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Changeset 0:00d4ea6b6c71 (2023-03-06)

Next changeset 1:93203a7af11b (2023-03-15)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit afc6220b1e5f402f872338bbab440e4a1fe04ccd

added:
kreport2mpa.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/combined_kreport.tabular
test-data/mpa_output.tabular
test-data/mpa_output_intermediate.tabular
test-data/mpa_output_percentages.tabular
test-data/only_combined_count.tabular
test-data/output.tabular
test-data/output_intermediate.tabular
test-data/sample.tabular

diff -r 000000000000 -r 00d4ea6b6c71 kreport2mpa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kreport2mpa.xml Mon Mar 06 21:22:31 2023 +0000

[

@@ -0,0 +1,92 @@
+<tool id="krakentools_kreport2mpa" name="Krakentools: Convert kraken report file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>to MetaPhlAn-style</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+kreport2mpa.py
+    --report '$report'
+    --output '$output'
+    $intermediate_ranks
+    $percentages
+    ]]></command>
+    <inputs>
+        <param argument="--report" type="data" format="tabular" label="Kraken report file" />
+        <param argument="--intermediate-ranks" type="boolean" checked="false" truevalue="--intermediate-ranks" falsevalue="" label="Include intermediate ranks" help="Include non-standard levels. Default only outputs standard levels [D,P,C,O,F,G,S]." />
+        <param argument="--percentages" type="boolean" checked="false" truevalue="--percentages" falsevalue="" label="Use percentage of total reads for output." help="Outputs percentages of reads instead of total reads."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <output name="output" file="mpa_output.tabular"/>
+        </test>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <param name="intermediate_ranks" value="--intermediate-ranks"/>
+            <output name="output" file="mpa_output_intermediate.tabular"/>
+        </test>
+        <test>
+            <param name="report" value="sample.tabular"/>
+            <param name="percentages" value="--percentages"/>
+            <output name="output" file="mpa_output_percentages.tabular"/>
+        </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 takes a Kraken report file and prints out a MetaPhlAn-style TEXT file.
+
+Input
+------
+A Kraken report file
+
+Output
+------
+A MetaPhlAn-style TEXT file
+
+**Example output:**
+
+``--no-intermediate-ranks``
+
+::
+
+    k__Eukaryota 756
+    k__Eukaryota|k__Metazoa 402
+    k__Eukaryota|k__Metazoa|p__Chordata 402
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia 402
+
+
+``--intermediate-ranks``
+
+::
+
+    x__cellular_organisms 836
+    x__cellular_organisms|k__Eukaryota 756
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta 747
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa 402
+    x__cellular_organisms|k__Eukaryota|x__Opisthokonta|k__Metazoa|x__Eumetazoa 402
+
+``--percentages``
+
+::
+
+    k__Eukaryota 56.0
+    k__Eukaryota|k__Metazoa 29.78
+    k__Eukaryota|k__Metazoa|p__Chordata 29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia 29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates 29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae 29.78
+    k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo 29.78
+
+    ]]></help>
+    <expand macro="citations"/>
+    <creator>
+        <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
+    </creator>
+</tool>

diff -r 000000000000 -r 00d4ea6b6c71 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/beta_bracken_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_1.tabular Mon Mar 06 21:22:31 2023 +0000

[

diff -r 000000000000 -r 00d4ea6b6c71 test-data/beta_bracken_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_2.tabular Mon Mar 06 21:22:31 2023 +0000

[

diff -r 000000000000 -r 00d4ea6b6c71 test-data/beta_bracken_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_3.tabular Mon Mar 06 21:22:31 2023 +0000

diff -r 000000000000 -r 00d4ea6b6c71 test-data/beta_kreport_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_1.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/beta_kreport_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_2.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/beta_kreport_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_3.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/beta_krona_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_1.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/beta_krona_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_2.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/bracken_abundance.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bracken_abundance.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/combined_kreport.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combined_kreport.tabular Mon Mar 06 21:22:31 2023 +0000

