t Euglenozoa\n+ 0.00\t1\t0\t1197\t43\tC\t5653\t Kinetoplastea\n+ 0.00\t1\t0\t1197\t43\tC1\t2704647\t Metakinetoplastina\n+ 0.00\t1\t0\t1197\t43\tO\t2704949\t Trypanosomatida\n+ 0.00\t1\t0\t1197\t43\tF\t5654\t Trypanosomatidae\n+ 0.00\t1\t0\t1177\t30\tF1\t1286322\t Leishmaniinae\n+ 0.00\t1\t1\t1177\t30\tG\t5658\t Leishmania\n+ 0.00\t11\t0\t4589\t665\tD\t2157\t Archaea\n+ 0.00\t11\t0\t4325\t494\tP\t28890\t Euryarchaeota\n+ 0.00\t9\t0\t1463\t273\tP1\t2283794\t Methanomada group\n+ 0.00\t9\t0\t1407\t229\tC\t183925\t Methanobacteria\n+ 0.00\t9\t0\t1407\t229\tO\t2158\t Methanobacteriales\n+ 0.00\t9\t0\t1407\t229\tF\t2159\t Methanobacteriaceae\n+ 0.00\t9\t0\t1371\t202\tG\t2172\t Methanobrevibacter\n+ 0.00\t9\t7\t1344\t182\tS\t2173\t Methanobrevibacter smithii\n+ 0.00\t2\t2\t63\t61\tS1\t420247\t Methanobrevibacter smithii ATCC 35061\n+ 0.00\t2\t0\t236\t185\tP1\t2290931\t Stenosarchaea group\n+ 0.00\t2\t0\t123\t100\tC\t183963\t Halobacteria\n+ 0.00\t2\t0\t48\t39\tO\t2235\t Halobacteriales\n+ 0.00\t2\t0\t21\t20\tF\t1963268\t Haloarculaceae\n+ 0.00\t2\t0\t4\t3\tG\t146825\t Halorhabdus\n+ 0.00\t2\t0\t2\t1\tS\t146826\t Halorhabdus utahensis\n+ 0.00\t2\t2\t2\t1\tS1\t519442\t Halorhabdus utahensis DSM 12940\n+ 0.00\t12\t0\t3306\t594\tD\t10239\t Viruses\n+ 0.00\t12\t0\t1510\t524\tD1\t2731341\t Duplodnaviria\n+ 0.00\t12\t0\t1510\t524\tK\t2731360\t Heunggongvirae\n+ 0.00\t12\t0\t1495\t517\tP\t2731618\t Uroviricota\n+ 0.00\t12\t0\t1495\t517\tC\t2731619\t Caudoviricetes\n+ 0.00\t12\t0\t1495\t517\tO\t28883\t Caudovirales\n+ 0.00\t8\t0\t350\t254\tF\t10744\t Podoviridae\n+ 0.00\t8\t0\t345\t251\tF1\t196895\t unclassified Podoviridae\n+ 0.00\t8\t0\t345\t251\tF2\t1978007\t crAss-like viruses\n+ 0.00\t4\t0\t162\t147\tF3\t2315857\t environmental samples\n+ 0.00\t4\t4\t162\t147\tS\t1211417\t uncultured crAssphage\n+ 0.00\t3\t3\t45\t16\tS\t2831617\t CrAss-like virus sp.\n+ 0.00\t1\t1\t1\t1\tS\t2772070\t crAssphage cr110_1\n+ 0.00\t3\t0\t176\t152\tF\t10699\t Siphoviridae\n+ 0.00\t1\t0\t18\t16\tF1\t196894\t unclassified Siphoviridae\n+ 0.00\t1\t1\t5\t5\tS\t537874\t Streptococcus phage PH15\n+ 0.00\t1\t1\t58\t58\tG\t2843470\t Vedamuthuvirus\n+ 0.00\t1\t0\t64\t49\tG\t1623303\t Brussowvirus\n+ 0.00\t1\t0\t18\t9\tG1\t2267560\t unclassified Brussowvirus\n+ 0.00\t1\t1\t18\t9\tS\t1385385\t Streptococcus phage TP-778L\n+ 0.00\t1\t0\t59\t45\tF\t10662\t Myoviridae\n+ 0.00\t1\t0\t1\t1\tF1\t857479\t Peduovirinae\n+ 0.00\t1\t0\t1\t1\tG\t2732988\t Reginaelenavirus\n+ 0.00\t1\t0\t1\t1\tS\t2734071\t Reginaelenavirus rv3LV2017\n+ 0.00\t1\t1\t1\t1\tS1\t1960657\t Klebsiella phage 3LV2017\n+ 0.00\t8\t0\t98\t44\tR1\t2787854\t other entries\n+ 0.00\t8\t6\t98\t44\tR2\t28384\t other sequences\n+ 0.00\t2\t0\t17\t11\tR3\t36549\t plasmids\n+ 0.00\t2\t2\t10\t6\tS\t2524\t Plasmid pAM77\n'

diff -r 000000000000 -r fc2077c654fb test-data/beta_krona_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_1.tabular Fri Jan 13 13:21:51 2023 +0000

[

b'@@ -0,0 +1,8485 @@\n+21579435\tUnclassified\n+165218\tk__Bacteria\n+339823\tk__Bacteria\tp__Firmicutes\n+3097\tk__Bacteria\tp__Firmicutes\tc__Clostridia\n+390954\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\n+1058423\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\n+16689\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Mediterraneibacter\n+7691179\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Mediterraneibacter\ts__[Ruminococcus]_gnavus\n+252163\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Mediterraneibacter\ts__[Ruminococcus]_torques\n+2210\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerostipes\n+3603595\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerostipes\ts__Anaerostipes_hadrus\n+11765\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerostipes\ts__Anaerostipes_caccae\n+10999\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerostipes\ts__Anaerostipes_rhamnosivorans\n+370273\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\n+738429\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_obeum\n+374191\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_sp._SC05B48\n+102408\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_sp._NBRC_113351\n+439939\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_argi\n+285036\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_massiliensis\n+193377\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_hansenii\n+106549\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_producta\n+58164\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_pseudococcoides\n+17828\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Blautia\ts__Blautia_liquoris\n+17874\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Coprococcus\n+543570\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Coprococcus\ts__Coprococcus_comes\n+203082\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Coprococcus\ts__Coprococcus_catus\n+63068\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Coprococcus\ts__Coprococcus_sp._ART55/1\n+23305\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Coprococcus\ts__Coprococcus_eutactus\n+0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerobutyricum\n+838713\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Anaerobutyricum\ts__Anaerobutyricum_hallii\n+3844\