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Changeset 0:519e0835abd7 (2023-03-15)

Next changeset 1:f329328da134 (2023-06-20)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 92c58a65005708fbd56b27b86969c01a1258ddb9

diff -r 000000000000 -r 519e0835abd7 extract_kraken_reads.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_kraken_reads.xml Wed Mar 15 18:18:27 2023 +0000

[

b'@@ -0,0 +1,251 @@\n+<tool id="krakentools_extract_kraken_reads" name="Krakentools: Extract Kraken Reads By ID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>\n+ Extract reads that were classified by the Kraken family at specified taxonomic IDs\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ <requirement type="package" version="1.12">gzip</requirement>\n+ </expand>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ ##set input\n+ #if $library.type == \'paired\':\n+ #set input_1 = $library.input_1\n+ #set input_2 = $library.input_2\n+ #else if $library.type == \'paired_collection\'\n+ #set input_1 = $library.input_1.forward\n+ #set input_2 = $library.input_1.reverse\n+ #else\n+ #set input_1 = $library.input_1\n+ #end if\n+\n+ ## name output according to --fastq_output param\n+ ## tests fails if file does not have correct ending\n+ #if str($fastq_output) == \'\':\n+ #set temp_output_1 = \'output_1.fasta\'\n+ #set temp_output_2 = \'output_2.fasta\'\n+ #else:\n+ #set temp_output_1 = \'output_1.fastq\'\n+ #set temp_output_2 = \'output_2.fastq\'\n+ #end if\n+\n+ ## do not quote $taxid\n+ extract_kraken_reads.py\n+ -k \'$results\'\n+ -s \'$input_1\'\n+ -o \'$temp_output_1\'\n+ --taxid $taxid\n+ --max \'$max\'\n+ $include_parents\n+ $include_children\n+ $exclude\n+ $fastq_output\n+\n+ #if str( $library.type ) != "single":\n+ -s2 \'$input_2\'\n+ -o2 \'$temp_output_2\'\n+ #end if\n+ #if $include_parents or $include_children:\n+ --report \'$report\'\n+ #end if\n+\n+ ##compress output\n+ && gzip -cvf \'$temp_output_1\' > output_1.gz\n+\n+ #if str( $library.type ) != "single":\n+ && gzip -cvf \'$temp_output_2\' > output_2.gz\n+ #end if\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ \n+ <conditional name="library">\n+ <param name="type" type="select" label="Single or paired reads?">\n+ <option value="single">\n+ Single\n+ </option>\n+ <option value="paired">\n+ Paired\n+ </option>\n+ <option value="paired_collection">\n+ Paired Collection\n+ </option>\n+ </param>\n+ <when value="single">\n+ <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A file" help="FASTQ or FASTQ input reads (may be gzipped)" />\n+ </when>\n+ <when value="paired">\n+ <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A forward file" help="FASTQ or FASTQ input reads (may be gzipped)" />\n+ <param name="input_2" format="fastq,fasta" type="data" label="FASTQ/A reverse file" help="FASTQ or FASTQ input reads (for paired reads, may be gzipped)" />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="input_1" format="fastq,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection (may be gzipped)" />\n+ </when>\n+ </conditional>\n+ <param name="results" argument="-k" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" />\n+ <param argument="--report" format="tabular" type="data" label="Report" optional="true" help="Report file from Kraken/KrakenUniq/Kraken2" />\n+ <param argument="--taxid" type="text" value="" label="Taxonomic ID(s) to match" help="Space-delimited list of taxonomic IDs for which to extract matching reads">\n+ <validator type="regex" message="Enter a space-separated list of n'..b' />\n+ <param name="include_children" value="True" />\n+ <param name="exclude" value="True" />\n+ <output name="output_1" file="extract_kraken_reads/out1.k1.e10386.children.fa" decompress="true" ftype="fasta.gz" />\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />\n+ <param name="library|type" value="single" />\n+ <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />\n+ <param name="taxid" value="11176" />\n+ <param name="max" value="2" />\n+ <output name="output_1" file="extract_kraken_reads/out1.k2.11176.max2.fa" decompress="true" ftype="fasta.gz" />\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />\n+ <param name="library|type" value="single" />\n+ <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />\n+ <param name="taxid" value="11176" />\n+ <param name="include_parents" value="True" />\n+ <param name="report" value="extract_kraken_reads/kraken2.report" ftype="tabular" />\n+ <output name="output_1" file="extract_kraken_reads/out1.k2.11176.parents.fa" decompress="true" ftype="fasta.gz" />\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />\n+ <param name="library|type" value="single" />\n+ <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />\n+ <param name="taxid" value="10386 11176" />\n+ <param name="exclude" value="True" />\n+ <param name="include_parents" value="True" />\n+ <param name="report" value="extract_kraken_reads/kraken2.report" ftype="tabular" />\n+ <output name="output_1" file="extract_kraken_reads/out1.k2.exclude_both.fa" decompress="true" ftype="fasta.gz" />\n+ </test>\n+ \n+ <test expect_failure="true">\n+ <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />\n+ <param name="library|type" value="single" />\n+ <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />\n+ <param name="taxid" value="10386 f5" />\n+ </test>\n+ \n+ <test expect_num_outputs="1">\n+ <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />\n+ <param name="library|type" value="single" />\n+ <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />\n+ <param name="taxid" value="11176" />\n+ <param name="fastq_output" value="true" />\n+ <output name="output_1" file="extract_kraken_reads/out1.k2.11176.fq" decompress="true" ftype="fastq.gz" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+**What it does**\n+-------------------\n+After running Kraken, Kraken2, or KrakenUniq, users may use the\n+`extract_kraken_reads.py` program to extract the FASTA or FASTQ reads\n+classified as a specific taxonomy ID. For example, this program can be used to\n+extract all bacterial reads or only reads assigned to Escherichia coli. Users\n+must provide (at minimum) the original sequence file(s), at least one taxonomy\n+ID, and the Kraken output file.\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+ <creator>\n+ <person givenName="Jeremy" familyName="Volkening" url="https://github.com/jvolkening" />\n+ <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />\n+ </creator>\n+</tool>\n'

diff -r 000000000000 -r 519e0835abd7 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Mar 15 18:18:27 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 519e0835abd7 test-data/1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/beta_bracken_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_1.tabular Wed Mar 15 18:18:27 2023 +0000

[

diff -r 000000000000 -r 519e0835abd7 test-data/beta_bracken_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_2.tabular Wed Mar 15 18:18:27 2023 +0000

[

diff -r 000000000000 -r 519e0835abd7 test-data/beta_bracken_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_bracken_3.tabular Wed Mar 15 18:18:27 2023 +0000

diff -r 000000000000 -r 519e0835abd7 test-data/beta_kreport_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_1.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/beta_kreport_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_2.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/beta_kreport_3.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_kreport_3.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/beta_krona_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_1.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/beta_krona_2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/beta_krona_2.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/bracken_abundance.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bracken_abundance.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/combined_kreport.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combined_kreport.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/extract_kraken_reads/R1.fq.gz

Binary file test-data/extract_kraken_reads/R1.fq.gz has changed

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/R2.fq.gz

Binary file test-data/extract_kraken_reads/R2.fq.gz has changed

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/kraken1.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/kraken1.report Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,18 @@
+  6.79 38 38 U 0 unclassified
+ 93.21 522 0 - 1 root
+ 93.21 522 0 D 10239   Viruses
+ 88.75 497 0 - 35237     dsDNA viruses, no RNA stage
+ 88.75 497 0 O 548681       Herpesvirales
+ 88.75 497 0 F 10292         Herpesviridae
+ 88.75 497 0 - 10293           Alphaherpesvirinae
+ 88.75 497 0 G 180255             Iltovirus
+ 88.75 497 497 S 10386               Gallid herpesvirus 1
+  4.46 25 0 - 439488     ssRNA viruses
+  4.46 25 0 - 35301       ssRNA negative-strand viruses
+  4.46 25 0 O 11157         Mononegavirales
+  4.46 25 0 F 11158           Paramyxoviridae
+  4.46 25 0 G 260963             Avulavirus
+  3.57 20 0 - 336096               unclassified Avulavirus
+  3.57 20 20 S 204987                 Goose paramyxovirus SF02
+  0.89 5 0 S 11176               Newcastle disease virus
+  0.89 5 5 - 139270                 Newcastle disease virus B1

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/kraken1.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/kraken1.results Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,560 @@\n+U\tC_II_XVIIIb-101\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-99\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-97\t204987\t301\t0:120 A:31 0:72 204987:2 0:46\n+C\tC_II_XVIIIb-95\t204987\t301\t0:87 204987:24 0:9 A:31 0:120\n+U\tC_II_XVIIIb-93\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-91\t204987\t301\t0:80 204987:2 0:38 A:31 0:120\n+C\tC_II_XVIIIb-89\t204987\t301\t0:120 A:31 0:60 204987:2 0:58\n+C\tC_II_XVIIIb-87\t139270\t301\t0:58 139270:9 0:53 A:31 0:120\n+U\tC_II_XVIIIb-85\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-83\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-81\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-79\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-77\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-75\t204987\t301\t0:120 A:31 0:54 204987:18 0:48\n+U\tC_II_XVIIIb-73\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-71\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-69\t204987\t301\t0:26 204987:2 0:92 A:31 0:120\n+U\tC_II_XVIIIb-67\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-65\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-63\t204987\t301\t0:43 139270:3 0:74 A:31 0:58 204987:14 0:48\n+C\tC_II_XVIIIb-61\t204987\t301\t0:71 204987:22 0:27 A:31 0:108 204987:12\n+U\tC_II_XVIIIb-59\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-57\t204987\t301\t0:34 204987:14 0:72 A:31 0:120\n+U\tC_II_XVIIIb-55\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-53\t139270\t301\t0:120 A:31 0:91 139270:2 0:27\n+C\tC_II_XVIIIb-51\t204987\t301\t0:9 204987:16 0:95 A:31 0:72 139270:3 0:45\n+C\tC_II_XVIIIb-49\t204987\t301\t0:41 204987:2 0:77 A:31 0:120\n+U\tC_II_XVIIIb-47\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-45\t204987\t301\t0:65 204987:12 260963:2 0:41 A:31 0:120\n+C\tC_II_XVIIIb-43\t204987\t301\t0:120 A:31 0:23 204987:3 0:94\n+U\tC_II_XVIIIb-41\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-39\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-37\t139270\t301\t0:120 A:31 0:116 139270:4\n+C\tC_II_XVIIIb-35\t204987\t301\t0:120 A:31 0:45 204987:11 0:64\n+C\tC_II_XVIIIb-33\t204987\t301\t0:32 204987:3 0:85 A:31 0:46 204987:18 0:56\n+U\tC_II_XVIIIb-31\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-29\t204987\t301\t0:120 A:31 0:82 204987:9 0:29\n+U\tC_II_XVIIIb-27\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-25\t139270\t301\t0:120 A:31 0:88 139270:1 0:31\n+C\tC_II_XVIIIb-23\t139270\t301\t0:44 139270:2 0:74 A:31 0:120\n+U\tC_II_XVIIIb-21\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-19\t204987\t301\t0:34 204987:9 0:77 A:31 0:23 204987:13 0:84\n+U\tC_II_XVIIIb-17\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-15\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-13\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-11\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-9\t0\t301\t0:120 A:31 0:120\n+U\tC_II_XVIIIb-7\t0\t301\t0:120 A:31 0:120\n+C\tC_II_XVIIIb-5\t204987\t301\t0:120 A:31 0:77 204987:28 0:15\n+C\tC_II_XVIIIb-3\t204987\t301\t0:99 204987:2 0:19 A:31 0:105 204987:2 0:13\n+C\tC_II_XVIIIb-1\t204987\t301\t0:109 204987:5 0:6 A:31 0:103 204987:5 0:12\n+C\tHQ630064-1017\t10386\t301\t0:32 10386:88 A:31 0:32 10386:23 0:31 10386:34\n+C\tHQ630064-1015\t10386\t301\t0:48 10386:72 A:31 0:22 10386:98\n+C\tHQ630064-1013\t10386\t301\t0:19 10386:101 A:31 0:22 10386:98\n+C\tHQ630064-1011\t10386\t301\t0:31 10386:89 A:31 0:50 10386:8 0:31 10386:31\n+C\tHQ630064-1009\t10386\t301\t0:31 10386:89 A:31 0:39 10386:65 0:16\n+C\tHQ630064-1007\t10386\t301\t0:1 10386:2 0:31 10386:86 A:31 0:28 10386:92\n+C\tHQ630064-1005\t10386\t301\t0:22 10386:16 0:31 10386:51 A:31 0:18 10386:2 0:40 10386:12 0:48\n+C\tHQ630064-1003\t10386\t301\t0:31 10386:89 A:31 0:99 10386:21\n+C\tHQ630064-1001\t10386\t301\t0:30 10386:17 0:31 10386:42 A:31 0:34 10386:77 0:9\n+C\tHQ630064-999\t10386\t301\t0:1 10386:1 0:55 10386:63 A:31 0:37 10386:83\n+C\tHQ630064-997\t10386\t301\t0:37 10386:61 0:22 A:31 0:19 10386:31 0:52 10386:18\n+C\tHQ630064-995\t10386\t301\t0:32 10386:1 0:31 10386:56 A:31 0:33 10386:53 0:31 10386:3\n+C\tHQ630064-993\t10386\t301\t0:30 10386:90 A:31 0:39 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10386:57\n+C\tHQ630064-23\t10386\t301\t0:26 10386:35 0:31 10386:28 A:31 0:23 10386:97\n+C\tHQ630064-21\t10386\t301\t0:25 10386:95 A:31 0:28 10386:40 0:31 10386:21\n+C\tHQ630064-19\t10386\t301\t0:32 10386:88 A:31 0:22 10386:98\n+C\tHQ630064-17\t10386\t301\t0:32 10386:88 A:31 0:26 10386:16 0:31 10386:47\n+C\tHQ630064-15\t10386\t301\t0:59 10386:61 A:31 0:21 10386:21 0:39 10386:39\n+C\tHQ630064-13\t10386\t301\t0:33 10386:87 A:31 0:35 10386:85\n+U\tHQ630064-11\t0\t301\t0:120 A:31 0:120\n+C\tHQ630064-9\t10386\t301\t0:22 10386:98 A:31 0:33 10386:1 0:31 10386:55\n+C\tHQ630064-7\t10386\t301\t0:30 10386:90 A:31 0:63 10386:57\n+C\tHQ630064-5\t10386\t301\t0:15 10386:47 0:58 A:31 0:14 10386:28 0:31 10386:4 0:43\n+U\tHQ630064-3\t0\t301\t0:120 A:31 0:120\n+C\tHQ630064-1\t10386\t301\t0:45 10386:31 0:44 A:31 0:120\n'