b'@@ -0,0 +1,11351 @@\n+24.8031\t21685466\t21685466\t21579435\t21579435\t106031\t106031\tU\t0\tunclassified\n+75.1969\t65745113\t77216\t38851676\t12709\t26893437\t64507\tR\t1\troot\n+74.5575\t65186014\t5846\t38357104\t5793\t26828910\t53\tR1\t131567\t cellular organisms\n+74.5382\t65169137\t558022\t38340776\t116876\t26828361\t441146\tD\t2\t Bacteria\n+71.7741\t62752518\t92639\t37924629\t48321\t24827889\t44318\tD1\t1783272\t Terrabacteria group\n+66.2740\t57943749\t504093\t33161332\t339823\t24782417\t164270\tP\t1239\t Firmicutes\n+38.5054\t33665471\t1015370\t9055341\t5860\t24610130\t1009510\tC\t91061\t Bacilli\n+37.1469\t32477789\t145939\t8923148\t11674\t23554641\t134265\tO\t186826\t Lactobacillales\n+26.7162\t23358109\t22391\t53780\t73\t23304329\t22318\tF\t81852\t Enterococcaceae\n+26.6869\t23332499\t3854263\t52357\t3033\t23280142\t3851230\tG\t1350\t Enterococcus\n+21.9036\t19150441\t19054995\t33130\t32928\t19117311\t19022067\tS\t1352\t Enterococcus faecium\n+0.0631\t55161\t55161\t175\t175\t54986\t54986\tS1\t1305849\t Enterococcus faecium Aus0085\n+0.0203\t17782\t17782\t27\t27\t17755\t17755\tS1\t333849\t Enterococcus faecium DO\n+0.0158\t13797\t13797\t0\t0\t13797\t13797\tS1\t565663\t Enterococcus faecium Com15\n+0.0044\t3869\t3869\t0\t0\t3869\t3869\tS1\t1158600\t Enterococcus faecium ATCC 8459 = NRRL B-2354\n+0.0038\t3314\t3314\t0\t0\t3314\t3314\tS1\t1328870\t Enterococcus faecium UC7251\n+0.0017\t1523\t1523\t0\t0\t1523\t1523\tS1\t1344042\t Enterococcus faecium T110\n+0.2121\t185426\t185426\t327\t327\t185099\t185099\tS\t33945\t Enterococcus avium\n+0.0402\t35146\t34886\t11427\t11420\t23719\t23466\tS\t1351\t Enterococcus faecalis\n+0.0001\t64\t64\t1\t1\t63\t63\tS1\t936153\t Enterococcus faecalis 62\n+0.0001\t57\t57\t1\t1\t56\t56\tS1\t699186\t Enterococcus faecalis R712\n+0.0000\t42\t42\t0\t0\t42\t42\tS1\t1201292\t Enterococcus faecalis ATCC 29212\n+0.0000\t42\t42\t2\t2\t40\t40\tS1\t565651\t Enterococcus faecalis ARO1/DG\n+0.0000\t24\t24\t0\t0\t24\t24\tS1\t1287066\t Enterococcus faecalis DENG1\n+0.0000\t20\t20\t3\t3\t17\t17\tS1\t1206105\t Enterococcus faecalis D32\n+0.0000\t6\t6\t0\t0\t6\t6\tS1\t226185\t Enterococcus faecalis V583\n+0.0000\t5\t5\t0\t0\t5\t5\tS1\t1157365\t Enterococcus faecalis EnGen0107\n+0.0251\t21913\t21913\t350\t350\t21563\t21563\tS\t53345\t Enterococcus durans\n+0.0215\t18784\t18546\t214\t214\t18570\t18332\tS\t1354\t Enterococcus hirae\n+0.0003\t238\t238\t0\t0\t238\t238\tS1\t768486\t Enterococcus hirae ATCC 9790\n+0.0166\t14552\t14552\t100\t100\t14452\t14452\tS\t357441\t