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\n+222110\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\ts__[Clostridium]_scindens\n+77562\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\ts__[Clostridium]_hylemonae\n+38261\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\ts__Lachnoclostridium_phocaeense\n+36261\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\ts__Lachnoclostridium_sp._YL32\n+6578\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Lachnoclostridium\ts__Lachnoclostridium_phytofermentans\n+0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Eubacteriales\tf__Lachnospiraceae\tg__Dorea\n+329338\tk__Bacteria\tp__Firmicutes\tc__Clostridia'..b'k__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Myoviridae\tg__Eneladusvirus\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Myoviridae\tg__Eneladusvirus\ts__Eneladusvirus_Yen904\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Herelleviridae\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Herelleviridae\tg__Tybeckvirus\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Herelleviridae\tg__Tybeckvirus\ts__Tybeckvirus_tv521B\n+0\tk__Viruses\tp__Peploviricota\n+0\tk__Viruses\tp__Peploviricota\tc__Herviviricetes\n+0\tk__Viruses\tp__Peploviricota\tc__Herviviricetes\to__Herpesvirales\n+0\tk__Viruses\tp__Peploviricota\tc__Herviviricetes\to__Herpesvirales\tf__Alloherpesviridae\n+0\tk__Viruses\tp__Peploviricota\tc__Herviviricetes\to__Herpesvirales\tf__Alloherpesviridae\tg__Batrachovirus\n+1\tk__Viruses\tp__Peploviricota\tc__Herviviricetes\to__Herpesvirales\tf__Alloherpesviridae\tg__Batrachovirus\ts__Ranid_herpesvirus_3\n+0\tk__Viruses\tp__Kitrinoviricota\n+0\tk__Viruses\tp__Kitrinoviricota\tc__Alsuviricetes\n+0\tk__Viruses\tp__Kitrinoviricota\tc__Alsuviricetes\to__Martellivirales\n+0\tk__Viruses\tp__Kitrinoviricota\tc__Alsuviricetes\to__Martellivirales\tf__Closteroviridae\n+0\tk__Viruses\tp__Kitrinoviricota\tc__Alsuviricetes\to__Martellivirales\tf__Closteroviridae\tg__Crinivirus\n+31\tk__Viruses\tp__Kitrinoviricota\tc__Alsuviricetes\to__Martellivirales\tf__Closteroviridae\tg__Crinivirus\ts__Lettuce_infectious_yellows_virus\n+0\tk__Viruses\tp__Pisuviricota\n+0\tk__Viruses\tp__Pisuviricota\tc__Pisoniviricetes\n+0\tk__Viruses\tp__Pisuviricota\tc__Pisoniviricetes\to__Nidovirales\n+0\tk__Viruses\tp__Pisuviricota\tc__Pisoniviricetes\to__Nidovirales\tf__Coronaviridae\n+0\tk__Viruses\tp__Pisuviricota\tc__Pisoniviricetes\to__Nidovirales\tf__Coronaviridae\tg__Alphacoronavirus\n+1\tk__Viruses\tp__Pisuviricota\tc__Pisoniviricetes\to__Nidovirales\tf__Coronaviridae\tg__Alphacoronavirus\ts__Rhinolophus_bat_coronavirus_HKU2\n+2\tk__Viruses\ts__Beihai_sobemo-like_virus_16\n+0\tk__Viruses\tp__Nucleocytoviricota\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Imitervirales\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Imitervirales\tf__Mimiviridae\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Imitervirales\tf__Mimiviridae\tg__Mimivirus\n+21\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Imitervirales\tf__Mimiviridae\tg__Mimivirus\ts__Megavirus_chiliensis\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Algavirales\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Algavirales\tf__Phycodnaviridae\n+1\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Algavirales\tf__Phycodnaviridae\ts__Chrysochromulina_ericina_virus\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Pimascovirales\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Pimascovirales\tf__Iridoviridae\n+1\tk__Viruses\tp__Nucleocytoviricota\tc__Megaviricetes\to__Pimascovirales\tf__Iridoviridae\tg__Chloriridovirus\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\tf__Poxviridae\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\tf__Poxviridae\tg__Yatapoxvirus\n+1\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\tf__Poxviridae\tg__Yatapoxvirus\ts__Tanapox_virus\n+0\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\tf__Poxviridae\tg__Betaentomopoxvirus\n+1\tk__Viruses\tp__Nucleocytoviricota\tc__Pokkesviricetes\to__Chitovirales\tf__Poxviridae\tg__Betaentomopoxvirus\ts__Choristoneura_rosaceana_entomopoxvirus\n+0\tk__Viruses\tp__Phixviricota\n+0\tk__Viruses\tp__Phixviricota\tc__Malgrandaviricetes\n+0\tk__Viruses\tp__Phixviricota\tc__Malgrandaviricetes\to__Petitvirales\n+0\tk__Viruses\tp__Phixviricota\tc__Malgrandaviricetes\to__Petitvirales\tf__Microviridae\n+2\tk__Viruses\tp__Phixviricota\tc__Malgrandaviricetes\to__Petitvirales\tf__Microviridae\ts__Parabacteroides_phage_YZ-2015b\n'