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/kraken2.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/kraken2.report Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,73 @@
+  4.29 24 24 U 0 unclassified
+ 95.71 536 0 R 1 root
+ 95.00 532 0 D 10239   Viruses
+ 88.75 497 0 D1 2731341     Duplodnaviria
+ 88.75 497 0 D2 2731360       Heunggongvirae
+ 88.75 497 0 P 2731361         Peploviricota
+ 88.75 497 0 C 2731363           Herviviricetes
+ 88.75 497 0 O 548681             Herpesvirales
+ 88.75 497 0 F 10292               Herpesviridae
+ 88.75 497 0 F1 10293                 Alphaherpesvirinae
+ 88.75 497 0 G 180255                   Iltovirus
+ 88.75 497 497 S 10386                     Gallid alphaherpesvirus 1
+  6.25 35 0 D1 2559587     Riboviria
+  6.25 35 0 K 2732396       Orthornavirae
+  6.25 35 0 P 2497569         Negarnaviricota
+  6.25 35 0 P1 2497570           Haploviricotina
+  6.25 35 0 C 2497574             Monjiviricetes
+  6.25 35 0 O 11157               Mononegavirales
+  6.25 35 0 F 11158                 Paramyxoviridae
+  6.25 35 12 G 260963                   Avulavirus
+  2.68 15 0 G1 336096                     unclassified Avulavirus
+  2.68 15 15 S 204987                       Goose paramyxovirus SF02
+  1.25 7 7 S 11176                     Avian avulavirus 1
+  0.18 1 1 S 1305716                     Avian avulavirus 12
+  0.71 4 0 R1 131567   cellular organisms
+  0.36 2 0 D 2     Bacteria
+  0.36 2 0 P 1224       Proteobacteria
+  0.36 2 0 C 1236         Gammaproteobacteria
+  0.36 2 0 O 72274           Pseudomonadales
+  0.36 2 0 F 468             Moraxellaceae
+  0.36 2 0 G 469               Acinetobacter
+  0.36 2 0 G1 909768                 Acinetobacter calcoaceticus/baumannii complex
+  0.36 2 2 S 470                   Acinetobacter baumannii
+  0.36 2 0 D 2759     Eukaryota
+  0.18 1 0 D1 33154       Opisthokonta
+  0.18 1 0 K 33208         Metazoa
+  0.18 1 0 K1 6072           Eumetazoa
+  0.18 1 0 K2 33213             Bilateria
+  0.18 1 0 K3 33511               Deuterostomia
+  0.18 1 0 P 7711                 Chordata
+  0.18 1 0 P1 89593                   Craniata
+  0.18 1 0 P2 7742                     Vertebrata
+  0.18 1 0 P3 7776                       Gnathostomata
+  0.18 1 0 P4 117570                         Teleostomi
+  0.18 1 0 P5 117571                           Euteleostomi
+  0.18 1 0 P6 8287                             Sarcopterygii
+  0.18 1 0 P7 1338369                               Dipnotetrapodomorpha
+  0.18 1 0 P8 32523                                 Tetrapoda
+  0.18 1 0 P9 32524                                   Amniota
+  0.18 1 0 C 40674                                     Mammalia
+  0.18 1 0 C1 32525                                       Theria
+  0.18 1 0 C2 9347                                         Eutheria
+  0.18 1 0 C3 1437010                                           Boreoeutheria
+  0.18 1 0 C4 314146                                             Euarchontoglires
+  0.18 1 0 O 9443                                               Primates
+  0.18 1 0 O1 376913                                                 Haplorrhini
+  0.18 1 0 O2 314293                                                   Simiiformes
+  0.18 1 0 O3 9526                                                     Catarrhini
+  0.18 1 0 O4 314295                                                       Hominoidea
+  0.18 1 0 F 9604                                                         Hominidae
+  0.18 1 0 F1 207598                                                           Homininae
+  0.18 1 0 G 9605                                                             Homo
+  0.18 1 1 S 9606                                                               Homo sapiens
+  0.18 1 0 D1 2698737       Sar
+  0.18 1 0 D2 33630         Alveolata
+  0.18 1 0 P 5794           Apicomplexa
+  0.18 1 0 C 422676             Aconoidasida
+  0.18 1 0 O 5819               Haemosporida
+  0.18 1 0 F 1639119                 Plasmodiidae
+  0.18 1 0 G 5820                   Plasmodium
+  0.18 1 0 G1 418103                     Plasmodium (Plasmodium)
+  0.18 1 0 S 5850                       Plasmodium knowlesi
+  0.18 1 1 S1 5851                         Plasmodium knowlesi strain H