Enterococcus lactis\n+0.0160\t14027\t13743\t441\t439\t13586\t13304\tS\t53346\t Enterococcus mundtii\n+0.0003\t284\t284\t2\t2\t282\t282\tS1\t1300150\t Enterococcus mundtii QU 25\n+0.0130\t11387\t11342\t124\t119\t11263\t11223\tS\t37734\t Enterococcus casseliflavus\n+0.0001\t45\t45\t5\t5\t40\t40\tS1\t565655\t Enterococcus casseliflavus EC20\n+0.0115\t10044\t9\t397\t9\t9647\t0\tG1\t2608891\t unclassified Enterococcus\n+0.0062\t5439\t5439\t76\t76\t5363\t5363\tS\t2060307\t Enterococcus sp. FDAARGOS_375\n+0.0043\t3725\t3725\t0\t0\t3725\t3725\tS\t2603296\t Enterococcus sp. DA9\n+0.0005\t435\t435\t96\t96\t339\t339\tS\t2420313\t Enterococcus sp. FDAARGOS_553\n+0.0004\t366\t366\t204\t204\t162\t162\tS\t2582830\t Enterococcus sp. M190262\n+0.0001\t70\t70\t12\t12\t58\t58\tS\t2057791\t Enterococcus sp. CR-Ec1\n+0.0063\t5491\t5491\t34\t34\t5457\t5457\tS\t417368\t Enterococcus thailandicus\n+0.0056\t4928\t4928\t2123\t2123\t2805\t2805\tS\t44008\t Enterococcus cecorum\n+0.0027\t2394\t2394\t16\t16\t2378\t2378\tS\t1805431\t Enterococcus saigonensis\n+0.0015\t1355\t1355\t55\t55\t1300\t1300\tS\t118060\t Enterococcus rotai\n+0.0014\t1241\t1241\t139\t139\t1102\t1102\tS\t71452\t Enterococcus raffinosus\n+0.0005\t455'..b"10942\t Lactobacillus phage 521B\n+0.0000\t1\t0\t1\t0\t0\t0\tP\t2731361\t Peploviricota\n+0.0000\t1\t0\t1\t0\t0\t0\tC\t2731363\t Herviviricetes\n+0.0000\t1\t0\t1\t0\t0\t0\tO\t548681\t Herpesvirales\n+0.0000\t1\t0\t1\t0\t0\t0\tF\t548682\t Alloherpesviridae\n+0.0000\t1\t0\t1\t0\t0\t0\tG\t692605\t Batrachovirus\n+0.0000\t1\t1\t1\t1\t0\t0\tS\t1987509\t Ranid herpesvirus 3\n+0.0000\t34\t0\t34\t0\t0\t0\tD1\t2559587\t Riboviria\n+0.0000\t32\t0\t32\t0\t0\t0\tK\t2732396\t Orthornavirae\n+0.0000\t31\t0\t31\t0\t0\t0\tP\t2732406\t Kitrinoviricota\n+0.0000\t31\t0\t31\t0\t0\t0\tC\t2732461\t Alsuviricetes\n+0.0000\t31\t0\t31\t0\t0\t0\tO\t2732544\t Martellivirales\n+0.0000\t31\t0\t31\t0\t0\t0\tF\t69973\t Closteroviridae\n+0.0000\t31\t0\t31\t0\t0\t0\tG\t67753\t Crinivirus\n+0.0000\t31\t31\t31\t31\t0\t0\tS\t31713\t Lettuce infectious yellows virus\n+0.0000\t1\t0\t1\t0\t0\t0\tP\t2732408\t Pisuviricota\n+0.0000\t1\t0\t1\t0\t0\t0\tC\t2732506\t Pisoniviricetes\n+0.0000\t1\t0\t1\t0\t0\t0\tO\t76804\t Nidovirales\n+0.0000\t1\t0\t1\t0\t0\t0\tO1\t2499399\t Cornidovirineae\n+0.0000\t1\t0\t1\t0\t0\t0\tF\t11118\t Coronaviridae\n+0.0000\t1\t0\t1\t0\t0\t0\tF1\t2501931\t Orthocoronavirinae\n+0.0000\t1\t0\t1\t0\t0\t0\tG\t693996\t Alphacoronavirus\n+0.0000\t1\t0\t1\t0\t0\t0\tG1\t2509509\t Rhinacovirus\n+0.0000\t1\t1\t1\t1\t0\t0\tS\t693998\t