diff -r 000000000000 -r fc2077c654fb test-data/beta_krona_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_2.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,2720 @@\n+106031\tUnclassified\n+485465\tk__Bacteria\n+164270\tk__Bacteria\tp__Firmicutes\n+1009510\tk__Bacteria\tp__Firmicutes\tc__Bacilli\n+134265\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\n+22318\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\n+3851230\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\n+19117311\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_faecium\n+185099\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_avium\n+23719\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_faecalis\n+21563\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_durans\n+18570\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_hirae\n+14452\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_lactis\n+13586\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_mundtii\n+11263\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_casseliflavus\n+5363\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_sp._FDAARGOS_375\n+3725\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_sp._DA9\n+339\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_sp._FDAARGOS_553\n+162\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_sp._M190262\n+58\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_sp._CR-Ec1\n+5457\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_thailandicus\n+2805\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_cecorum\n+2378\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_saigonensis\n+1300\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_rotai\n+1102\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_raffinosus\n+246\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_gilvus\n+190\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_gallinarum\n+147\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_wangshanyuanii\n+72\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_innesii\n+5\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Enterococcus\ts__Enterococcus_italicus\n+44\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\n+693\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_carniphilus\n+281\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_fluvialis\n+62\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_penaei\n+52\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_teuberi\n+33\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_lutrae\n+25\tk__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Enterococcaceae\tg__Vagococcus\ts__Vagococcus_xie'..b'ida\to__Eucoccidiorida\tf__Sarcocystidae\n+0\tk__Eukaryota\tp__Apicomplexa\tc__Conoidasida\to__Eucoccidiorida\tf__Sarcocystidae\tg__Toxoplasma\n+1\tk__Eukaryota\tp__Apicomplexa\tc__Conoidasida\to__Eucoccidiorida\tf__Sarcocystidae\tg__Toxoplasma\ts__Toxoplasma_gondii\n+0\tk__Eukaryota\tp__Apicomplexa\tc__Conoidasida\to__Eucoccidiorida\tf__Sarcocystidae\tg__Neospora\n+1\tk__Eukaryota\tp__Apicomplexa\tc__Conoidasida\to__Eucoccidiorida\tf__Sarcocystidae\tg__Neospora\ts__Neospora_caninum\n+0\tk__Eukaryota\tp__Bacillariophyta\n+0\tk__Eukaryota\tp__Bacillariophyta\tc__Bacillariophyceae\n+0\tk__Eukaryota\tp__Bacillariophyta\tc__Bacillariophyceae\to__Naviculales\n+0\tk__Eukaryota\tp__Bacillariophyta\tc__Bacillariophyceae\to__Naviculales\tf__Phaeodactylaceae\n+0\tk__Eukaryota\tp__Bacillariophyta\tc__Bacillariophyceae\to__Naviculales\tf__Phaeodactylaceae\tg__Phaeodactylum\n+2\tk__Eukaryota\tp__Bacillariophyta\tc__Bacillariophyceae\to__Naviculales\tf__Phaeodactylaceae\tg__Phaeodactylum\ts__Phaeodactylum_tricornutum\n+0\tk__Eukaryota\tp__Evosea\n+0\tk__Eukaryota\tp__Evosea\tc__Eumycetozoa\n+0\tk__Eukaryota\tp__Evosea\tc__Eumycetozoa\to__Dictyosteliales\n+0\tk__Eukaryota\tp__Evosea\tc__Eumycetozoa\to__Dictyosteliales\tf__Dictyosteliaceae\n+0\tk__Eukaryota\tp__Evosea\tc__Eumycetozoa\to__Dictyosteliales\tf__Dictyosteliaceae\tg__Dictyostelium\n+1\tk__Eukaryota\tp__Evosea\tc__Eumycetozoa\to__Dictyosteliales\tf__Dictyosteliaceae\tg__Dictyostelium\ts__Dictyostelium_discoideum\n+0\tk__Eukaryota\tp__Euglenozoa\n+0\tk__Eukaryota\tp__Euglenozoa\tc__Kinetoplastea\n+0\tk__Eukaryota\tp__Euglenozoa\tc__Kinetoplastea\to__Trypanosomatida\n+0\tk__Eukaryota\tp__Euglenozoa\tc__Kinetoplastea\to__Trypanosomatida\tf__Trypanosomatidae\n+1\tk__Eukaryota\tp__Euglenozoa\tc__Kinetoplastea\to__Trypanosomatida\tf__Trypanosomatidae\tg__Leishmania\n+0\tk__Archaea\n+0\tk__Archaea\tp__Euryarchaeota\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanobacteria\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanobacteria\to__Methanobacteriales\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanobacteria\to__Methanobacteriales\tf__Methanobacteriaceae\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanobacteria\to__Methanobacteriales\tf__Methanobacteriaceae\tg__Methanobrevibacter\n+9\tk__Archaea\tp__Euryarchaeota\tc__Methanobacteria\to__Methanobacteriales\tf__Methanobacteriaceae\tg__Methanobrevibacter\ts__Methanobrevibacter_smithii\n+0\tk__Archaea\tp__Euryarchaeota\tc__Halobacteria\n+0\tk__Archaea\tp__Euryarchaeota\tc__Halobacteria\to__Halobacteriales\n+0\tk__Archaea\tp__Euryarchaeota\tc__Halobacteria\to__Halobacteriales\tf__Haloarculaceae\n+0\tk__Archaea\tp__Euryarchaeota\tc__Halobacteria\to__Halobacteriales\tf__Haloarculaceae\tg__Halorhabdus\n+2\tk__Archaea\tp__Euryarchaeota\tc__Halobacteria\to__Halobacteriales\tf__Haloarculaceae\tg__Halorhabdus\ts__Halorhabdus_utahensis\n+0\tk__Viruses\n+0\tk__Viruses\tp__Uroviricota\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Podoviridae\n+4\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Podoviridae\ts__uncultured_crAssphage\n+3\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Podoviridae\ts__CrAss-like_virus_sp.\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Podoviridae\ts__crAssphage_cr110_1\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Siphoviridae\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Siphoviridae\ts__Streptococcus_phage_PH15\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Siphoviridae\tg__Vedamuthuvirus\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Siphoviridae\tg__Brussowvirus\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Siphoviridae\tg__Brussowvirus\ts__Streptococcus_phage_TP-778L\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Myoviridae\n+0\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Myoviridae\tg__Reginaelenavirus\n+1\tk__Viruses\tp__Uroviricota\tc__Caudoviricetes\to__Caudovirales\tf__Myoviridae\tg__Reginaelenavirus\ts__Reginaelenavirus_rv3LV2017\n'