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/kraken2.results
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/kraken2.results Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,560 @@\n+C\tC_II_XVIIIb-101\t5851\t150|150\t0:116 |:| 0:17 5851:5 0:94\n+C\tC_II_XVIIIb-99\t260963\t150|150\t0:40 260963:5 0:71 |:| 0:116\n+C\tC_II_XVIIIb-97\t260963\t150|150\t0:116 |:| 0:75 260963:1 0:40\n+C\tC_II_XVIIIb-95\t204987\t150|150\t0:63 260963:3 0:21 204987:20 0:9 |:| 0:116\n+C\tC_II_XVIIIb-93\t260963\t150|150\t0:116 |:| 0:82 260963:3 0:31\n+C\tC_II_XVIIIb-91\t204987\t150|150\t0:65 260963:2 0:49 |:| 0:18 204987:2 0:96\n+C\tC_II_XVIIIb-89\t204987\t150|150\t0:11 204987:5 0:38 260963:3 0:59 |:| 0:56 260963:5 0:55\n+C\tC_II_XVIIIb-87\t260963\t150|150\t0:23 260963:4 0:58 260963:2 0:1 260963:5 0:23 |:| 0:116\n+C\tC_II_XVIIIb-85\t260963\t150|150\t0:42 260963:3 0:3 260963:5 0:1 260963:5 0:57 |:| 0:116\n+U\tC_II_XVIIIb-83\t0\t150|150\t0:116 |:| 0:116\n+U\tC_II_XVIIIb-81\t0\t150|150\t0:116 |:| 0:116\n+U\tC_II_XVIIIb-79\t0\t150|150\t0:116 |:| 0:116\n+U\tC_II_XVIIIb-77\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-75\t260963\t150|150\t0:59 260963:1 0:7 260963:3 0:7 260963:3 0:36 |:| 0:52 260963:16 0:48\n+C\tC_II_XVIIIb-73\t1305716\t150|150\t0:116 |:| 0:53 1305716:4 0:59\n+U\tC_II_XVIIIb-71\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-69\t204987\t150|150\t0:11 260963:2 0:67 204987:3 0:33 |:| 0:116\n+U\tC_II_XVIIIb-67\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-65\t11176\t150|150\t0:103 11176:3 0:1 11176:2 0:7 |:| 0:31 260963:6 11176:5 0:5 11176:4 260963:1 11176:5 0:8 11176:2 0:1 11176:3 0:45\n+C\tC_II_XVIIIb-63\t204987\t150|150\t0:39 260963:5 0:72 |:| 0:58 204987:12 0:1 204987:5 0:23 260963:3 0:14\n+C\tC_II_XVIIIb-61\t204987\t150|150\t0:45 260963:3 0:23 204987:18 0:27 |:| 0:108 204987:8\n+U\tC_II_XVIIIb-59\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-57\t11176\t150|150\t0:31 260963:13 0:1 260963:6 0:16 11176:1 0:48 |:| 0:102 11176:1 0:13\n+C\tC_II_XVIIIb-55\t204987\t150|150\t0:67 204987:6 0:43 |:| 0:113 204987:3\n+C\tC_II_XVIIIb-53\t204987\t150|150\t0:55 260963:5 0:10 260963:2 204987:5 0:7 260963:5 0:27 |:| 0:28 260963:1 0:65 260963:5 0:17\n+C\tC_II_XVIIIb-51\t204987\t150|150\t0:8 204987:13 0:95 |:| 0:21 260963:4 0:33 260963:3 0:7 260963:5 0:43\n+C\tC_II_XVIIIb-49\t11176\t150|150\t0:35 260963:1 0:80 |:| 0:30 11176:5 0:5 11176:3 0:73\n+U\tC_II_XVIIIb-47\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-45\t11176\t150|150\t0:28 11176:1 0:35 260963:13 0:39 |:| 0:98 11176:7 0:1 260963:5 0:5\n+C\tC_II_XVIIIb-43\t260963\t150|150\t0:99 260963:12 0:5 |:| 0:20 260963:4 0:51 260963:2 0:21 260963:1 0:17\n+C\tC_II_XVIIIb-41\t204987\t150|150\t0:116 |:| 0:77 204987:6 0:33\n+U\tC_II_XVIIIb-39\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-37\t204987\t150|150\t0:110 204987:5 0:1 |:| 0:116\n+C\tC_II_XVIIIb-35\t204987\t150|150\t0:48 204987:5 0:5 204987:1 0:42 260963:4 0:11 |:| 0:19 260963:7 0:17 260963:10 0:56 260963:4 0:3\n+C\tC_II_XVIIIb-33\t260963\t150|150\t0:32 260963:7 0:77 |:| 0:46 260963:16 0:54\n+C\tC_II_XVIIIb-31\t204987\t150|150\t0:113 204987:3 |:| 0:116\n+C\tC_II_XVIIIb-29\t260963\t150|150\t0:116 |:| 0:74 260963:16 0:6 260963:1 0:11 260963:5 0:3\n+U\tC_II_XVIIIb-27\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-25\t204987\t150|150\t0:106 260963:5 0:5 |:| 0:61 204987:7 0:48\n+C\tC_II_XVIIIb-23\t204987\t150|150\t0:47 260963:5 0:31 260963:5 0:7 204987:5 260963:2 0:10 260963:4 |:| 0:57 260963:12 0:9 260963:1 0:37\n+U\tC_II_XVIIIb-21\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-19\t260963\t150|150\t0:24 260963:1 0:6 260963:16 0:69 |:| 0:19 260963:15 0:82\n+C\tC_II_XVIIIb-17\t11176\t150|150\t0:116 |:| 0:79 11176:2 0:7 11176:12 260963:1 11176:6 0:9\n+U\tC_II_XVIIIb-15\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-13\t470\t150|150\t0:116 |:| 0:22 470:2 0:5 470:2 0:37 470:5 0:42 470:1\n+C\tC_II_XVIIIb-11\t470\t150|150\t0:49 470:5 0:42 470:6 0:10 260963:1 0:3 |:| 0:116\n+C\tC_II_XVIIIb-9\t11176\t150|150\t0:116 |:| 0:25 11176:3 0:4 11176:8 0:76\n+U\tC_II_XVIIIb-7\t0\t150|150\t0:116 |:| 0:116\n+C\tC_II_XVIIIb-5\t260963\t150|150\t0:116 |:| 0:73 260963:32 0:11\n+C\tC_II_XVIIIb-3\t260963\t150|150\t0:33 260963:5 0:55 260963:1 0:22 |:| 0:108 260963:1 0:7\n+C\tC_II_XVIIIb-1\t11176\t150|150\t0:36 260963:5 0:11 204987:1 0:54 260963:4 0:5 |:| 0:38 11176:3 0:5 11176:5 0:51 260963:4 0:10\n+C\tHQ630064-1017\t10386\t150|150\t0:29 10386:87 |:| 0:26 10386:33 0:1 10386:5 0:9 10386:3 0:8 10386:31\n+C\tHQ630064'..b'86\t150|150\t0:32 10386:84 |:| 0:45 10386:5 0:1 10386:3 0:3 10386:59\n+C\tHQ630064-77\t10386\t150|150\t0:33 10386:83 |:| 10386:1 0:5 10386:2 0:27 10386:7 0:1 10386:73\n+C\tHQ630064-75\t10386\t150|150\t0:28 10386:88 |:| 0:28 10386:21 0:31 10386:5 0:5 10386:26\n+C\tHQ630064-73\t10386\t150|150\t0:10 10386:1 0:5 10386:20 0:23 10386:1 0:8 10386:48 |:| 10386:50 0:21 10386:11 0:3 10386:31\n+C\tHQ630064-71\t10386\t150|150\t0:28 10386:1 0:17 10386:70 |:| 0:18 10386:19 0:23 10386:3 0:7 10386:46\n+C\tHQ630064-69\t10386\t150|150\t0:31 10386:36 0:4 10386:2 0:28 10386:15 |:| 0:47 10386:69\n+C\tHQ630064-67\t10386\t150|150\t0:23 10386:93 |:| 0:3 10386:1 0:15 10386:7 0:4 10386:86\n+C\tHQ630064-65\t10386\t150|150\t0:16 10386:100 |:| 0:19 10386:5 0:9 10386:83\n+C\tHQ630064-63\t10386\t150|150\t0:23 10386:93 |:| 0:62 10386:20 0:2 10386:5 0:1 10386:5 0:17 10386:4\n+C\tHQ630064-61\t10386\t150|150\t0:7 10386:1 0:4 10386:104 |:| 0:23 10386:1 0:7 10386:1 0:12 10386:72\n+C\tHQ630064-59\t10386\t150|150\t0:19 10386:1 0:5 10386:91 |:| 0:27 10386:89\n+C\tHQ630064-57\t10386\t150|150\t0:31 10386:76 0:6 10386:3 |:| 0:4 10386:1 0:53 10386:26 0:3 10386:5 0:24\n+C\tHQ630064-55\t10386\t150|150\t0:29 10386:87 |:| 0:15 10386:3 0:5 10386:3 0:1 10386:89\n+C\tHQ630064-53\t10386\t150|150\t0:9 10386:1 0:16 10386:90 |:| 0:14 10386:1 0:3 10386:8 0:3 10386:1 0:1 10386:5 0:13 10386:5 0:3 10386:28 0:9 10386:5 0:9 10386:8\n+C\tHQ630064-51\t10386\t150|150\t0:25 10386:12 0:10 10386:1 0:13 10386:2 0:8 10386:45 |:| 0:27 10386:12 0:71 10386:6\n+C\tHQ630064-49\t10386\t150|150\t0:16 10386:5 0:12 10386:83 |:| 0:116\n+C\tHQ630064-47\t10386\t150|150\t0:16 10386:4 0:11 10386:27 0:3 10386:9 0:19 10386:27 |:| 0:19 10386:5 0:7 10386:48 0:31 10386:6\n+C\tHQ630064-45\t10386\t150|150\t0:20 10386:25 0:17 10386:22 0:32 |:| 0:26 10386:5 0:15 10386:1 0:11 10386:37 0:21\n+C\tHQ630064-43\t10386\t150|150\t0:27 10386:1 0:5 10386:28 0:8 10386:2 0:25 10386:2 0:11 10386:7 |:| 0:25 10386:30 0:20 10386:1 0:10 10386:30\n+C\tHQ630064-41\t10386\t150|150\t0:26 10386:15 0:21 10386:5 0:1 10386:48 |:| 0:31 10386:81 0:1 10386:3\n+C\tHQ630064-39\t10386\t150|150\t0:40 10386:76 |:| 0:14 10386:102\n+C\tHQ630064-37\t10386\t150|150\t0:20 10386:6 0:3 10386:87 |:| 0:46 10386:45 0:25\n+C\tHQ630064-35\t10386\t150|150\t0:33 10386:83 |:| 0:7 10386:109\n+C\tHQ630064-33\t10386\t150|150\t0:10 10386:5 0:4 10386:97 |:| 0:13 10386:5 0:33 10386:65\n+C\tHQ630064-31\t10386\t150|150\t0:13 10386:5 0:4 10386:13 0:12 10386:11 0:10 10386:12 0:7 10386:9 0:13 10386:1 0:4 10386:2 |:| 0:18 10386:1 0:4 10386:93\n+C\tHQ630064-29\t10386\t150|150\t0:23 10386:46 0:35 10386:12 |:| 0:12 10386:2 0:10 10386:53 0:1 10386:5 0:33\n+C\tHQ630064-27\t10386\t150|150\t0:24 10386:2 0:6 10386:4 0:17 10386:7 0:1 10386:1 0:1 10386:1 0:10 10386:42 |:| 0:19 10386:46 0:2 10386:5 0:12 10386:4 0:11 10386:13 0:4\n+C\tHQ630064-25\t10386\t150|150\t0:20 10386:2 0:8 10386:86 |:| 0:51 10386:1 0:5 10386:1 0:5 10386:53\n+C\tHQ630064-23\t10386\t150|150\t0:18 10386:5 0:1 10386:34 0:12 10386:1 0:5 10386:5 0:5 10386:5 0:1 10386:24 |:| 0:23 10386:93\n+C\tHQ630064-21\t10386\t150|150\t0:7 10386:1 0:12 10386:2 0:1 10386:93 |:| 0:20 10386:44 0:9 10386:1 0:7 10386:7 0:10 10386:18\n+C\tHQ630064-19\t10386\t150|150\t0:32 10386:84 |:| 0:19 10386:97\n+C\tHQ630064-17\t10386\t150|150\t0:28 10386:88 |:| 0:23 10386:15 0:5 10386:3 0:13 10386:5 0:5 10386:47\n+C\tHQ630064-15\t10386\t150|150\t0:43 10386:1 0:12 10386:60 |:| 0:6 10386:3 0:12 10386:21 0:7 10386:1 0:15 10386:1 0:3 10386:6 0:5 10386:36\n+C\tHQ630064-13\t10386\t150|150\t0:25 10386:1 0:1 10386:89 |:| 0:17 10386:1 0:1 10386:5 0:1 10386:1 0:1 10386:1 0:3 10386:85\n+U\tHQ630064-11\t0\t150|150\t0:116 |:| 0:116\n+C\tHQ630064-9\t10386\t150|150\t0:19 10386:97 |:| 0:15 10386:3 0:5 10386:1 0:1 10386:2 0:16 10386:11 0:9 10386:53\n+C\tHQ630064-7\t10386\t150|150\t0:15 10386:10 0:2 10386:89 |:| 0:35 10386:3 0:23 10386:55\n+C\tHQ630064-5\t10386\t150|150\t0:1 10386:1 0:5 10386:1 0:6 10386:48 0:29 10386:7 0:1 10386:7 0:7 10386:3 |:| 0:13 10386:25 0:5 10386:5 0:7 10386:7 0:1 10386:7 0:3 10386:2 0:28 10386:9 0:3 10386:1\n+U\tHQ630064-3\t0\t150|150\t0:116 |:| 0:116\n+C\tHQ630064-1\t10386\t150|150\t0:35 10386:5 0:5 10386:28 0:4 10386:3 0:36 |:| 0:116\n'