Rhinolophus bat coronavirus HKU2\n+0.0000\t2\t0\t2\t0\t0\t0\tD2\t2585030\t unclassified Riboviria\n+0.0000\t2\t0\t2\t0\t0\t0\tD3\t1922348\t unclassified RNA viruses ShiM-2016\n+0.0000\t2\t2\t2\t2\t0\t0\tS\t1922687\t Beihai sobemo-like virus 16\n+0.0000\t25\t0\t25\t0\t0\t0\tD1\t2732004\t Varidnaviria\n+0.0000\t25\t0\t25\t0\t0\t0\tK\t2732005\t Bamfordvirae\n+0.0000\t25\t0\t25\t0\t0\t0\tP\t2732007\t Nucleocytoviricota\n+0.0000\t23\t0\t23\t0\t0\t0\tC\t2732523\t Megaviricetes\n+0.0000\t21\t0\t21\t0\t0\t0\tO\t2732554\t Imitervirales\n+0.0000\t21\t0\t21\t0\t0\t0\tF\t549779\t Mimiviridae\n+0.0000\t21\t0\t21\t0\t0\t0\tG\t315393\t Mimivirus\n+0.0000\t21\t0\t21\t0\t0\t0\tG1\t2501774\t unclassified Mimivirus\n+0.0000\t21\t21\t21\t21\t0\t0\tS\t1094892\t Megavirus chiliensis\n+0.0000\t1\t0\t1\t0\t0\t0\tO\t2732555\t Pimascovirales\n+0.0000\t1\t0\t1\t0\t0\t0\tF\t10486\t Iridoviridae\n+0.0000\t1\t0\t1\t0\t0\t0\tF1\t2017757\t Betairidovirinae\n+0.0000\t1\t1\t1\t1\t0\t0\tG\t10491\t Chloriridovirus\n+0.0000\t1\t0\t1\t0\t0\t0\tO\t2732524\t Algavirales\n+0.0000\t1\t0\t1\t0\t0\t0\tF\t10501\t Phycodnaviridae\n+0.0000\t1\t0\t1\t0\t0\t0\tF1\t455363\t unclassified Phycodnaviridae\n+0.0000\t1\t1\t1\t1\t0\t0\tS\t455364\t Chrysochromulina ericina virus\n+0.0000\t2\t0\t2\t0\t0\t0\tC\t2732525\t Pokkesviricetes\n+0.0000\t2\t0\t2\t0\t0\t0\tO\t2732527\t Chitovirales\n+0.0000\t2\t0\t2\t0\t0\t0\tF\t10240\t Poxviridae\n+0.0000\t1\t0\t1\t0\t0\t0\tF1\t10284\t Entomopoxvirinae\n+0.0000\t1\t0\t1\t0\t0\t0\tG\t10286\t Betaentomopoxvirus\n+0.0000\t1\t0\t1\t0\t0\t0\tS\t1993631\t Choristoneura rosaceana entomopoxvirus\n+0.0000\t1\t1\t1\t1\t0\t0\tS1\t1293539\t Choristoneura rosaceana entomopoxvirus 'L'\n+0.0000\t1\t0\t1\t0\t0\t0\tF1\t10241\t Chordopoxvirinae\n+0.0000\t1\t0\t1\t0\t0\t0\tG\t10282\t Yatapoxvirus\n+0.0000\t1\t1\t1\t1\t0\t0\tS\t99000\t Tanapox virus\n+0.0000\t2\t0\t2\t0\t0\t0\tD1\t2731342\t Monodnaviria\n+0.0000\t2\t0\t2\t0\t0\t0\tK\t2732091\t Sangervirae\n+0.0000\t2\t0\t2\t0\t0\t0\tP\t2732412\t Phixviricota\n+0.0000\t2\t0\t2\t0\t0\t0\tC\t2732413\t Malgrandaviricetes\n+0.0000\t2\t0\t2\t0\t0\t0\tO\t2732414\t Petitvirales\n+0.0000\t2\t0\t2\t0\t0\t0\tF\t10841\t Microviridae\n+0.0000\t2\t0\t2\t0\t0\t0\tF1\t117574\t unclassified Microviridae\n+0.0000\t2\t2\t2\t2\t0\t0\tS\t1655645\t Parabacteroides phage YZ-2015b\n+0.0000\t30\t0\t22\t0\t8\t0\tR1\t2787854\t other entries\n+0.0000\t30\t28\t22\t22\t8\t6\tR2\t28384\t other sequences\n+0.0000\t2\t0\t0\t0\t2\t0\tR3\t36549\t plasmids\n+0.0000\t2\t2\t0\t0\t2\t2\tS\t2524\t Plasmid pAM77\n"