diff -r 000000000000 -r fc2077c654fb test-data/bracken_abundance.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bracken_abundance.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,176 @@\n+name\ttaxonomy_id\ttaxonomy_lvl\tkraken_assigned_reads\tadded_reads\tnew_est_reads\tfraction_total_reads\n+Streptococcus sanguinis\t1305\tS\t21\t0\t21\t0.00000\n+Streptococcus suis\t1307\tS\t22\t1\t23\t0.00000\n+Streptococcus gordonii\t1302\tS\t10\t0\t10\t0.00000\n+Vibrio cholerae\t666\tS\t10\t4\t14\t0.00000\n+Bacillus methylotrophicus\t492670\tS\t23\t0\t23\t0.00000\n+Streptococcus thermophilus\t1308\tS\t34\t0\t34\t0.00000\n+Streptococcus mutans\t1309\tS\t10\t0\t10\t0.00000\n+Burkholderia xenovorans\t36873\tS\t34\t0\t34\t0.00000\n+Sinorhizobium medicae\t110321\tS\t54\t0\t54\t0.00000\n+Burkholderia phymatum\t148447\tS\t655478\t1228\t656706\t0.02503\n+Borrelia burgdorferi\t139\tS\t36\t0\t36\t0.00000\n+Nostoc punctiforme\t272131\tS\t590086\t562\t590648\t0.02251\n+Shewanella frigidimarina\t56812\tS\t23\t0\t23\t0.00000\n+Clostridium novyi\t1542\tS\t211808\t388\t212196\t0.00809\n+Mycobacterium tuberculosis\t1773\tS\t20647\t274350\t294997\t0.01124\n+Mycobacterium smegmatis\t1772\tS\t239\t0\t239\t0.00001\n+Rhodopseudomonas palustris\t1076\tS\t823190\t1106\t824296\t0.03141\n+Bacteroides thetaiotaomicron\t818\tS\t392179\t3490\t395669\t0.01508\n+Mycobacterium abscessus\t36809\tS\t78\t0\t78\t0.00000\n+Burkholderia multivorans\t87883\tS\t30\t5\t35\t0.00000\n+Citrobacter koseri\t545\tS\t576\t17\t593\t0.00002\n+Bordetella pertussis\t520\tS\t632\t732\t1364\t0.00005\n+Chlamydia trachomatis\t813\tS\t71933\t284\t72217\t0.00275\n+Pseudomonas aeruginosa\t287\tS\t42\t1\t43\t0.00000\n+Chlamydia pneumoniae\t83558\tS\t78615\t83\t78698\t0.00300\n+Haloquadratum walsbyi\t293091\tS\t223986\t31\t224017\t0.00854\n+Streptococcus pyogenes\t1314\tS\t252007\t4976\t256983\t0.00979\n+Streptococcus pneumoniae\t1313\tS\t177347\t1168\t178515\t0.00680\n+Pelodictyon luteolum\t1100\tS\t157283\t1662\t158945\t0.00606\n+Streptococcus agalactiae\t1311\tS\t159789\t4251\t164040\t0.00625\n+Pseudomonas protegens\t380021\tS\t18\t0\t18\t0.00000\n+Salmonella enterica\t28901\tS\t387186\t4916\t392102\t0.01494\n+Francisella tularensis\t263\tS\t120338\t554\t120892\t0.00461\n+Clostridium botulinum\t1491\tS\t281791\t594\t282385\t0.01076\n+Alkaliphilus metalliredigens\t208226\tS\t368065\t432\t368497\t0.01404\n+Shewanella denitrificans\t192073\tS\t17\t0\t17\t0.00000\n+Shewanella sp. MR-7\t60481\tS\t224465\t86579\t311044\t0.01185\n+Bacillus licheniformis\t1402\tS\t13\t0\t13\t0.00000\n+Burkholderia ambifaria\t152480\tS\t27\t3\t30\t0.00000\n+Alkalilimnicola ehrlichii\t351052\tS\t226337\t74\t226411\t0.00863\n+Corynebacterium jeikeium\t38289\tS\t20\t0\t20\t0.00000\n+Pediococcus pentosaceus\t1255\tS\t13\t0\t13\t0.00000\n+Bacillus anthracis\t1392\tS\t151306\t277437\t428743\t0.01634\n+Hyphomonas neptunium\t81032\tS\t262956\t33\t262989\t0.01002\n+Borrelia afzelii\t29518\tS\t37\t0\t37\t0.00000\n+Pseudomonas fluorescens\t294\tS\t21\t1\t22\t0.00000\n+Corynebacterium urealyticum\t43771\tS\t168078\t3426\t171504\t0.00654\n+Bacillus clausii\t79880\tS\t281618\t346\t281964\t0.01075\n+Campylobacter concisus\t199\tS\t157661\t329\t157990\t0.00602\n+Shewanella baltica\t62322\tS\t108\t1\t109\t0.00000\n+Pseudomonas stutzeri\t316\tS\t293151\t1980\t295131\t0.01125\n+Cytophaga hutchinsonii\t985\tS\t307508\t31\t307539\t0.01172\n+Cyanothece sp. ATCC 51142\t43989\tS\t372257\t54\t372311\t0.01419\n+Thermus thermophilus\t274\tS\t152701\t13\t152714\t0.00582\n+Bacillus cytotoxicus\t580165\tS\t643\t5\t648\t0.00002\n+Clostridium acetobutylicum\t1488\tS\t13\t0\t13\t0.00000\n+Burkholderia cenocepacia\t95486\tS\t29\t50\t79\t0.00000\n+Corynebacterium efficiens\t152794\tS\t233423\t670\t234093\t0.00892\n+Chromobacterium violaceum\t536\tS\t330985\t434\t331419\t0.01263\n+Ureaplasma parvum\t134821\tS\t47612\t5\t47617\t0.00181\n+Bacillus pumilus\t1408\tS\t20\t0\t20\t0.00000\n+Enterobacter sp. 638\t399742\tS\t290\t1\t291\t0.00001\n+Bordetella avium\t521\tS\t81\t0\t81\t0.00000\n+Bacillus cereus\t1396\tS\t1086754\t202070\t1288824\t0.04912\n+Ochrobactrum anthropi\t529\tS\t381841\t1054\t382895\t0.01459\n+Thermosipho melanesiensis\t46541\tS\t128132\t53\t128185\t0.00489\n+Mycobacterium marinum\t1781\tS\t281340\t152004\t433344\t0.01651\n+Nostoc sp. PCC 7120\t103690\tS\t247\t7\t254\t0.00001\n+Pseudomonas mendocina\t300\tS\t14\t1\t15\t0.00000\n+Lactococcus lactis\t1358\tS\t404921\t2772\t407693\t0.01554\n+Pseudomonas putida\t303\tS\t511201\t4777\t515978\t0.01966\n+Sinorhizobium meliloti\t382\tS\t420783\t3928\t424711\t0.01619\n+Clostridium