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/krakenU.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/krakenU.report Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,1305 @@\n+# KrakenUniq v0.5.8 DATE:2021-09-21T05:28:21Z DB:./db1 ./db2 ./db3 ./db4 ./db5 ./db6 ./db7 ./db8 ./db9 DB_SIZE:43487608 WD:/tmp/nxf.LS2KtRM0fv\n+# CL:perl /opt/conda/envs/nf/bin/krakenuniq --db db1 --db db2 --db db3 --db db4 --db db5 --db db6 --db db7 --db db8 --db db9 --threads 64 --report-file lowfilt.report.pre --output lowfilt.results --paired lowfilt.qfilt.R1_val_1.rmspikein.fq lowfilt.qfilt.R2_val_2.rmspikein.fq\n+\n+%\treads\ttaxReads\tkmers\tdup\tcov\ttaxID\trank\ttaxName\n+2.18\t1681\t1681\t12617084\t1.2\tNA\t0\tno rank\tunclassified\n+97.82\t75426\t277\t1886797\t1.23\t7.482e-05\t1\tno rank\troot\n+95.62\t73730\t29\t1742828\t1.21\t7.188e-05\t131567\tno rank\t cellular organisms\n+93.26\t71908\t380\t1704354\t1.21\t9.69e-05\t2\tsuperkingdom\t Bacteria\n+44.5\t34310\t59\t797434\t1.21\t0.0001228\t1783272\tclade\t Terrabacteria group\n+29.93\t23076\t82\t557233\t1.2\t0.0002134\t1239\tphylum\t Firmicutes\n+20.77\t16015\t73\t379200\t1.22\t0.0003627\t91061\tclass\t Bacilli\n+12.81\t9880\t45\t253369\t1.19\t0.0003098\t1385\torder\t Bacillales\n+4.103\t3164\t10\t102496\t1.16\t0.00027\t186817\tfamily\t Bacillaceae\n+4.088\t3152\t963\t100677\t1.16\t0.001024\t1386\tgenus\t Bacillus\n+2.521\t1944\t1944\t46683\t1.13\t0.07898\t1963032\tspecies\t Bacillus intestinalis\n+0.284\t219\t150\t4091\t1.26\t0.0002188\t86661\tspecies group\t Bacillus cereus group\n+0.05447\t42\t42\t1083\t1.29\t0.001994\t2026186\tspecies\t Bacillus paranthracis\n+0.009078\t7\t7\t226\t1.29\t0.0004816\t2026188\tspecies\t Bacillus tropicus\n+0.007781\t6\t6\t208\t1.21\t0.00036\t2026190\tspecies\t Bacillus mobilis\n+0.005188\t4\t4\t170\t1.21\t4.36e-05\t1396\tspecies\t Bacillus cereus\n+0.003891\t3\t3\t75\t1.29\t0.0001177\t2026189\tspecies\t Bacillus albus\n+0.002594\t2\t2\t56\t1.16\t0.0001006\t2026193\tspecies\t Bacillus nitratireducens\n+0.002594\t2\t2\t62\t1.27\t0.0002833\t1392\tspecies\t Bacillus anthracis\n+0.001297\t1\t1\t44\t1.27\t0.0001063\t2026191\tspecies\t Bacillus luti\n+0.001297\t1\t1\t66\t1.26\t8.275e-05\t1890302\tspecies\t Bacillus wiedmannii\n+0.001297\t1\t1\t70\t1.19\t5.253e-05\t1428\tspecies\t Bacillus thuringiensis\n+0.01816\t14\t0\t1824\t1.22\t5.778e-05\t185979\tno rank\t unclassified Bacillus (in: Bacteria)\n+0.01167\t9\t9\t1141\t1.25\t0.002064\t2597270\tspecies\t Bacillus sp. P16(2019)\n+0.006484\t5\t5\t681\t1.19\t4.507e-05\t1409\tspecies\t Bacillus sp. (in: Bacteria)\n+0.01038\t8\t6\t3457\t1.41\t0.0003944\t653685\tspecies group\t Bacillus subtilis group\n+0.002594\t2\t2\t1721\t1.15\t0.002671\t483913\tspecies\t Bacillus inaquosorum\n+0.002594\t2\t2\t119\t1.18\t0.0002753\t230954\tspecies\t Bacillus thermozeamaize\n+0.001297\t1\t1\t179\t1.23\t0.0004264\t408580\tspecies\t Bacillus coahuilensis\n+0.001297\t1\t1\t61\t1.36\t0.000156\t2039284\tspecies\t Bacillus fungorum\n+0.001297\t1\t0\t42\t1.17\t4.106e-06\t84406\tgenus\t Virgibacillus\n+0.001297\t1\t1\t37\t1.19\t6.655e-05\t1638645\tspecies\t Virgibacillus kapii\n+0.001297\t1\t0\t5\t1\t1.141e-06\t704093\tgenus\t Anaerobacillus\n+0.001297\t1\t0\t2\t1\t8.059e-07\t2625356\tno rank\t unclassified Anaerobacillus\n+0.001297\t1\t1\t2\t1\t8.059e-07\t1872506\tspecies\t Anaerobacillus sp.\n+3.84\t2961\t27\t58221\t1.28\t0.001726\t90964\tfamily\t Staphylococcaceae\n+3.803\t2932\t321\t56780\t1.27\t0.002658\t1279\tgenus\t Staphylococcus\n+1.935\t1492\t1492\t25704\t1.26\t0.07286\t1280\tspecies\t Staphylococcus aureus\n+1.414\t1090\t1090\t20177\t1.19\t0.06293\t1282\tspecies\t Staphylococcus epidermidis\n+0.01038\t8\t8\t231\t1.31\t0.0002607\t1283\tspecies\t Staphylococcus haemolyticus\n+0.007781\t6\t6\t92\t1.54\t0.0002367\t29388\tspecies\t Staphylococcus capitis\n+0.005188\t4\t4\t121\t1.34\t0.0001435\t246432\tspecies\t Staphylococcus equorum\n+0.003891\t3\t3\t197\t1.42\t0.'..b'illevirus\n+0.001297\t1\t0\t8\t1\t3.411e-05\t2315196\tno rank\t unclassified Bastillevirus\n+0.001297\t1\t1\t8\t1\t0.0009028\t2282408\tspecies\t Bacillus phage Maceta\n+0.01167\t9\t0\t944\t1.61\t2.861e-05\t2731361\tphylum\t Peploviricota\n+0.01167\t9\t0\t944\t1.61\t2.861e-05\t2731363\tclass\t Herviviricetes\n+0.01167\t9\t0\t944\t1.61\t2.861e-05\t548681\torder\t Herpesvirales\n+0.01167\t9\t0\t944\t1.61\t3.27e-05\t10292\tfamily\t Herpesviridae\n+0.01167\t9\t0\t935\t1.62\t8.081e-05\t10357\tsubfamily\t Betaherpesvirinae\n+0.01167\t9\t0\t935\t1.62\t0.0001562\t10358\tgenus\t Cytomegalovirus\n+0.01038\t8\t8\t783\t1.65\t0.0003119\t10359\tspecies\t Human betaherpesvirus 5\n+0.001297\t1\t1\t152\t1.47\t0.0003854\t47929\tspecies\t Macacine betaherpesvirus 3\n+0.1945\t150\t53\t13859\t1.21\t0.0002668\t12333\tno rank\t unclassified bacterial viruses\n+0.05058\t39\t39\t3891\t1.28\t0.186\t2716355\tspecies\t Escherichia phage 503046\n+0.02334\t18\t18\t1490\t1.29\t0.05535\t2783517\tspecies\t Escherichia phage 204576\n+0.02334\t18\t18\t3311\t1.13\t0.1106\t129862\tspecies\t Phage Gifsy-2\n+0.02205\t17\t17\t1867\t1.24\t0.05953\t129861\tspecies\t Phage Gifsy-1\n+0.002594\t2\t2\t269\t1.07\t0.01331\t2859565\tspecies\t Enterococcus phage VEsP-2\n+0.001297\t1\t1\t22\t1\t0.01401\t356350\tspecies\t Phage 258-320\n+0.001297\t1\t1\t191\t1\t0.1322\t2558708\tspecies\t Streptococcus satellite phage Javan449\n+0.001297\t1\t1\t67\t1\t0.001649\t128975\tspecies\t Salmonella phage Fels-1\n+0.006484\t5\t0\t444\t1.01\t1.139e-05\t2731342\tclade\t Monodnaviria\n+0.006484\t5\t0\t431\t1\t0.0004848\t2732090\tkingdom\t Loebvirae\n+0.006484\t5\t0\t431\t1\t0.0004848\t2732410\tphylum\t Hofneiviricota\n+0.006484\t5\t0\t431\t1\t0.0004848\t2732411\tclass\t Faserviricetes\n+0.006484\t5\t0\t431\t1\t0.0004848\t2732094\torder\t Tubulavirales\n+0.006484\t5\t3\t431\t1\t0.0005104\t10860\tfamily\t Inoviridae\n+0.001297\t1\t0\t83\t1\t0.0001515\t456491\tno rank\t unclassified Inoviridae\n+0.001297\t1\t1\t83\t1\t0.01283\t2686285\tspecies\t Pseudomonas phage pf8_ST274-AUS411\n+0.001297\t1\t0\t77\t1\t0.00601\t2732875\tgenus\t Primolicivirus\n+0.001297\t1\t1\t77\t1\t0.00601\t2011081\tspecies\t Pseudomonas virus Pf1\n+0.005188\t4\t0\t210\t2.23\t4.643e-06\t12429\tno rank\t unclassified viruses\n+0.005188\t4\t0\t210\t2.23\t5.953e-06\t2204151\tno rank\t unclassified DNA viruses\n+0.005188\t4\t0\t210\t2.23\t0.0009295\t79205\tno rank\t unclassified dsDNA phages\n+0.005188\t4\t4\t210\t2.23\t0.01276\t320831\tspecies\t Staphylococcus phage PT1028\n+0.003891\t3\t0\t150\t1.22\t5.186e-07\t2559587\tclade\t Riboviria\n+0.003891\t3\t0\t144\t1.23\t6.207e-07\t2732396\tkingdom\t Orthornavirae\n+0.002594\t2\t0\t100\t1.12\t4.316e-06\t2732405\tphylum\t Duplornaviricota\n+0.002594\t2\t0\t83\t1.1\t2.868e-05\t2732458\tclass\t Chrymotiviricetes\n+0.002594\t2\t0\t83\t1.1\t2.868e-05\t2732540\torder\t Ghabrivirales\n+0.002594\t2\t0\t83\t1.1\t3.981e-05\t11006\tfamily\t Totiviridae\n+0.002594\t2\t0\t83\t1.1\t0.0002877\t11007\tgenus\t Totivirus\n+0.002594\t2\t2\t83\t1.1\t0.002982\t11008\tspecies\t Saccharomyces cerevisiae virus L-A\n+0.001297\t1\t0\t24\t1.71\t2.937e-07\t2732408\tphylum\t Pisuviricota\n+0.001297\t1\t0\t20\t1.85\t3.197e-07\t2732506\tclass\t Pisoniviricetes\n+0.001297\t1\t0\t20\t1.85\t5.285e-07\t464095\torder\t Picornavirales\n+0.001297\t1\t0\t20\t1.85\t9.652e-07\t12058\tfamily\t Picornaviridae\n+0.001297\t1\t0\t20\t1.85\t1.591e-06\t12059\tgenus\t Enterovirus\n+0.001297\t1\t1\t20\t1.85\t1.107e-05\t138950\tspecies\t Enterovirus C\n+0.001297\t1\t0\t63\t1.35\t3.295e-06\t186616\tno rank\t environmental samples\n+0.001297\t1\t1\t16\t1.69\t1.073e-05\t340016\tspecies\t uncultured virus\n+0.6575\t507\t0\t45700\t1.63\t0.006306\t2787854\tno rank\t other entries\n+0.6575\t507\t0\t45700\t1.63\t0.006306\t28384\tno rank\t other sequences\n+0.6575\t507\t0\t45700\t1.63\t0.006306\t81077\tno rank\t artificial sequences\n+0.6575\t507\t507\t45700\t1.63\t0.006306\t32630\tspecies\t synthetic construct\n'

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/krona.k2.int.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/krona.k2.int.tsv Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,73 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diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/krona.k2.noint.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/krona.k2.noint.tsv Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,36 @@
+24 Unclassified
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diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k1.11176.children.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k1.11176.children.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,20 @@
+>C_II_XVIIIb-87/1
+TTTACCAAGAGTCCCAAATCATGATATATATATTGTCAGTGCTAGGGGGGGCATTGAGGG
+ATTATGCCAGAAGCTATGGACAATGATCTCAATTGCTACAATCCAACTTGCTGCAGCAAG
+ATCACACTGTCGTGTTGCCTGCATGGTACA
+>C_II_XVIIIb-53/1
+CACTCGGATACCCTCATTTGATATGAGTACTACTCACTACTGTTATACTCACAATGTTAT
+ACTATCTGGTTGTAGAGATCACTCACACTCACACCAATACTTAGCACTTGGTGTGCTTCG
+GGTATCTGCGACAGGGAGGGTATTCTTTTC
+>C_II_XVIIIb-37/1
+GGCTGCATTGTTGGCACATGACATAACAGTGTTTTCACTAAGGTCACCTGATATTAGCAC
+TAATTTAGATGAGTTTTTGAGGACCTGACTGAGTATTGCTCCGTCTTTGAATATTCGTTT
+GCTATATATGAAGAATGTGTCTGACCTGAT
+>C_II_XVIIIb-25/1
+ACAAATTTCGGAAGATTGAAAGGAAGATTCAGAGTCACAATACAAGGTATGGAGAATTGT
+TCACAAAGCTGTGCACACATATTGAAAAGAAATTGCTAGGATCATCTCGATCTAATAATG
+TCCCACGGTCAGAAGAATTCAGTAGCATCC
+>C_II_XVIIIb-23/1
+TCACACTGCTGGAGTTTCGATTTTGGGTGTCATCTAAATTGATAGAACGCAGAGTAGAAA
+AGAATACCCTCCCTGTCGCAGATACCCGAAGCACACCAAGTGCTAAGTATTGGTGTGAGT
+GTGAGTGATCTCTACAACCAGATAGTATAA