diff -r 000000000000 -r 00d4ea6b6c71 test-data/mpa_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output.tabular Mon Mar 06 21:22:31 2023 +0000

diff -r 000000000000 -r 00d4ea6b6c71 test-data/mpa_output_intermediate.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_intermediate.tabular Mon Mar 06 21:22:31 2023 +0000

diff -r 000000000000 -r 00d4ea6b6c71 test-data/mpa_output_percentages.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_percentages.tabular Mon Mar 06 21:22:31 2023 +0000

diff -r 000000000000 -r 00d4ea6b6c71 test-data/only_combined_count.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_combined_count.tabular Mon Mar 06 21:22:31 2023 +0000

b'@@ -0,0 +1,11351 @@\n+24.8031\t21685466\t21685466\tU\t0\tunclassified\n+75.1969\t65745113\t77216\tR\t1\troot\n+74.5575\t65186014\t5846\tR1\t131567\t cellular organisms\n+74.5382\t65169137\t558022\tD\t2\t Bacteria\n+71.7741\t62752518\t92639\tD1\t1783272\t Terrabacteria group\n+66.2740\t57943749\t504093\tP\t1239\t Firmicutes\n+38.5054\t33665471\t1015370\tC\t91061\t Bacilli\n+37.1469\t32477789\t145939\tO\t186826\t Lactobacillales\n+26.7162\t23358109\t22391\tF\t81852\t Enterococcaceae\n+26.6869\t23332499\t3854263\tG\t1350\t Enterococcus\n+21.9036\t19150441\t19054995\tS\t1352\t Enterococcus faecium\n+0.0631\t55161\t55161\tS1\t1305849\t Enterococcus faecium Aus0085\n+0.0203\t17782\t17782\tS1\t333849\t Enterococcus faecium DO\n+0.0158\t13797\t13797\tS1\t565663\t Enterococcus faecium Com15\n+0.0044\t3869\t3869\tS1\t1158600\t Enterococcus faecium ATCC 8459 = NRRL B-2354\n+0.0038\t3314\t3314\tS1\t1328870\t Enterococcus faecium UC7251\n+0.0017\t1523\t1523\tS1\t1344042\t Enterococcus faecium T110\n+0.2121\t185426\t185426\tS\t33945\t Enterococcus avium\n+0.0402\t35146\t34886\tS\t1351\t Enterococcus faecalis\n+0.0001\t64\t64\tS1\t936153\t Enterococcus faecalis 62\n+0.0001\t57\t57\tS1\t699186\t Enterococcus faecalis R712\n+0.0000\t42\t42\tS1\t1201292\t Enterococcus faecalis ATCC 29212\n+0.0000\t42\t42\tS1\t565651\t Enterococcus faecalis ARO1/DG\n+0.0000\t24\t24\tS1\t1287066\t Enterococcus faecalis DENG1\n+0.0000\t20\t20\tS1\t1206105\t Enterococcus faecalis D32\n+0.0000\t6\t6\tS1\t226185\t Enterococcus faecalis V583\n+0.0000\t5\t5\tS1\t1157365\t Enterococcus faecalis EnGen0107\n+0.0251\t21913\t21913\tS\t53345\t Enterococcus durans\n+0.0215\t18784\t18546\tS\t1354\t Enterococcus hirae\n+0.0003\t238\t238\tS1\t768486\t Enterococcus hirae ATCC 9790\n+0.0166\t14552\t14552\tS\t357441\t Enterococcus lactis\n+0.0160\t14027\t13743\tS\t53346\t Enterococcus mundtii\n+0.0003\t284\t284\tS1\t1300150\t Enterococcus mundtii QU 25\n+0.0130\t11387\t11342\tS\t37734\t Enterococcus