beijerinckii\t1520\tS\t418932\t1011\t419943\t0.01600\n+Geobacillus thermodenitrificans\t33940\tS\t'..b' meningitidis\t487\tS\t143635\t11544\t155179\t0.00591\n+Herpetosiphon aurantiacus\t65\tS\t427279\t27\t427306\t0.01628\n+Leptospira borgpetersenii\t174\tS\t242592\t345\t242937\t0.00926\n+Leptospira interrogans\t173\tS\t13\t0\t13\t0.00000\n+Photobacterium profundum\t74109\tS\t12\t1\t13\t0.00000\n+Lysinibacillus sphaericus\t1421\tS\t47\t0\t47\t0.00000\n+Clostridium perfringens\t1502\tS\t17\t0\t17\t0.00000\n+Bacillus subtilis\t1423\tS\t265462\t2267\t267729\t0.01020\n+Lawsonia intracellularis\t29546\tS\t114759\t23\t114782\t0.00437\n+Lactobacillus casei\t1582\tS\t11\t0\t11\t0.00000\n+Bacillus thuringiensis\t1428\tS\t187882\t159705\t347587\t0.01325\n+Psychrobacter arcticus\t334543\tS\t78\t0\t78\t0.00000\n+Oceanobacillus iheyensis\t182710\tS\t15\t0\t15\t0.00000\n+Lactobacillus helveticus\t1587\tS\t12\t0\t12\t0.00000\n+Lactobacillus delbrueckii\t1584\tS\t153860\t3163\t157023\t0.00598\n+Histophilus somni\t731\tS\t136275\t317\t136592\t0.00521\n+Wigglesworthia glossinidia\t51229\tS\t66219\t57\t66276\t0.00253\n+Cronobacter sakazakii\t28141\tS\t270\t3\t273\t0.00001\n+Yersinia enterocolitica\t630\tS\t101\t0\t101\t0.00000\n+Bacillus halodurans\t86665\tS\t269485\t450\t269935\t0.01029\n+Yersinia pestis\t632\tS\t61383\t252873\t314256\t0.01198\n+Burkholderia vietnamiensis\t60552\tS\t26\t5\t31\t0.00000\n+Photorhabdus luminescens\t29488\tS\t51\t0\t51\t0.00000\n+Bacillus weihenstephanensis\t86662\tS\t1934\t51\t1985\t0.00008\n+Idiomarina loihiensis\t135577\tS\t187227\t435\t187662\t0.00715\n+Prochlorococcus marinus\t1219\tS\t307019\t266\t307285\t0.01171\n+Ignicoccus hospitalis\t160233\tS\t87443\t14\t87457\t0.00333\n+Burkholderia lata\t482957\tS\t16\t2\t18\t0.00000\n+Lactobacillus salivarius\t1624\tS\t139242\t326\t139568\t0.00532\n+Syntrophomonas wolfei\t863\tS\t193716\t30\t193746\t0.00738\n+Burkholderia thailandensis\t57975\tS\t1133\t49\t1182\t0.00005\n+Haemophilus influenzae\t727\tS\t117883\t629\t118512\t0.00452\n+Cupriavidus necator\t106590\tS\t29061\t136\t29197\t0.00111\n+Acinetobacter sp. ADP1\t62977\tS\t11\t0\t11\t0.00000\n+Ruminiclostridium thermocellum\t1515\tS\t260096\t100\t260196\t0.00992\n+Erwinia tasmaniensis\t338565\tS\t322076\t1182\t323258\t0.01232\n+Clostridium tetani\t1513\tS\t16\t0\t16\t0.00000\n+Psychrobacter cryohalolentis\t330922\tS\t413504\t4426\t417930\t0.01593\n+Borrelia bavariensis\t664662\tS\t78122\t1938\t80060\t0.00305\n+Shewanella loihica\t359303\tS\t10\t0\t10\t0.00000\n+Pasteurella multocida\t747\tS\t12\t0\t12\t0.00000\n+Treponema denticola\t158\tS\t183744\t23\t183767\t0.00700\n+Yersinia pseudotuberculosis\t633\tS\t709\t1324\t2033\t0.00008\n+Pseudomonas entomophila\t312306\tS\t52\t0\t52\t0.00000\n+Halorhodospira halophila\t1053\tS\t11\t0\t11\t0.00000\n+Lachnoclostridium phytofermentans\t66219\tS\t10\t0\t10\t0.00000\n+Buchnera aphidicola\t9\tS\t26192\t14\t26206\t0.00100\n+Escherichia coli\t562\tS\t717629\t732184\t1449813\t0.05525\n+Coxiella burnetii\t777\tS\t135506\t22\t135528\t0.00516\n+Geobacter sulfurreducens\t35554\tS\t244079\t217\t244296\t0.00931\n+Anabaena variabilis\t1172\tS\t433603\t12868\t446471\t0.01701\n+Synechococcus elongatus\t32046\tS\t466278\t215\t466493\t0.01778\n+Serratia proteamaculans\t28151\tS\t117\t0\t117\t0.00000\n+Burkholderia pseudomallei\t28450\tS\t224374\t228836\t453210\t0.01727\n+Neisseria gonorrhoeae\t485\tS\t135601\t16923\t152524\t0.00581\n+Thiobacillus denitrificans\t36861\tS\t226889\t122\t227011\t0.00865\n+Burkholderia mallei\t13373\tS\t193\t3075\t3268\t0.00012\n+Pectobacterium atrosepticum\t29471\tS\t96\t0\t96\t0.00000\n+Listeria welshimeri\t1643\tS\t176044\t4791\t180835\t0.00689\n+Mycobacterium gilvum\t1804\tS\t236\t8\t244\t0.00001\n+Mycobacterium sp. JLS\t164757\tS\t326114\t373821\t699935\t0.02667\n+Staphylococcus aureus\t1280\tS\t1192940\t19301\t1212241\t0.04620\n+Staphylococcus haemolyticus\t1283\tS\t33\t0\t33\t0.00000\n+Staphylococcus epidermidis\t1282\tS\t53\t2\t55\t0.00000\n+Psychromonas ingrahamii\t357794\tS\t287498\t273\t287771\t0.01097\n+Shewanella amazonensis\t60478\tS\t18\t0\t18\t0.00000\n+Mycobacterium vanbaalenii\t110539\tS\t244\t4\t248\t0.00001\n+Shewanella sediminis\t271097\tS\t12\t0\t12\t0.00000\n+Acinetobacter baumannii\t470\tS\t257301\t727\t258028\t0.00983\n+Mycobacterium leprae\t1769\tS\t31\t0\t31\t0.00000\n+Mycobacterium bovis\t1765\tS\t15035\t264359\t279394\t0.01065\n+Mycobacterium ulcerans\t1809\tS\t525\t376\t901\t0.00003\n+Vibrio campbellii\t680\tS\t11\t3\t14\t0.00000\n+Mycobacterium avium\t1764\tS\t310855\t356\t311211\t0.01186\n+Shewanella sp. ANA-3\t94122\tS\t405\t42\t447\t0.00002\n'