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k1.e10386.children.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k1.e10386.children.fa Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,252 @@\n+>C_II_XVIIIb-101/1\n+AGTGACATAGTAATGGGGGAGAGGAGGCGCATTACAGTCTTAGGAACGCAACTTACTTCC\n+TGAAGGGATTGTACTTAGCAATGGTATGTCTCTTCTCTATCTTAGTAGAGGTGACTTCAT\n+GATCAGCGGTCACTGCGACAGCGCGCTGAG\n+>C_II_XVIIIb-99/1\n+ATCCAATCACCCATTAGTCTGCTCTATTAAGTGTTCGCTGACGCTAGCAGACTATGCCCG\n+GAACAGAAGCTGGTCACCTTTGACAGGGGGTAGGAAGATACTAGGCGTATCTAATCCTGA\n+CACCATAGAACTTGTGGAAGGAGAGATTCT\n+>C_II_XVIIIb-97/1\n+TGAGTCATGCATAGAGTACGACCCCATTACCAATCTAAGCATGTTCTTAAAGGACAAGGC\n+AATCGCACATCCGAAAGATAACTGGCTCGCCTCATTCAGGCGGAACCTCCTCTCTGAGGA\n+CCAAAAGAAACAGATAAAAGAGGCGACCTC\n+>C_II_XVIIIb-95/1\n+GTCATATTCCACACTGGAGCTCATGAAAATTCTTTCAATCTCTAGCGGAAAGTTGATCGG\n+CCAATCAGTGGTTTCTTATGATGAAGATACCTCTATAAAGAATGATGCTATAATAGTGTA\n+TGACAACACACGAAATTGGATCAGTGAGGC\n+>C_II_XVIIIb-93/1\n+GTCGCAAGTTGATCTGATAGCCTTTGGTTCGACCCCGGAGGAATCTCAATGTCGCAATGC\n+AGTAATGCTACAGACCTGTGGGGCACTACAGATGTGATATATCCCACTGCTCTATCTGAA\n+GTCAGGTCGCTTTCTTCTGCATTCTCTCTC\n+>C_II_XVIIIb-91/1\n+CTTCGCCTGCCTTCCTGCATTACTATCTAACTTGGTAATAGTCTATCTTGATTGCTTATA\n+GCTAGTTCACCTGTCTATCTAATTAGAAAAAACACGGGTAGAAGAGTCTGGAACCTAACT\n+AGCACATTCTGAACGCAATATGGGCTCCAA\n+>C_II_XVIIIb-89/1\n+GGCTATTGCATGTCGGCCTGATATGGCAGTGGAGAAGGACACTGTCCGTGCATTAATCAC\n+CTCTCGCCCAATGCATCCAAGCTCCTCAGCTAAGCTCCTGAGCAAGCTGGATGCAGCCAG\n+GTCGATTGAAGAGATCAGGAAGATCAAACG\n+>C_II_XVIIIb-87/1\n+TTTACCAAGAGTCCCAAATCATGATATATATATTGTCAGTGCTAGGGGGGGCATTGAGGG\n+ATTATGCCAGAAGCTATGGACAATGATCTCAATTGCTACAATCCAACTTGCTGCAGCAAG\n+ATCACACTGTCGTGTTGCCTGCATGGTACA\n+>C_II_XVIIIb-85/1\n+TAGGTTGAACAAGCTGCAAGGGCACCCAGACGTCGGGGATGGAGAGACCCAATTCCTAGA\n+TTTTATGAGAGCAGTGGCGAACAGCGTGCGAGAAGCGTCAAATCCCGCACAAAACGTCAC\n+CCCTCTAGAGCCTCCCCCAACTCCTGGGCC\n+>C_II_XVIIIb-83/1\n+AGGTAGTTTCCCTTGGCAAGAATCAGCAAGATGCCCTAACTCATGCGTCACTGGAGTCTA\n+TACTGATCCGTATCCCTTAGTCTTCAATCGGAATCATACCCTACGAGGGGTATTCGGGAC\n+AATGCTTGATGATGGACAGGCAAGACTCAA\n+>C_II_XVIIIb-81/1\n+GGCCGCCGGCCCACTGAGTGGGGCCGCCTTCTCGGGTGCGGACGGCTGTTTGTCTGGTCT\n+GGCTTGTTGGTCGGGGGCGTCCTGGCCGGCATTTGATTGGACACTCCCGTGCTTCTCCCA\n+TGCAGTGCTCAGAGCCTTGGTCTTGCCTTG\n+>C_II_XVIIIb-79/1\n+GCTTGTAAAGCATGGACAGAAGATAGTTGCTTGCTCCGGTATTGAGCTGTATGTCGCCGG\n+CCTCGCCTGCAGCCTGGGTGGGAGAGGACTCGGTGGATGTGGCCGGCGGGTCACTGTGTT\n+GGGCCGCCTGCTCGGGTGCGGACGGCTGTT\n+>C_II_XVIIIb-77/1\n+TGCTAGGAAGATGAAAGCACGTAACCTTCTCATCTCCACTGTCACACTTTGTGCACCCTC\n+CACTGACACTGAGAATCTCTCCTTCCACAAGTTCTATGGTGTCAGGATTAGATACGCCTA\n+GTATCTTCCTACCCCCTGTCAAAGGTGACC\n+>C_II_XVIIIb-75/1\n+CAATCTGGATGATAACGGACTAGCGCCCGGAGATGACTTAAGGATGAAATGTTGGCGCAA\n+CCGGGGTCCAGAATTTTCATCATGCCTAAGTTGGCTTCCATGATCGCAACAGATGTTTTA\n+AGCTGTTGGATTTCAGACCGCATCATAGGG\n+>C_II_XVIIIb-73/1\n+CAGACGCGGAATGCTCAGCAGTCACTCAATACCTATTGTCGGATGCTGTGAGACCATTGC\n+TTAGGTCGGAACAAGTGAACTCTATCATATCTCCCAACATAATCACATTTCCCGCCAATC\n+TATATTACATGTCCAGGAAGAGTCTTAATC\n+>C_II_XVIIIb-71/1\n+GGGTTAACTCTGAGGCTCAGGGGAGAATGTGATGCAACTTATCAAAAGGATATCTCAATA\n+TTAGATTCTCAAGTCATCGTGACCGGCAATCTCGTTATATCAACTGAGCTTGGAAATGTC\n+AACAATTCAATAAGCAATGCCTTGGATAAG\n+>C_II_XVIIIb-69/1\n+CTTAAAGCTAGTTCACCTGTCTATCTAATTAGAAAAAACACGGGTAGAAGAGTCTGGAAC\n+CTAACTAGCACATTCTGAACGCAATATGGGCTCCAAACCTTCTACCAGGATTCCAGTACC\n+TCTGATGCTGATCATTCGGACTATGCTGAT\n+>C_II_XVIIIb-67/1\n+CTATCTCGGCATCTGTAGCGGTGGCCATCTTCACACTAATCTACTAGGTAGAAGAGAGAA\n+CAGAGACTTTGGTGACTCGTCCTGGTCTCCAGGTGTCTCCCTTCTACCCGTATTTTTTTC\n+TAATACCTCGGGCTCTGAGTGGATTGTTGG\n+>C_II_XVIIIb-65/1\n+ACCCCCACCTGTTGAGTAGGAATATCCATGCAGCCAATTTCTTCAGACACTCGTTGGGCA\n+GCAGCCGCCAGACCTCTCCTTGCTGCCGGAGTCAGTTTTAGTTCAGCAGCCATGTCTTCA\n+TTGATGCTACTTCCCTGAGCCTGAGCATAC\n+>C_II_XVIIIb-63/1\n+GTATGATCCTAGGCCTACGTCAGAAAAGGATCGTGCAAGATTCGACTTAGCTATCTTCAA\n+GAGTTATGAGCTTAATTTGGAGTCATATTCCACACTGGAGCTGATGAACATTCTTTCAAT\n+CTCTAGCGGAAAGTTGATCGGCCAATCAGT\n+>C_II_XVIIIb-61/1\n+GCTGATGAACATTTTGACAATCCCTATCGGAACGTTGATCGGCCAATCAGTGGTTTCTTA\n+TGATGAAGATCCCTCTATAAAGAATGATGCTATAATAGTGTATGACAACACACGAAATTG\n+GATCAGTGAGGCCCAGAATTCAGATGTGGT\n+>C_II_XVIIIb-59/1\n+TACCACAAGAGTTCATCTGCCCTCGAATTTGAGACATGCATAGAGTATGACCCCGTTACC\n+AATCTAAGCATGTTCTTAAAGGACAAGGCAATCGCACATCCGAAAGATAACTGGCTCGCC\n+TCATTCAGGCGGAACCTCCTCTCTGAGGAC\n+>C_II_XVIIIb-57/1\n+CGGGAGCCCAGTTAATTTCCAGTAATAGAGCAACTTGTGCTTGACCAATGGAGAGGATAG\n+ATGTGACTCTGGTAGGATAATCTGGTGCTCTGCCCTTTCGGGACCAGA'..b'TATAA\n+>C_II_XVIIIb-21/1\n+TTCTCTGAACGTTCGACCCGTAGATTGCTGCTTAGTTTCTTATACCCGTCAGTTTTTTCT\n+TGAGTTTTCGATCTGACAGGCTGTCAGAATTGACATACAGGCTGCTGCTGTATGTGCATC\n+CAATTCTCATTTGCGGTCATGCTCTTGTAT\n+>C_II_XVIIIb-19/1\n+GGCACAGACGCGAACAGAGCTTGTCATGGACTATGGAAGGAGTCACAACCATCAGCTGGT\n+GCAACCCCTCATGTGCCCCAGTCAGGGCAGAACCAAGACAATACTCCTGCACCTGTGGAT\n+CATGTCCAGCTACCTGTCGACTTTGTGCAA\n+>C_II_XVIIIb-17/1\n+GAATTTGAATCTGTGAGGCCCAGAATTCAGATGTGGTCCGCTTATTCGAATATGCGGCAC\n+TCGAGGTGCTCCTTGACTGTTCTTACCAACTCTACTATCTGAGAGTGAGAGGCCTAAACA\n+ACATCGTCTTATACATGAGTGACCTATACA\n+>C_II_XVIIIb-15/1\n+TGAGCCGCGATCTTAAAAGCCGAGGATAAGTTCACGACTTTGCTCAGTTCTAGCCAAGAT\n+GTGACAGATAGGATATATAAACAGGTGGCTCTTGAATCTCCGCTAGCGCTACTAAACACC\n+GAATCTATAATTATGAATGCAATAACATCC\n+>C_II_XVIIIb-13/1\n+CCTCACAGTAGCGTCTTGTGAACGACATTCTATCCAGTCCCCTACCGAGGCTGATGAAGT\n+TCTTGGGAGAAAATATTGATGCTGCACTGATCGCAGCAGGGGGACAGCCCGTCCGTCCCT\n+TTTGTGCAGAAAGTTTGGTGAGCACACTAA\n+>C_II_XVIIIb-11/1\n+TGTGCACGGTTTAATTGACGTCATCTTTTTCCCGTCTGTAGAGAGGTTATAAGGAGTAAA\n+TAAGAATACTGTGTCAGCAAGGTCCCCCTCGGCATCCATGTAGATCACAGATCTAATGAC\n+TGTGTCAATGTGGCTGGCAATTATCTGAGT\n+>C_II_XVIIIb-9/1\n+GACTAATCATGTCAGTGTCGTTAGACTGTGCCTACCCGGCAGCACGGGATCTGGGCTTGT\n+GTTGATATTCAGTTTGACTCTTGGCATCGCGAAAGATATTCAGTGCCACATCATTCTTCC\n+AGCCGTCCTATGGCTGACTCAATTGGCTGG\n+>C_II_XVIIIb-7/1\n+GCCATGGTGATTAAGCAGTTCCTAATCCTCTGAACAAGTATCGTACTAAGTAATCTTCCT\n+TTGGGTTTGGTAGTGTGTGCTCGGGGCAAATCTCGCTAAGCGTAAATGCATCATACCTTG\n+CTGGAGCAGTCAAATCTAGCTCTTGTATAA\n+>C_II_XVIIIb-5/1\n+TAGAAACTATTATAGCATCATTGTTTTTATAGGTATCTTCATCATAAGAAACCACTGATT\n+GGCCGATCAACTTTCCGCTAGAGATTGAAAGAATGTTCATCAGCTCCAGTGTGGAATATG\n+ACTCCAAATTAAGCTCATAACTCTTGAAGA\n+>C_II_XVIIIb-3/1\n+CAGATAAAAGAGACGACCCTAACTTATCGCCTCTTGATTGAGTTTTTAGAATCAAATGAT\n+TTTGATCCATACAAGGAGATGGAATACTTGACAACCCTTGAGTACCTAAGAGATGACAGT\n+GTGGCAGTATCATATTCACTTAAAGAGAAG\n+>C_II_XVIIIb-1/1\n+CTTGCTCATTGGCTCATGATTGCGGTTTGTGGAAACTCTCTCTTTGCAGTCGGTGATACG\n+TTTCTTATTGCTGTTGAAGGACAGTTGACTCATTGCCAACATACTCTTAGTCAAGGATAT\n+GCTATCTTGAATGACCCCATTTCCTTGGAA\n+>HQ630064-957/1\n+CAAAGCAAATTTTGTAGCTTAAGATAAAGGGGGCCCTAAAGAAGAAGCAACATCGTCTCG\n+GGCTGTGTTTCCGACGTTGGGGTGCATTATGCGATTTTACTACCAGTGTTTGGTGTGGTG\n+TGGTAAGGGGAAATGAGACGAGAATTTTTC\n+>HQ630064-665/1\n+CCCCGGGAGCTTTTTAGCGCGGCGTCACGTATAAATGCACAGAAGCTTCGTCAGTAACGA\n+AGCGCCTCTGCCAGAGTTATTAACATTAGGACTCGAGAGAGTCTCGAGAAGAGACTTCCC\n+AAAGAGAGTGCCGCTTTGATCTCCAGATCA\n+>HQ630064-403/1\n+TGTCTACCTGTCTGTCAAATTGTGACTACCACGTACCAACTCCTCCCCAAAGTTCTACCC\n+TTTTCCTTAAAAACACATTTAAAATGTCAAAATACCGATCCTTATATTTGTGTGTTATGT\n+TTTCTTTTGCCTTCTAGGATTGATTGAATT\n+>HQ630064-343/1\n+ACGAAAGAAAGAAAGGAAAAGGCCTCAAAGTTAATTTTGTAGCTTAAAAAAGAGGGGGCC\n+CTAAAGAAGAAGCAACATCGTCTCGGGCTGTGTTTCCGACGTTGGGGTGCATTATGCGAT\n+TTTACTACCAGTGTTTGGTGTGGTGTGGTA\n+>HQ630064-307/1\n+TCGTGTGTTTGCTCGCGTGCTTTGGATGTTGGGATGAGGCCTTGGTGTTGCCAGGCTCCG\n+GTTTCTTAAAGGTTATCCGAGGGGGAAGTTCCACGTGTTCTTTTAGCTTTTCTCCATATT\n+CCGGTCTACGGGTACAAATGTCCTCTGGAT\n+>HQ630064-241/1\n+CGTGACCTCATTTACAAGATGTCGGTGGCACCCAGCTACGTCACGTTCGCACCGAGGGTC\n+CAACATTTTCCTAAAATGGCAAAGCGGGACTTGGGTCCGTGGGTAAATTTTCTAATTTTT\n+TCCCACGGTCTGTCGCAAGAGCGTATTCTC\n+>HQ630064-217/1\n+AACTTTGGGGAGGAATTGGTACGTGGTAGACACAATTTGACAGACAGGTAGACAGACAAC\n+GAATTACAAGCGGCCTAGGGTAATAGCGCTGAGCCCATGATGTGTCCGTGCATATGAGAC\n+GACTAATAAGGTAGTCACGTAAACCCCCGT\n+>HQ630064-199/1\n+AGAAGCAGTATTGTGATCTTTCTCTCTTTCGCATGAATCGCTAGGAAGAGGAATTTTGGA\n+AGCATCTGGATACCTTACAGGAGATTTAGAAATCTCGGTAGTTATGACATGTTCATCAGA\n+TGAGGAAGATAGCAAGCGTGACGGTGTTTT\n+>HQ630064-111/1\n+GTGTCTCCGAGTTGTGCTCTCTCGAAACTCACTTTGCCCTCACTTGTTGGCTTTATGGAG\n+GTCGTAATGATCATCGATGGAGTACTTATATAATATTGTGCTCTGCCGGCCATCTCTCCG\n+TGGTCGCAGAACTCCAACACCTTGTTGGCG\n+>HQ630064-105/1\n+AGTTTAAACTTTGTCCGCGCGCCAATCTTGAAGTGATATTAGGACATAGTCAACCAACCG\n+ACGTACGTTGAACCATTTGCGGGCAGCGCTGAGGGAAGACGAGATGTATGGACAACACAA\n+CGACCGGAGAAGAGGGCGTAAAGAACATCA\n+>HQ630064-11/1\n+GAAAGAAAGAAAGGAAAAGGCCTCAAAGCAAATTTTGTAGCTTAAAAAAGAGGGGGCCCT\n+AAAGAAGAAGCAACATCGTCTCGGGCTGTGTTTCCGACGTTGGGGTGCATTATGCGATTT\n+TACTACCAGTGTTTGGTGTGGTGTGGTAAG\n+>HQ630064-3/1\n+AGGACTGTCGCTCATATCTTGCGTACTGTGTCTTATTTACTCGTGTTGTCTTTCCGCAGG\n+GAATGCGCGGTTCGAGTAGGCCGTGGTTTGCGGCCGTTCTCGGATAAGCACAAAATATCG\n+CCCTACTCGTGTGTCAAAAAGGAAAAGTCT\n'