casseliflavus\n+0.0001\t45\t45\tS1\t565655\t Enterococcus casseliflavus EC20\n+0.0115\t10044\t9\tG1\t2608891\t unclassified Enterococcus\n+0.0062\t5439\t5439\tS\t2060307\t Enterococcus sp. FDAARGOS_375\n+0.0043\t3725\t3725\tS\t2603296\t Enterococcus sp. DA9\n+0.0005\t435\t435\tS\t2420313\t Enterococcus sp. FDAARGOS_553\n+0.0004\t366\t366\tS\t2582830\t Enterococcus sp. M190262\n+0.0001\t70\t70\tS\t2057791\t Enterococcus sp. CR-Ec1\n+0.0063\t5491\t5491\tS\t417368\t Enterococcus thailandicus\n+0.0056\t4928\t4928\tS\t44008\t Enterococcus cecorum\n+0.0027\t2394\t2394\tS\t1805431\t Enterococcus saigonensis\n+0.0015\t1355\t1355\tS\t118060\t Enterococcus rotai\n+0.0014\t1241\t1241\tS\t71452\t Enterococcus raffinosus\n+0.0005\t455\t455\tS\t1353\t Enterococcus gallinarum\n+0.0004\t337\t337\tS\t160453\t Enterococcus gilvus\n+0.0003\t227\t227\tS\t2005703\t Enterococcus wangshanyuanii\n+0.0001\t76\t76\tS\t2839759\t Enterococcus innesii\n+0.0000\t12\t12\tS\t246144\t Enterococcus italicus\n+0.0026\t2276\t51\tG\t2737\t Vagococcus\n+0.0012\t1009\t1009\tS\t218144\t Vagococcus carniphilus\n+0.0006\t557\t557\tS\t2738\t Vagococcus fluvialis\n+0.0002\t142\t142\tS\t633807\t Vagococcus penaei\n+0.0002\t135\t135\tS\t2571750\t Vagococcus zengguangii\n+0.0002\t133\t133\tS\t2562451\t Vagococcus xieshaowenii\n+0.0001\t89\t89\tS\t519472\t Vagococcus teuberi\n+0.0001\t87\t87\tS\t81947\t Vagococcus lutrae\n+0.0000\t27\t27\tS\t2714947\t '..b"\t1\t0\tG\t2560128\t Eneladusvirus\n+0.0000\t1\t0\tS\t2560849\t Eneladusvirus Yen904\n+0.0000\t1\t1\tS1\t2052742\t Yersinia phage fHe-Yen9-04\n+0.0000\t1\t0\tG\t2733142\t Yoloswagvirus\n+0.0000\t1\t0\tG1\t2788656\t unclassified Yoloswagvirus\n+0.0000\t1\t1\tS\t2797313\t Erwinia phage pEa_SNUABM_5\n+0.0000\t1\t0\tF\t2560065\t Herelleviridae\n+0.0000\t1\t0\tG\t2843105\t Tybeckvirus\n+0.0000\t1\t0\tS\t2845127\t Tybeckvirus tv521B\n+0.0000\t1\t1\tS1\t2510942\t Lactobacillus phage 521B\n+0.0000\t1\t0\tP\t2731361\t Peploviricota\n+0.0000\t1\t0\tC\t2731363\t Herviviricetes\n+0.0000\t1\t0\tO\t548681\t Herpesvirales\n+0.0000\t1\t0\tF\t548682\t Alloherpesviridae\n+0.0000\t1\t0\tG\t692605\t Batrachovirus\n+0.0000\t1\t1\tS\t1987509\t Ranid herpesvirus 3\n+0.0000\t34\t0\tD1\t2559587\t Riboviria\n+0.0000\t32\t0\tK\t2732396\t Orthornavirae\n+0.0000\t31\t0\tP\t2732406\t Kitrinoviricota\n+0.0000\t31\t0\tC\t2732461\t Alsuviricetes\n+0.0000\t31\t0\tO\t2732544\t Martellivirales\n+0.0000\t31\t0\tF\t69973\t Closteroviridae\n+0.0000\t31\t0\tG\t67753\t Crinivirus\n+0.0000\t31\t31\tS\t31713\t Lettuce infectious yellows virus\n+0.0000\t1\t0\tP\t2732408\t Pisuviricota\n+0.0000\t1\t0\tC\t2732506\t Pisoniviricetes\n+0.0000\t1\t0\tO\t76804\t Nidovirales\n+0.0000\t1\t0\tO1\t2499399\t