diff -r 000000000000 -r fc2077c654fb test-data/output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,213 @@\n+513\tUnclassified\n+7\tk__Eukaryota\n+0\tk__Eukaryota\tp__Chordata\n+0\tk__Eukaryota\tp__Chordata\tc__Mammalia\n+0\tk__Eukaryota\tp__Chordata\tc__Mammalia\to__Primates\n+0\tk__Eukaryota\tp__Chordata\tc__Mammalia\to__Primates\tf__Hominidae\n+0\tk__Eukaryota\tp__Chordata\tc__Mammalia\to__Primates\tf__Hominidae\tg__Homo\n+402\tk__Eukaryota\tp__Chordata\tc__Mammalia\to__Primates\tf__Hominidae\tg__Homo\ts__Homo_sapiens\n+0\tk__Eukaryota\tp__Ascomycota\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\n+1\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\n+3\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\n+11\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Saccharomyces\n+293\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Saccharomyces\ts__Saccharomyces_cerevisiae\n+15\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Saccharomyces\ts__Saccharomyces_paradoxus\n+10\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Saccharomyces\ts__Saccharomyces_eubayanus\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Kluyveromyces\n+1\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Saccharomycetaceae\tg__Kluyveromyces\ts__Kluyveromyces_marxianus\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Trichomonascaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Trichomonascaceae\tg__Sugiyamaella\n+1\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Trichomonascaceae\tg__Sugiyamaella\ts__Sugiyamaella_lignohabitans\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Debaryomycetaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Debaryomycetaceae\tg__Candida\n+1\tk__Eukaryota\tp__Ascomycota\tc__Saccharomycetes\to__Saccharomycetales\tf__Debaryomycetaceae\tg__Candida\ts__Candida_dubliniensis\n+1\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Sordariales\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Sordariales\tf__Sordariaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Sordariales\tf__Sordariaceae\tg__Neurospora\n+1\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Sordariales\tf__Sordariaceae\tg__Neurospora\ts__Neurospora_crassa\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Magnaporthales\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Magnaporthales\tf__Pyriculariaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Magnaporthales\tf__Pyriculariaceae\tg__Pyricularia\n+1\tk__Eukaryota\tp__Ascomycota\tc__Sordariomycetes\to__Magnaporthales\tf__Pyriculariaceae\tg__Pyricularia\ts__Pyricularia_pennisetigena\n+0\tk__Eukaryota\tp__Ascomycota\tc__Eurotiomycetes\n+0\tk__Eukaryota\tp__Ascomycota\tc__Eurotiomycetes\to__Eurotiales\n+0\tk__Eukaryota\tp__Ascomycota\tc__Eurotiomycetes\to__Eurotiales\tf__Aspergillaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Eurotiomycetes\to__Eurotiales\tf__Aspergillaceae\tg__Aspergillus\n+1\tk__Eukaryota\tp__Ascomycota\tc__Eurotiomycetes\to__Eurotiales\tf__Aspergillaceae\tg__Aspergillus\ts__Aspergillus_luchuensis\n+0\tk__Eukaryota\tp__Ascomycota\tc__Schizosaccharomycetes\n+0\tk__Eukaryota\tp__Ascomycota\tc__Schizosaccharomycetes\to__Schizosaccharomycetales\n+0\tk__Eukaryota\tp__Ascomycota\tc__Schizosaccharomycetes\to__Schizosaccharomycetales\tf__Schizosaccharomycetaceae\n+0\tk__Eukaryota\tp__Ascomycota\tc__Schizosaccharomycetes\to__Schizosaccharomycetales\tf__Schizosaccharomycetaceae\tg__Schizosaccharomyces\n+1\tk__Eukaryota\tp__Ascomycota\tc__Schizosaccharomycetes\to__Schizosaccharomycetales\tf__Schizosaccharomycetaceae\tg__Schizosaccharomyces\ts__Schizosaccharomyces_pombe\n+0\tk__Eukaryota\tp__Apicomplexa\n+0\tk__Eukaryota\tp__Apicomplexa\tc__Aconoidasida\n+0\tk__Eukaryota\tp__Apicomplexa\tc__Aconoidasida\to__Haemosporida\n+0\tk__Eukaryota\tp__Apicomplexa\tc__Aconoidasida\to__Haemospori'..b'obacter\ts__Campylobacter_hepaticus\n+0\tk__Bacteria\tp__Bacteroidetes\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Blattabacteriaceae\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Blattabacteriaceae\tg__Blattabacterium\n+1\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Blattabacteriaceae\tg__Blattabacterium\ts__Blattabacterium_cuenoti\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Flavobacteriaceae\n+1\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Flavobacteriaceae\tg__Olleya\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Weeksellaceae\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Weeksellaceae\tg__Chryseobacterium\n+1\tk__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Weeksellaceae\tg__Chryseobacterium\ts__Chryseobacterium_sp._DH-B6\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Bacteroidia\n+2\tk__Bacteria\tp__Bacteroidetes\tc__Bacteroidia\to__Bacteroidales\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Sphingobacteriaceae\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Sphingobacteriaceae\tg__Sphingobacterium\n+1\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Sphingobacteriaceae\tg__Sphingobacterium\ts__Sphingobacterium_multivorum\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Cytophagia\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Flammeovirgaceae\n+0\tk__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Flammeovirgaceae\tg__Flammeovirga\n+1\tk__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Flammeovirgaceae\tg__Flammeovirga\ts__Flammeovirga_kamogawensis\n+0\tk__Bacteria\tp__Fusobacteria\n+0\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\n+0\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\n+0\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\n+0\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\n+1\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\ts__Fusobacterium_nucleatum\n+1\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\ts__Fusobacterium_hwasookii\n+0\tk__Bacteria\tp__Spirochaetes\n+0\