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k2.11176.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k2.11176.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,28 @@
+>C_II_XVIIIb-65/1
+ACCCCCACCTGTTGAGTAGGAATATCCATGCAGCCAATTTCTTCAGACACTCGTTGGGCA
+GCAGCCGCCAGACCTCTCCTTGCTGCCGGAGTCAGTTTTAGTTCAGCAGCCATGTCTTCA
+TTGATGCTACTTCCCTGAGCCTGAGCATAC
+>C_II_XVIIIb-57/1
+CGGGAGCCCAGTTAATTTCCAGTAATAGAGCAACTTGTGCTTGACCAATGGAGAGGATAG
+ATGTGACTCTGGTAGGATAATCTGGTGCTCTGCCCTTTCGGGACCAGAGCCTGCCATGTC
+CTACCCGTGCTTTCTTTTGTGTGTTGGTTT
+>C_II_XVIIIb-49/1
+ATTTAGATCCATACAATGAGATGGAATCTTTGACAACCCTTGAGTACCTAAGAGATGACA
+GTGTGGCAGTATCATATTCACTTAAAGAGAAGGAGGTGAAAGTGAATGGGCGAATTTTTG
+CTAAGTTGACAAAGAAGCTAAGGAACTGCC
+>C_II_XVIIIb-45/1
+GAGAAGATAGTTGATTGGTGTGTGATTGCCTGTAAGAGTCATTGTTACTGTAATATCCCT
+TTGCTGCATTACCTATGGTTTTCATGTAGAATTTTTGTTGAGCACGAGTTAAATAGAGTG
+AAGAGGTATCTGTAAATATTTCTTTGAGTT
+>C_II_XVIIIb-17/1
+GAATTTGAATCTGTGAGGCCCAGAATTCAGATGTGGTCCGCTTATTCGAATATGCGGCAC
+TCGAGGTGCTCCTTGACTGTTCTTACCAACTCTACTATCTGAGAGTGAGAGGCCTAAACA
+ACATCGTCTTATACATGAGTGACCTATACA
+>C_II_XVIIIb-9/1
+GACTAATCATGTCAGTGTCGTTAGACTGTGCCTACCCGGCAGCACGGGATCTGGGCTTGT
+GTTGATATTCAGTTTGACTCTTGGCATCGCGAAAGATATTCAGTGCCACATCATTCTTCC
+AGCCGTCCTATGGCTGACTCAATTGGCTGG
+>C_II_XVIIIb-1/1
+CTTGCTCATTGGCTCATGATTGCGGTTTGTGGAAACTCTCTCTTTGCAGTCGGTGATACG
+TTTCTTATTGCTGTTGAAGGACAGTTGACTCATTGCCAACATACTCTTAGTCAAGGATAT
+GCTATCTTGAATGACCCCATTTCCTTGGAA

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k2.11176.fq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k2.11176.fq Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,28 @@
+@C_II_XVIIIb-65/1
+ACCCCCACCTGTTGAGTAGGAATATCCATGCAGCCAATTTCTTCAGACACTCGTTGGGCAGCAGCCGCCAGACCTCTCCTTGCTGCCGGAGTCAGTTTTAGTTCAGCAGCCATGTCTTCATTGATGCTACTTCCCTGAGCCTGAGCATAC
++
+G9;G*GGG3GGG*GGF+G#GFG*<G#GD,EB#GGGGFGGGGC8GCG:FGDGFC5G7AGGFGGGGFEGGGGCGDE@G>DGGGGFGGGGGG77FGGG,GGGGFGCGGFG>GGGGCFGGAGGG7GGGGGGGGGGGEGGEGGF<EFGGGF,GFG
+@C_II_XVIIIb-57/1
+CGGGAGCCCAGTTAATTTCCAGTAATAGAGCAACTTGTGCTTGACCAATGGAGAGGATAGATGTGACTCTGGTAGGATAATCTGGTGCTCTGCCCTTTCGGGACCAGAGCCTGCCATGTCCTACCCGTGCTTTCTTTTGTGTGTTGGTTT
++
+FGGGF#GFEGGGG,FE,GGGFGCGGGEG+FCGE#?G:EEGA9FGEGDGGCDFGGGGFF<GGGC:GGGGGD7GFGGGFG*A7EGGGFG@GGGFGGGGEFGGGGGGGGFGGFGGGCGFGGGGGGGGGGGGGGGGGG:GGGGGGGGGGGFGGG
+@C_II_XVIIIb-49/1
+ATTTAGATCCATACAATGAGATGGAATCTTTGACAACCCTTGAGTACCTAAGAGATGACAGTGTGGCAGTATCATATTCACTTAAAGAGAAGGAGGTGAAAGTGAATGGGCGAATTTTTGCTAAGTTGACAAAGAAGCTAAGGAACTGCC
++
+CGG9#G<:AG:GG?G@#0E#6:EGGGF##G=GGGGGG=GG<CFGGGDGCGGGG9GGGGGG7CFGGCEGFCFGFGFGGGGGD+C9=CGGGGGGGGFGGGFFGGGGCGGGG9GG<GGCGGGFGGGEEC,EGGG@GCGGCGGGGGGGGCGFGG
+@C_II_XVIIIb-45/1
+GAGAAGATAGTTGATTGGTGTGTGATTGCCTGTAAGAGTCATTGTTACTGTAATATCCCTTTGCTGCATTACCTATGGTTTTCATGTAGAATTTTTGTTGAGCACGAGTTAAATAGAGTGAAGAGGTATCTGTAAATATTTCTTTGAGTT
++
+GGGGFGFDG>:FGFF*;GCGG#?GGEGFEGC#G<G<GEGGGGFGFGGGGGFGGGFG1C+G9FGGGFGGGGFECGGGGCGC+GGGG9G+DGGFGGGGGGGGCCDFGGGCGGFG:GG4*F8EGGGGGG7GDGGG7GGGGFGGGCGG=E,=G<
+@C_II_XVIIIb-17/1
+GAATTTGAATCTGTGAGGCCCAGAATTCAGATGTGGTCCGCTTATTCGAATATGCGGCACTCGAGGTGCTCCTTGACTGTTCTTACCAACTCTACTATCTGAGAGTGAGAGGCCTAAACAACATCGTCTTATACATGAGTGACCTATACA
++
+GEG#*#F#GGG*G=EG9GG*FGE#GGGGCFGCGFE9GGCGG+GFF5EGG*GDG@EGGGEGG6FFGGGGGGGEG?GGCGGGGF<GGFGGFGGGGFACGG@GCGGGGFGG4FGGGGGGGGGGGG9C?CFGGGGGGEGGGGFGGGF:GGGGGG
+@C_II_XVIIIb-9/1
+GACTAATCATGTCAGTGTCGTTAGACTGTGCCTACCCGGCAGCACGGGATCTGGGCTTGTGTTGATATTCAGTTTGACTCTTGGCATCGCGAAAGATATTCAGTGCCACATCATTCTTCCAGCCGTCCTATGGCTGACTCAATTGGCTGG
++
+ECGGGF1CG:5GCG?)G>#GG6EFE#GG58#GGGFGGGGCGCGFBCGGGGGFGDG@FGGGGGCFGGGCFGFD8CGDFGDGGGACDGFGFGGGG:FGG>GGGG>GGGCFGG4GGCBGGGGFFGEGGGGGGGGGGGGGGGGGGGG:GGGGGG
+@C_II_XVIIIb-1/1
+CTTGCTCATTGGCTCATGATTGCGGTTTGTGGAAACTCTCTCTTTGCAGTCGGTGATACGTTTCTTATTGCTGTTGAAGGACAGTTGACTCATTGCCAACATACTCTTAGTCAAGGATATGCTATCTTGAATGACCCCATTTCCTTGGAA
++
+GFFGG@G#G#GG#GGGC;EGGGGGGE#FG#+GGGGG*GGGGDGGGFCFGG8CCGG1FGGEGGGFGGGGGF*GGGCGGFGGGGG/GF:EGGGGFF@GGG*GE+DGGGFGGCGGGGGGGG@GDGGGGG,GF,CG4FFGGGGFGGGGCFGGGG

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k2.11176.max2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k2.11176.max2.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,8 @@
+>C_II_XVIIIb-65/1
+ACCCCCACCTGTTGAGTAGGAATATCCATGCAGCCAATTTCTTCAGACACTCGTTGGGCA
+GCAGCCGCCAGACCTCTCCTTGCTGCCGGAGTCAGTTTTAGTTCAGCAGCCATGTCTTCA
+TTGATGCTACTTCCCTGAGCCTGAGCATAC
+>C_II_XVIIIb-57/1
+CGGGAGCCCAGTTAATTTCCAGTAATAGAGCAACTTGTGCTTGACCAATGGAGAGGATAG
+ATGTGACTCTGGTAGGATAATCTGGTGCTCTGCCCTTTCGGGACCAGAGCCTGCCATGTC
+CTACCCGTGCTTTCTTTTGTGTGTTGGTTT