Cornidovirineae\n+0.0000\t1\t0\tF\t11118\t Coronaviridae\n+0.0000\t1\t0\tF1\t2501931\t Orthocoronavirinae\n+0.0000\t1\t0\tG\t693996\t Alphacoronavirus\n+0.0000\t1\t0\tG1\t2509509\t Rhinacovirus\n+0.0000\t1\t1\tS\t693998\t Rhinolophus bat coronavirus HKU2\n+0.0000\t2\t0\tD2\t2585030\t unclassified Riboviria\n+0.0000\t2\t0\tD3\t1922348\t unclassified RNA viruses ShiM-2016\n+0.0000\t2\t2\tS\t1922687\t Beihai sobemo-like virus 16\n+0.0000\t25\t0\tD1\t2732004\t Varidnaviria\n+0.0000\t25\t0\tK\t2732005\t Bamfordvirae\n+0.0000\t25\t0\tP\t2732007\t Nucleocytoviricota\n+0.0000\t23\t0\tC\t2732523\t Megaviricetes\n+0.0000\t21\t0\tO\t2732554\t Imitervirales\n+0.0000\t21\t0\tF\t549779\t Mimiviridae\n+0.0000\t21\t0\tG\t315393\t Mimivirus\n+0.0000\t21\t0\tG1\t2501774\t unclassified Mimivirus\n+0.0000\t21\t21\tS\t1094892\t Megavirus chiliensis\n+0.0000\t1\t0\tO\t2732555\t Pimascovirales\n+0.0000\t1\t0\tF\t10486\t Iridoviridae\n+0.0000\t1\t0\tF1\t2017757\t Betairidovirinae\n+0.0000\t1\t1\tG\t10491\t Chloriridovirus\n+0.0000\t1\t0\tO\t2732524\t Algavirales\n+0.0000\t1\t0\tF\t10501\t Phycodnaviridae\n+0.0000\t1\t0\tF1\t455363\t unclassified Phycodnaviridae\n+0.0000\t1\t1\tS\t455364\t Chrysochromulina ericina virus\n+0.0000\t2\t0\tC\t2732525\t Pokkesviricetes\n+0.0000\t2\t0\tO\t2732527\t Chitovirales\n+0.0000\t2\t0\tF\t10240\t Poxviridae\n+0.0000\t1\t0\tF1\t10284\t Entomopoxvirinae\n+0.0000\t1\t0\tG\t10286\t Betaentomopoxvirus\n+0.0000\t1\t0\tS\t1993631\t Choristoneura rosaceana entomopoxvirus\n+0.0000\t1\t1\tS1\t1293539\t Choristoneura rosaceana entomopoxvirus 'L'\n+0.0000\t1\t0\tF1\t10241\t Chordopoxvirinae\n+0.0000\t1\t0\tG\t10282\t Yatapoxvirus\n+0.0000\t1\t1\tS\t99000\t Tanapox virus\n+0.0000\t2\t0\tD1\t2731342\t Monodnaviria\n+0.0000\t2\t0\tK\t2732091\t Sangervirae\n+0.0000\t2\t0\tP\t2732412\t Phixviricota\n+0.0000\t2\t0\tC\t2732413\t Malgrandaviricetes\n+0.0000\t2\t0\tO\t2732414\t Petitvirales\n+0.0000\t2\t0\tF\t10841\t Microviridae\n+0.0000\t2\t0\tF1\t117574\t unclassified Microviridae\n+0.0000\t2\t2\tS\t1655645\t Parabacteroides phage YZ-2015b\n+0.0000\t30\t0\tR1\t2787854\t other entries\n+0.0000\t30\t28\tR2\t28384\t other sequences\n+0.0000\t2\t0\tR3\t36549\t plasmids\n+0.0000\t2\t2\tS\t2524\t Plasmid pAM77\n"

diff -r 000000000000 -r 00d4ea6b6c71 test-data/output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/output_intermediate.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_intermediate.tabular Mon Mar 06 21:22:31 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 00d4ea6b6c71 test-data/sample.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.tabular Mon Mar 06 21:22:31 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'