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\n+0\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\n+0\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\n+0\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\tg__Brachyspira\n+1\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\tg__Brachyspira\ts__Brachyspira_hyodysenteriae\n+0\tk__Archaea\n+0\tk__Archaea\tp__Euryarchaeota\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanomicrobia\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanomicrobia\to__Methanosarcinales\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\n+0\tk__Archaea\tp__Euryarchaeota\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\tg__Methanosarcina\n+1\tk__Archaea\tp__Euryarchaeota\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\tg__Methanosarcina\ts__Methanosarcina_barkeri\n+0\tk__Archaea\tp__Thaumarchaeota\n+0\tk__Archaea\tp__Thaumarchaeota\tc__Nitrososphaeria\n+0\tk__Archaea\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\n+0\tk__Archaea\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\tf__Nitrososphaeraceae\n+0\tk__Archaea\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\tf__Nitrososphaeraceae\tg__Candidatus_Nitrosocosmicus\n'

diff -r 000000000000 -r fc2077c654fb test-data/output_intermediate.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_intermediate.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,300 @@\n+513\tUnclassified\n+1\tx__root\n+27\tx__root\tx__cellular_organisms\n+3\tx__root\tx__cellular_organisms\tk__Eukaryota\n+3\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\tc__Mammalia\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\tc__Mammalia\tx__Theria\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\tc__Mammalia\tx__Theria\tx__Eutheria\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\tc__Mammalia\tx__Theria\tx__Eutheria\tx__Boreoeutheria\n+0\tx__root\tx__cellular_organisms\tk__Eukaryota\tx__Opisthokonta\tx__Metazoa\tx__Eumetazoa\tx__Bilateria\tx__Deuterostomia\tp__Chordata\tx__Craniata\tx__Vertebrata\tx__Gnathostomata\tx__Teleostomi\tx__Euteleostomi\tx__Sarcopterygii\tx__Dipnotetrapodomorpha\tx__Tetrapoda\tx__Amniota\tc__Mammalia\tx__Theria\tx__Eu'..b'_organisms\tk__Bacteria\tx__FCB_group\tx__Bacteroidetes/Chlorobi_group\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Flammeovirgaceae\tg__Flammeovirga\n+1\tx__root\tx__cellular_organisms\tk__Bacteria\tx__FCB_group\tx__Bacteroidetes/Chlorobi_group\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Flammeovirgaceae\tg__Flammeovirga\ts__Flammeovirga_kamogawensis\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\ts__Fusobacterium_nucleatum\n+1\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\ts__Fusobacterium_nucleatum\tx__Fusobacterium_nucleatum_subsp._polymorphum\n+1\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Fusobacteriaceae\tg__Fusobacterium\ts__Fusobacterium_hwasookii\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\n+0\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\tg__Brachyspira\n+1\tx__root\tx__cellular_organisms\tk__Bacteria\tp__Spirochaetes\tc__Spirochaetia\to__Brachyspirales\tf__Brachyspiraceae\tg__Brachyspira\ts__Brachyspira_hyodysenteriae\n+0\tx__root\tx__cellular_organisms\tk__Archaea\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\to__Methanosarcinales\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\tg__Methanosarcina\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\tg__Methanosarcina\ts__Methanosarcina_barkeri\n+1\tx__root\tx__cellular_organisms\tk__Archaea\tp__Euryarchaeota\tx__Stenosarchaea_group\tc__Methanomicrobia\to__Methanosarcinales\tf__Methanosarcinaceae\tg__Methanosarcina\ts__Methanosarcina_barkeri\tx__Methanosarcina_barkeri_3\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\tc__Nitrososphaeria\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\tf__Nitrososphaeraceae\n+0\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\tf__Nitrososphaeraceae\tg__Candidatus_Nitrosocosmicus\n+1\tx__root\tx__cellular_organisms\tk__Archaea\tx__TACK_group\tp__Thaumarchaeota\tc__Nitrososphaeria\to__Nitrososphaerales\tf__Nitrososphaeraceae\tg__Candidatus_Nitrosocosmicus\ts__Candidatus_Nitrosocosmicus_franklandus\n'

diff -r 000000000000 -r fc2077c654fb test-data/sample.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.tabular Fri Jan 13 13:21:51 2023 +0000

b'@@ -0,0 +1,300 @@\n+ 38.00\t513\t513\tU\t0\tunclassified\n+ 62.00\t837\t1\tR\t1\troot\n+ 61.93\t836\t27\tR1\t131567\t cellular organisms\n+ 56.00\t756\t3\tD\t2759\t Eukaryota\n+ 55.33\t747\t3\tD1\t33154\t Opisthokonta\n+ 29.78\t402\t0\tK\t33208\t Metazoa\n+ 29.78\t402\t0\tK1\t6072\t Eumetazoa\n+ 29.78\t402\t0\tK2\t33213\t Bilateria\n+ 29.78\t402\t0\tK3\t33511\t Deuterostomia\n+ 29.78\t402\t0\tP\t7711\t Chordata\n+ 29.78\t402\t0\tP1\t89593\t Craniata\n+ 29.78\t402\t0\tP2\t7742\t Vertebrata\n+ 29.78\t402\t0\tP3\t7776\t Gnathostomata\n+ 29.78\t402\t0\tP4\t117570\t Teleostomi\n+ 29.78\t402\t0\tP5\t117571\t Euteleostomi\n+ 29.78\t402\t0\tP6\t8287\t Sarcopterygii\n+ 29.78\t402\t0\tP7\t1338369\t Dipnotetrapodomorpha\n+ 29.78\t402\t0\tP8\t32523\t Tetrapoda\n+ 29.78\t402\t0\tP9\t32524\t Amniota\n+ 29.78\t402\t0\tC\t40674\t Mammalia\n+ 29.78\t402\t0\tC1\t32525\t Theria\n+ 29.78\t402\t0\tC2\t9347\t Eutheria\n+ 