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k2.11176.parents.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k2.11176.parents.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,76 @@
+>C_II_XVIIIb-99/1
+ATCCAATCACCCATTAGTCTGCTCTATTAAGTGTTCGCTGACGCTAGCAGACTATGCCCG
+GAACAGAAGCTGGTCACCTTTGACAGGGGGTAGGAAGATACTAGGCGTATCTAATCCTGA
+CACCATAGAACTTGTGGAAGGAGAGATTCT
+>C_II_XVIIIb-97/1
+TGAGTCATGCATAGAGTACGACCCCATTACCAATCTAAGCATGTTCTTAAAGGACAAGGC
+AATCGCACATCCGAAAGATAACTGGCTCGCCTCATTCAGGCGGAACCTCCTCTCTGAGGA
+CCAAAAGAAACAGATAAAAGAGGCGACCTC
+>C_II_XVIIIb-93/1
+GTCGCAAGTTGATCTGATAGCCTTTGGTTCGACCCCGGAGGAATCTCAATGTCGCAATGC
+AGTAATGCTACAGACCTGTGGGGCACTACAGATGTGATATATCCCACTGCTCTATCTGAA
+GTCAGGTCGCTTTCTTCTGCATTCTCTCTC
+>C_II_XVIIIb-87/1
+TTTACCAAGAGTCCCAAATCATGATATATATATTGTCAGTGCTAGGGGGGGCATTGAGGG
+ATTATGCCAGAAGCTATGGACAATGATCTCAATTGCTACAATCCAACTTGCTGCAGCAAG
+ATCACACTGTCGTGTTGCCTGCATGGTACA
+>C_II_XVIIIb-85/1
+TAGGTTGAACAAGCTGCAAGGGCACCCAGACGTCGGGGATGGAGAGACCCAATTCCTAGA
+TTTTATGAGAGCAGTGGCGAACAGCGTGCGAGAAGCGTCAAATCCCGCACAAAACGTCAC
+CCCTCTAGAGCCTCCCCCAACTCCTGGGCC
+>C_II_XVIIIb-75/1
+CAATCTGGATGATAACGGACTAGCGCCCGGAGATGACTTAAGGATGAAATGTTGGCGCAA
+CCGGGGTCCAGAATTTTCATCATGCCTAAGTTGGCTTCCATGATCGCAACAGATGTTTTA
+AGCTGTTGGATTTCAGACCGCATCATAGGG
+>C_II_XVIIIb-65/1
+ACCCCCACCTGTTGAGTAGGAATATCCATGCAGCCAATTTCTTCAGACACTCGTTGGGCA
+GCAGCCGCCAGACCTCTCCTTGCTGCCGGAGTCAGTTTTAGTTCAGCAGCCATGTCTTCA
+TTGATGCTACTTCCCTGAGCCTGAGCATAC
+>C_II_XVIIIb-57/1
+CGGGAGCCCAGTTAATTTCCAGTAATAGAGCAACTTGTGCTTGACCAATGGAGAGGATAG
+ATGTGACTCTGGTAGGATAATCTGGTGCTCTGCCCTTTCGGGACCAGAGCCTGCCATGTC
+CTACCCGTGCTTTCTTTTGTGTGTTGGTTT
+>C_II_XVIIIb-49/1
+ATTTAGATCCATACAATGAGATGGAATCTTTGACAACCCTTGAGTACCTAAGAGATGACA
+GTGTGGCAGTATCATATTCACTTAAAGAGAAGGAGGTGAAAGTGAATGGGCGAATTTTTG
+CTAAGTTGACAAAGAAGCTAAGGAACTGCC
+>C_II_XVIIIb-45/1
+GAGAAGATAGTTGATTGGTGTGTGATTGCCTGTAAGAGTCATTGTTACTGTAATATCCCT
+TTGCTGCATTACCTATGGTTTTCATGTAGAATTTTTGTTGAGCACGAGTTAAATAGAGTG
+AAGAGGTATCTGTAAATATTTCTTTGAGTT
+>C_II_XVIIIb-43/1
+CCAGATAGTATAACATTGTGAGGATAACAGTAGTGAGTAGTACTCATATCAAATGAGGGT
+ATCCGAGTGCAACCAGACCCTGTAGTAGGGGCCGGGATAAAATTCAAGTGTTCTTGATAT
+GCGGAAGGATAAAATGATGTGACATCACTG
+>C_II_XVIIIb-33/1
+TCCGAACCCAGCATATTCTGGAATATGGAAACAGTCACAACCATCAGCTGGTGCAACCCC
+TCATGTGCCCCAGTCAGGGCAGAACCAAGACAATACTCCTGCACCTGTGGATCATGTCCA
+GCTACCTGTCGACTTTGTGCAAATGATGAT
+>C_II_XVIIIb-29/1
+TTTCCATGCTTGACAAGCTGAGCAATAATTCGTCCAATGCTAAAAAGGGCCCAAGGTCAG
+GCCCCCAAGAAGGGCACCATCAACCTCCGGTCCCACAACAAGGGAACCAGCCGAGCCATG
+GAAGCAACCAGGAAAGACCGCAGCACCAGG
+>C_II_XVIIIb-19/1
+GGCACAGACGCGAACAGAGCTTGTCATGGACTATGGAAGGAGTCACAACCATCAGCTGGT
+GCAACCCCTCATGTGCCCCAGTCAGGGCAGAACCAAGACAATACTCCTGCACCTGTGGAT
+CATGTCCAGCTACCTGTCGACTTTGTGCAA
+>C_II_XVIIIb-17/1
+GAATTTGAATCTGTGAGGCCCAGAATTCAGATGTGGTCCGCTTATTCGAATATGCGGCAC
+TCGAGGTGCTCCTTGACTGTTCTTACCAACTCTACTATCTGAGAGTGAGAGGCCTAAACA
+ACATCGTCTTATACATGAGTGACCTATACA
+>C_II_XVIIIb-9/1
+GACTAATCATGTCAGTGTCGTTAGACTGTGCCTACCCGGCAGCACGGGATCTGGGCTTGT
+GTTGATATTCAGTTTGACTCTTGGCATCGCGAAAGATATTCAGTGCCACATCATTCTTCC
+AGCCGTCCTATGGCTGACTCAATTGGCTGG
+>C_II_XVIIIb-5/1
+TAGAAACTATTATAGCATCATTGTTTTTATAGGTATCTTCATCATAAGAAACCACTGATT
+GGCCGATCAACTTTCCGCTAGAGATTGAAAGAATGTTCATCAGCTCCAGTGTGGAATATG
+ACTCCAAATTAAGCTCATAACTCTTGAAGA
+>C_II_XVIIIb-3/1
+CAGATAAAAGAGACGACCCTAACTTATCGCCTCTTGATTGAGTTTTTAGAATCAAATGAT
+TTTGATCCATACAAGGAGATGGAATACTTGACAACCCTTGAGTACCTAAGAGATGACAGT
+GTGGCAGTATCATATTCACTTAAAGAGAAG
+>C_II_XVIIIb-1/1
+CTTGCTCATTGGCTCATGATTGCGGTTTGTGGAAACTCTCTCTTTGCAGTCGGTGATACG
+TTTCTTATTGCTGTTGAAGGACAGTTGACTCATTGCCAACATACTCTTAGTCAAGGATAT
+GCTATCTTGAATGACCCCATTTCCTTGGAA