29.78\t402\t0\tC3\t1437010\t Boreoeutheria\n+ 29.78\t402\t0\tC4\t314146\t Euarchontoglires\n+ 29.78\t402\t0\tO\t9443\t Primates\n+ 29.78\t402\t0\tO1\t376913\t Haplorrhini\n+ 29.78\t402\t0\tO2\t314293\t Simiiformes\n+ 29.78\t402\t0\tO3\t9526\t Catarrhini\n+ 29.78\t402\t0\tO4\t314295\t Hominoidea\n+ 29.78\t402\t0\tF\t9604\t Hominidae\n+ 29.78\t402\t0\tF1\t207598\t Homininae\n+ 29.78\t402\t0\tG\t9605\t Homo\n+ 29.78\t402\t402\tS\t9606\t Homo sapiens\n+ 25.33\t342\t0\tK\t4751\t Fungi\n+ 25.33\t342\t1\tK1\t451864\t Dikarya\n+ 25.26\t341\t0\tP\t4890\t Ascomycota\n+ 25.19\t340\t0\tP1\t716545\t saccharomyceta\n+ 24.89\t336\t0\tP2\t147537\t Saccharomycotina\n+ 24.89\t336\t0\tC\t4891\t Saccharomycetes\n+ 24.89\t336\t1\tO\t4892\t Saccharomycetales\n+ 24.67\t333\t3\tF\t4893\t Saccharomycetaceae\n+ 24.37\t329\t11\tG\t4930\t Saccharomyces\n+ 21.70\t293\t0\tS\t4932\t Saccharomyces cerevisiae\n+ 21.70\t293\t293\tS1\t559292\t Saccharomyces cerevisiae S288C\n+ 1.11\t15\t15\tS\t27291\t Saccharomyces paradoxus\n+ 0.74\t10\t10\tS\t1080349\t Saccharomyces eubayanus\n+ 0.07\t1\t0\tG\t4910\t Kluyveromyces\n+ 0.07\t1\t0\tS\t4911\t Kluyveromyces marxianus\n+ 0.07\t1\t1\tS1\t1003335\t Kluyveromyces marxianus DMKU3-1042\n+ 0.07\t1\t0\tF\t410830\t Trichomonascaceae\n+ 0.07\t1\t0\tG\t410829\t Sugiyamaella\n+ 0.07\t1\t1\tS\t796027\t Sugiyamaella lignohabitans\n+ 0.07\t1\t0\tO1\t2916678\t CUG-Ser1 clade\n+ 0.07\t1\t0\tF\t766764\t Debaryomycetaceae\n+ 0.07\t1\t0\tF1\t1535325\t Candida/Lodderomyces clade\n+ 0.07\t1\t0\tG\t1535326\t Candida\n+ 0.07\t1\t0\tS\t42374\t Candida dubliniensis\n+ 0.07\t1\t1\tS1\t573826\t Candida dubliniensis CD36\n+ 0.30\t4\t0\tP2\t147538\t Pezizomycotina\n+ 0.30\t4\t0\tP3\t716546\t leotiomyceta\n+ 0.22\t3\t0\tP4\t715989\t sordariomyceta\n+ 0.22\t3\t0\tC\t147550\t Sordariomycetes\n+ 0.15\t2\t0\tC1\t222544\t Sordariomycetidae\n+ '..b'\t1\t0\tG1\t2639383\t unclassified Aggregatibacter\n+ 0.07\t1\t1\tS\t712150\t Aggregatibacter sp. oral taxon 513\n+ 0.15\t2\t0\tC\t28216\t Betaproteobacteria\n+ 0.07\t1\t0\tO\t80840\t Burkholderiales\n+ 0.07\t1\t0\tF\t119060\t Burkholderiaceae\n+ 0.07\t1\t0\tG\t106589\t Cupriavidus\n+ 0.07\t1\t1\tS\t68895\t Cupriavidus basilensis\n+ 0.07\t1\t0\tC1\t119066\t Betaproteobacteria incertae sedis\n+ 0.07\t1\t0\tG\t33055\t Candidatus Kinetoplastibacterium\n+ 0.07\t1\t1\tS\t33056\t Candidatus Kinetoplastibacterium crithidii\n+ 0.15\t2\t0\tP1\t68525\t delta/epsilon subdivisions\n+ 0.15\t2\t0\tC\t29547\t Epsilonproteobacteria\n+ 0.15\t2\t0\tO\t213849\t Campylobacterales\n+ 0.15\t2\t0\tF\t72294\t Campylobacteraceae\n+ 0.15\t2\t0\tG\t194\t Campylobacter\n+ 0.15\t2\t2\tS\t1813019\t Campylobacter hepaticus\n+ 0.52\t7\t0\tD1\t1783270\t FCB group\n+ 0.52\t7\t0\tD2\t68336\t Bacteroidetes/Chlorobi group\n+ 0.52\t7\t0\tP\t976\t Bacteroidetes\n+ 0.22\t3\t0\tC\t117743\t Flavobacteriia\n+ 0.22\t3\t0\tO\t200644\t Flavobacteriales\n+ 0.07\t1\t0\tF\t39782\t Blattabacteriaceae\n+ 0.07\t1\t0\tG\t34098\t Blattabacterium\n+ 0.07\t1\t1\tS\t1653831\t Blattabacterium cuenoti\n+ 0.07\t1\t0\tF\t49546\t Flavobacteriaceae\n+ 0.07\t1\t0\tG\t336276\t Olleya\n+ 0.07\t1\t1\tG1\t2615019\t unclassified Olleya\n+ 0.07\t1\t0\tF\t2762318\t Weeksellaceae\n+ 0.07\t1\t0\tF1\t2782232\t Chryseobacterium group\n+ 0.07\t1\t0\tG\t59732\t Chryseobacterium\n+ 0.07\t1\t0\tG1\t2593645\t unclassified Chryseobacterium\n+ 0.07\t1\t1\tS\t2759528\t Chryseobacterium sp. DH-B6\n+ 0.15\t2\t0\tC\t200643\t Bacteroidia\n+ 0.15\t2\t2\tO\t171549\t Bacteroidales\n+ 0.07\t1\t0\tC\t117747\t Sphingobacteriia\n+ 0.07\t1\t0\tO\t200666\t Sphingobacteriales\n+ 0.07\t1\t0\tF\t84566\t Sphingobacteriaceae\n+ 0.07\t1\t0\tG\t28453\t Sphingobacterium\n+ 0.07\t1\t1\tS\t28454\t Sphingobacterium multivorum\n+ 0.07\t1\t0\tC\t768503\t Cytophagia\n+ 0.07\t1\t0\tO\t768507\t Cytophagales\n+ 0.07\t1\t0\tF\t200667\t Flammeovirgaceae\n+ 0.07\t1\t0\tG\t59739\t Flammeovirga\n+ 0.07\t1\t1\tS\t373891\t Flammeovirga kamogawensis\n+ 0.15\t2\t0\tP\t32066\t Fusobacteria\n+ 0.15\t2\t0\tC\t203490\t Fusobacteriia\n+ 0.15\t2\t0\tO\t203491\t Fusobacteriales\n+ 0.15\t2\t0\tF\t203492\t Fusobacteriaceae\n+ 0.15\t2\t0\tG\t848\t Fusobacterium\n+ 0.07\t1\t0\tS\t851\t Fusobacterium nucleatum\n+ 0.07\t1\t1\tS1\t76857\t Fusobacterium nucleatum subsp. polymorphum\n+ 0.07\t1\t1\tS\t1583098\t Fusobacterium hwasookii\n+ 0.07\t1\t0\tP\t203691\t Spirochaetes\n+ 0.07\t1\t0\tC\t203692\t Spirochaetia\n+ 0.07\t1\t0\tO\t1643686\t Brachyspirales\n+ 0.07\t1\t0\tF\t143786\t Brachyspiraceae\n+ 0.07\t1\t0\tG\t29521\t Brachyspira\n+ 0.07\t1\t1\tS\t159\t Brachyspira hyodysenteriae\n+ 0.15\t2\t0\tD\t2157\t Archaea\n+ 0.07\t1\t0\tP\t28890\t Euryarchaeota\n+ 0.07\t1\t0\tP1\t2290931\t Stenosarchaea group\n+ 0.07\t1\t0\tC\t224756\t Methanomicrobia\n+ 0.07\t1\t0\tO\t94695\t Methanosarcinales\n+ 0.07\t1\t0\tF\t2206\t Methanosarcinaceae\n+ 0.07\t1\t0\tG\t2207\t Methanosarcina\n+ 0.07\t1\t0\tS\t2208\t Methanosarcina barkeri\n+ 0.07\t1\t1\tS1\t1434107\t Methanosarcina barkeri 3\n+ 0.07\t1\t0\tD1\t1783275\t TACK group\n+ 0.07\t1\t0\tP\t651137\t Thaumarchaeota\n+ 0.07\t1\t0\tC\t1643678\t Nitrososphaeria\n+ 0.07\t1\t0\tO\t1033996\t Nitrososphaerales\n+ 0.07\t1\t0\tF\t1033997\t Nitrososphaeraceae\n+ 0.07\t1\t0\tG\t1826864\t Candidatus Nitrosocosmicus\n+ 0.07\t1\t1\tS\t1798806\t Candidatus Nitrosocosmicus franklandus\n'