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out1.k2.exclude_both.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out1.k2.exclude_both.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,176 @@
+>C_II_XVIIIb-101/1
+AGTGACATAGTAATGGGGGAGAGGAGGCGCATTACAGTCTTAGGAACGCAACTTACTTCC
+TGAAGGGATTGTACTTAGCAATGGTATGTCTCTTCTCTATCTTAGTAGAGGTGACTTCAT
+GATCAGCGGTCACTGCGACAGCGCGCTGAG
+>C_II_XVIIIb-95/1
+GTCATATTCCACACTGGAGCTCATGAAAATTCTTTCAATCTCTAGCGGAAAGTTGATCGG
+CCAATCAGTGGTTTCTTATGATGAAGATACCTCTATAAAGAATGATGCTATAATAGTGTA
+TGACAACACACGAAATTGGATCAGTGAGGC
+>C_II_XVIIIb-91/1
+CTTCGCCTGCCTTCCTGCATTACTATCTAACTTGGTAATAGTCTATCTTGATTGCTTATA
+GCTAGTTCACCTGTCTATCTAATTAGAAAAAACACGGGTAGAAGAGTCTGGAACCTAACT
+AGCACATTCTGAACGCAATATGGGCTCCAA
+>C_II_XVIIIb-89/1
+GGCTATTGCATGTCGGCCTGATATGGCAGTGGAGAAGGACACTGTCCGTGCATTAATCAC
+CTCTCGCCCAATGCATCCAAGCTCCTCAGCTAAGCTCCTGAGCAAGCTGGATGCAGCCAG
+GTCGATTGAAGAGATCAGGAAGATCAAACG
+>C_II_XVIIIb-83/1
+AGGTAGTTTCCCTTGGCAAGAATCAGCAAGATGCCCTAACTCATGCGTCACTGGAGTCTA
+TACTGATCCGTATCCCTTAGTCTTCAATCGGAATCATACCCTACGAGGGGTATTCGGGAC
+AATGCTTGATGATGGACAGGCAAGACTCAA
+>C_II_XVIIIb-81/1
+GGCCGCCGGCCCACTGAGTGGGGCCGCCTTCTCGGGTGCGGACGGCTGTTTGTCTGGTCT
+GGCTTGTTGGTCGGGGGCGTCCTGGCCGGCATTTGATTGGACACTCCCGTGCTTCTCCCA
+TGCAGTGCTCAGAGCCTTGGTCTTGCCTTG
+>C_II_XVIIIb-79/1
+GCTTGTAAAGCATGGACAGAAGATAGTTGCTTGCTCCGGTATTGAGCTGTATGTCGCCGG
+CCTCGCCTGCAGCCTGGGTGGGAGAGGACTCGGTGGATGTGGCCGGCGGGTCACTGTGTT
+GGGCCGCCTGCTCGGGTGCGGACGGCTGTT
+>C_II_XVIIIb-77/1
+TGCTAGGAAGATGAAAGCACGTAACCTTCTCATCTCCACTGTCACACTTTGTGCACCCTC
+CACTGACACTGAGAATCTCTCCTTCCACAAGTTCTATGGTGTCAGGATTAGATACGCCTA
+GTATCTTCCTACCCCCTGTCAAAGGTGACC
+>C_II_XVIIIb-73/1
+CAGACGCGGAATGCTCAGCAGTCACTCAATACCTATTGTCGGATGCTGTGAGACCATTGC
+TTAGGTCGGAACAAGTGAACTCTATCATATCTCCCAACATAATCACATTTCCCGCCAATC
+TATATTACATGTCCAGGAAGAGTCTTAATC
+>C_II_XVIIIb-71/1
+GGGTTAACTCTGAGGCTCAGGGGAGAATGTGATGCAACTTATCAAAAGGATATCTCAATA
+TTAGATTCTCAAGTCATCGTGACCGGCAATCTCGTTATATCAACTGAGCTTGGAAATGTC
+AACAATTCAATAAGCAATGCCTTGGATAAG
+>C_II_XVIIIb-69/1
+CTTAAAGCTAGTTCACCTGTCTATCTAATTAGAAAAAACACGGGTAGAAGAGTCTGGAAC
+CTAACTAGCACATTCTGAACGCAATATGGGCTCCAAACCTTCTACCAGGATTCCAGTACC
+TCTGATGCTGATCATTCGGACTATGCTGAT
+>C_II_XVIIIb-67/1
+CTATCTCGGCATCTGTAGCGGTGGCCATCTTCACACTAATCTACTAGGTAGAAGAGAGAA
+CAGAGACTTTGGTGACTCGTCCTGGTCTCCAGGTGTCTCCCTTCTACCCGTATTTTTTTC
+TAATACCTCGGGCTCTGAGTGGATTGTTGG
+>C_II_XVIIIb-63/1
+GTATGATCCTAGGCCTACGTCAGAAAAGGATCGTGCAAGATTCGACTTAGCTATCTTCAA
+GAGTTATGAGCTTAATTTGGAGTCATATTCCACACTGGAGCTGATGAACATTCTTTCAAT
+CTCTAGCGGAAAGTTGATCGGCCAATCAGT
+>C_II_XVIIIb-61/1
+GCTGATGAACATTTTGACAATCCCTATCGGAACGTTGATCGGCCAATCAGTGGTTTCTTA
+TGATGAAGATCCCTCTATAAAGAATGATGCTATAATAGTGTATGACAACACACGAAATTG
+GATCAGTGAGGCCCAGAATTCAGATGTGGT
+>C_II_XVIIIb-59/1
+TACCACAAGAGTTCATCTGCCCTCGAATTTGAGACATGCATAGAGTATGACCCCGTTACC
+AATCTAAGCATGTTCTTAAAGGACAAGGCAATCGCACATCCGAAAGATAACTGGCTCGCC
+TCATTCAGGCGGAACCTCCTCTCTGAGGAC
+>C_II_XVIIIb-55/1
+AAGTGATCTCCGGGCGATAGTCCGATCTCATCAAGTTTTAATTTCGGGCCCTGGAGACCC
+ATCTCCTTATGTGACACAAGGGGGTGAAATGACACTCAATAAACTCTCACAACCGGTACA
+GCACCCTTCAGAGCTAGTTAAATCTGCTAC
+>C_II_XVIIIb-53/1
+CACTCGGATACCCTCATTTGATATGAGTACTACTCACTACTGTTATACTCACAATGTTAT
+ACTATCTGGTTGTAGAGATCACTCACACTCACACCAATACTTAGCACTTGGTGTGCTTCG
+GGTATCTGCGACAGGGAGGGTATTCTTTTC
+>C_II_XVIIIb-51/1
+GATCCGATCTCGTGTGTTGTCATACACTATTATAGCATCATTCTTTATAGAGGTATCTTC
+ATCATAAGAGACCACTGATTGGCCGATCAACTTTCCGCTAGAGATTGAAAGAATGTTCAT
+CAGCTCCAGTGTGGAATATGACTCCAAATT
+>C_II_XVIIIb-47/1
+ATAACCTGTGGCTCTGCCCTGTCGGGACTAGAGCCTGCCATGTCCTACCCGTGCTTTCTT
+TTGTGTGTTGGTTTCCTTTATATCTCAATGCTTTTTTTATTTTTTCTTAATAAAGTGGCC
+AAAAACAGGACTCAGACTAATCATGTCAGT
+>C_II_XVIIIb-41/1
+ACTTAGGCATGATGGAAAATCGCGACGCCGGCGGCGCCAACATTTCATCCTTAAGTGATC
+TCCGGGCGGTAGCCCGATCTCATCCAGTTTTAATTTCGGGCCCTGGAGACCCATCTCCTT
+ATGTGACACAAGGGGGTGAAATGACACTCA
+>C_II_XVIIIb-39/1
+TCCTCAGGGAGGAGGTTTCGCCTGAATGAGGCGAGCCAGTTATCTTTCGGATGTGCGATT
+GCCTTGTCCTTTAAGAACATGCTTAGATTGGTAACGGGGTCATACTCTATGCATGGCTCA
+AATTCGAGGGCAGATAAACTCTTGTACTCT
+>C_II_XVIIIb-37/1
+GGCTGCATTGTTGGCACATGACATAACAGTGTTTTCACTAAGGTCACCTGATATTAGCAC
+TAATTTAGATGAGTTTTTGAGGACCTGACTGAGTATTGCTCCGTCTTTGAATATTCGTTT
+GCTATATATGAAGAATGTGTCTGACCTGAT
+>C_II_XVIIIb-35/1
+GCGCTAGGCCGAAGCTCGAATCTTAGGGCACCTTCTACCGATATGTTGTCTGTCTTCGAC
+GAATACGAGCAGCTCCTCGCTGCCCAGACCCGTCCTAACGGAACTCACGGAGGAGGAGAG
+AAAGGGAGCACTTTAAAAGTTGAAGTCCCA
+>C_II_XVIIIb-31/1
+GCAGAAGTCAGGCGAATAGAAGAAGTGGGGGTGCTAAGTCCTAGTATTATGACCAACATC
+TTAACTAGGCCACCAGGCAATGGAGACTGGGCCAGCCTGTGCAACGACCCTTATTCCTTT
+AACTTTGAGACTGTTGCAAGCCCAAATATT
+>C_II_XVIIIb-27/1
+CACAGAGACAGATTAGCAGCCAGCTGAGCTAATAGACTTTGGTTAGACCCCGGAGGAATC
+TCAACGTCGCAATGCAGTAATGCTACAGACCTGTGGGGCACTACAGATGTGATATATCCC
+ACTGCTCTATCTGAAGTCAGGTCGCTTTCT
+>C_II_XVIIIb-25/1
+ACAAATTTCGGAAGATTGAAAGGAAGATTCAGAGTCACAATACAAGGTATGGAGAATTGT
+TCACAAAGCTGTGCACACATATTGAAAAGAAATTGCTAGGATCATCTCGATCTAATAATG
+TCCCACGGTCAGAAGAATTCAGTAGCATCC
+>C_II_XVIIIb-23/1
+TCACACTGCTGGAGTTTCGATTTTGGGTGTCATCTAAATTGATAGAACGCAGAGTAGAAA
+AGAATACCCTCCCTGTCGCAGATACCCGAAGCACACCAAGTGCTAAGTATTGGTGTGAGT
+GTGAGTGATCTCTACAACCAGATAGTATAA
+>C_II_XVIIIb-21/1
+TTCTCTGAACGTTCGACCCGTAGATTGCTGCTTAGTTTCTTATACCCGTCAGTTTTTTCT
+TGAGTTTTCGATCTGACAGGCTGTCAGAATTGACATACAGGCTGCTGCTGTATGTGCATC
+CAATTCTCATTTGCGGTCATGCTCTTGTAT
+>C_II_XVIIIb-15/1
+TGAGCCGCGATCTTAAAAGCCGAGGATAAGTTCACGACTTTGCTCAGTTCTAGCCAAGAT
+GTGACAGATAGGATATATAAACAGGTGGCTCTTGAATCTCCGCTAGCGCTACTAAACACC
+GAATCTATAATTATGAATGCAATAACATCC
+>C_II_XVIIIb-13/1
+CCTCACAGTAGCGTCTTGTGAACGACATTCTATCCAGTCCCCTACCGAGGCTGATGAAGT
+TCTTGGGAGAAAATATTGATGCTGCACTGATCGCAGCAGGGGGACAGCCCGTCCGTCCCT
+TTTGTGCAGAAAGTTTGGTGAGCACACTAA
+>C_II_XVIIIb-11/1
+TGTGCACGGTTTAATTGACGTCATCTTTTTCCCGTCTGTAGAGAGGTTATAAGGAGTAAA
+TAAGAATACTGTGTCAGCAAGGTCCCCCTCGGCATCCATGTAGATCACAGATCTAATGAC
+TGTGTCAATGTGGCTGGCAATTATCTGAGT
+>C_II_XVIIIb-7/1
+GCCATGGTGATTAAGCAGTTCCTAATCCTCTGAACAAGTATCGTACTAAGTAATCTTCCT
+TTGGGTTTGGTAGTGTGTGCTCGGGGCAAATCTCGCTAAGCGTAAATGCATCATACCTTG
+CTGGAGCAGTCAAATCTAGCTCTTGTATAA
+>HQ630064-957/1
+CAAAGCAAATTTTGTAGCTTAAGATAAAGGGGGCCCTAAAGAAGAAGCAACATCGTCTCG
+GGCTGTGTTTCCGACGTTGGGGTGCATTATGCGATTTTACTACCAGTGTTTGGTGTGGTG
+TGGTAAGGGGAAATGAGACGAGAATTTTTC
+>HQ630064-665/1
+CCCCGGGAGCTTTTTAGCGCGGCGTCACGTATAAATGCACAGAAGCTTCGTCAGTAACGA
+AGCGCCTCTGCCAGAGTTATTAACATTAGGACTCGAGAGAGTCTCGAGAAGAGACTTCCC
+AAAGAGAGTGCCGCTTTGATCTCCAGATCA
+>HQ630064-403/1
+TGTCTACCTGTCTGTCAAATTGTGACTACCACGTACCAACTCCTCCCCAAAGTTCTACCC
+TTTTCCTTAAAAACACATTTAAAATGTCAAAATACCGATCCTTATATTTGTGTGTTATGT
+TTTCTTTTGCCTTCTAGGATTGATTGAATT
+>HQ630064-343/1
+ACGAAAGAAAGAAAGGAAAAGGCCTCAAAGTTAATTTTGTAGCTTAAAAAAGAGGGGGCC
+CTAAAGAAGAAGCAACATCGTCTCGGGCTGTGTTTCCGACGTTGGGGTGCATTATGCGAT
+TTTACTACCAGTGTTTGGTGTGGTGTGGTA
+>HQ630064-307/1
+TCGTGTGTTTGCTCGCGTGCTTTGGATGTTGGGATGAGGCCTTGGTGTTGCCAGGCTCCG
+GTTTCTTAAAGGTTATCCGAGGGGGAAGTTCCACGTGTTCTTTTAGCTTTTCTCCATATT
+CCGGTCTACGGGTACAAATGTCCTCTGGAT
+>HQ630064-241/1
+CGTGACCTCATTTACAAGATGTCGGTGGCACCCAGCTACGTCACGTTCGCACCGAGGGTC
+CAACATTTTCCTAAAATGGCAAAGCGGGACTTGGGTCCGTGGGTAAATTTTCTAATTTTT
+TCCCACGGTCTGTCGCAAGAGCGTATTCTC
+>HQ630064-217/1
+AACTTTGGGGAGGAATTGGTACGTGGTAGACACAATTTGACAGACAGGTAGACAGACAAC
+GAATTACAAGCGGCCTAGGGTAATAGCGCTGAGCCCATGATGTGTCCGTGCATATGAGAC
+GACTAATAAGGTAGTCACGTAAACCCCCGT
+>HQ630064-199/1
+AGAAGCAGTATTGTGATCTTTCTCTCTTTCGCATGAATCGCTAGGAAGAGGAATTTTGGA
+AGCATCTGGATACCTTACAGGAGATTTAGAAATCTCGGTAGTTATGACATGTTCATCAGA
+TGAGGAAGATAGCAAGCGTGACGGTGTTTT
+>HQ630064-111/1
+GTGTCTCCGAGTTGTGCTCTCTCGAAACTCACTTTGCCCTCACTTGTTGGCTTTATGGAG
+GTCGTAATGATCATCGATGGAGTACTTATATAATATTGTGCTCTGCCGGCCATCTCTCCG
+TGGTCGCAGAACTCCAACACCTTGTTGGCG
+>HQ630064-105/1
+AGTTTAAACTTTGTCCGCGCGCCAATCTTGAAGTGATATTAGGACATAGTCAACCAACCG
+ACGTACGTTGAACCATTTGCGGGCAGCGCTGAGGGAAGACGAGATGTATGGACAACACAA
+CGACCGGAGAAGAGGGCGTAAAGAACATCA
+>HQ630064-11/1
+GAAAGAAAGAAAGGAAAAGGCCTCAAAGCAAATTTTGTAGCTTAAAAAAGAGGGGGCCCT
+AAAGAAGAAGCAACATCGTCTCGGGCTGTGTTTCCGACGTTGGGGTGCATTATGCGATTT
+TACTACCAGTGTTTGGTGTGGTGTGGTAAG
+>HQ630064-3/1
+AGGACTGTCGCTCATATCTTGCGTACTGTGTCTTATTTACTCGTGTTGTCTTTCCGCAGG
+GAATGCGCGGTTCGAGTAGGCCGTGGTTTGCGGCCGTTCTCGGATAAGCACAAAATATCG
+CCCTACTCGTGTGTCAAAAAGGAAAAGTCT

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k1.11176.children.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k1.11176.children.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,20 @@
+>C_II_XVIIIb-87/2
+AGAAGTTGTCACAAACTTTGTGAAGCTAACTTATCACCATATCCGGAGAATCATCTGACC
+TTACCTCTCTCGATACGGCTATTACTTGAATGTCACCTTGTACCATGCAGGCAAAACGAC
+AGTGTGATCTTGCTGCAGCAAGTTGGATTG
+>C_II_XVIIIb-53/2
+CTCTGAGACTTTAGTGCCCAGAACGTCACAACCTAAAGGAGTTGCACTCACACTGCAGGA
+CTTCCGACTTTGGGTGTCATCTAAGTTGATAGAACGCAGAGTAGAAAAGAATACCCTCCC
+TGTCGCAGATACCCGAAGCACACCAAGTGC
+>C_II_XVIIIb-37/2
+GATAGGTAAGGTCTGATGATTCTGCGGATCTGGTGTTAACTCAGCTGCACCAAGCTAGGG
+ATAACTTCTTTAAGGAATTAATTCATGTCAATCATCTGATTGGTCATAACTTGAAAGATC
+GTGAAACCATCAGGTCAGACACATTCTTCA
+>C_II_XVIIIb-25/2
+CAAAGACGTGGGGCATCTTATGAACTAACGTTACTAGCTTGGCGACTGCGGATCTTGTTC
+TTGCTGCTACAATCAGATGCCTTTGGACCTGTTTTATATGGAGCCATGCAAACTTGGCTC
+TGGACCACTTTGAGGGAAACCAGAATGCCG
+>C_II_XVIIIb-23/2
+ATGACCAGCATTATATCCGAGGGCTAGGCCGAGAACTCATAGTAAACGACACCAGTGATG
+TCACATCATTTTATCCTTCCGCATATCAAGAACACTTGAATTTTATCCCGGCGCCTTCTA
+CAGGGTCTGGTTGCACTCGGATACCCTCAT

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k1.e10386.children.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k1.e10386.children.fa Wed Mar 15 18:18:27 2023 +0000

b'@@ -0,0 +1,252 @@\n+>C_II_XVIIIb-101/2\n+GGGACCGCGTGCTAGCCCATAGCAAATGCCTCTCCACAGGTTGCTAAGATACTCTGGAGC\n+CAAACCGCGCACCTGCGGAGCGTGAAAGTCATCATTCAAGCTGGCACCCAGCGCGCTGTC\n+GCAGTGACCGCTGATCATGAAGTCACCTCT\n+>C_II_XVIIIb-99/2\n+TAGTGTTATCAGTCAGCTCCATGTTCCTTGGAAGATGAAAGCAAGTAAACTGCTCATCTC\n+CACTGTCACACTTTGTGCACCCTCCACTGACACTGAGAATCTCTCCTTCCACAAGTTCTA\n+TGGTGTCAGGATTAGAGACGCCTAGTATCT\n+>C_II_XVIIIb-97/2\n+GTCCCTAGCGTCTTCGTCTACTGAGGAAATATTCGCCCATTCACTCTCACCTCCTTCTCT\n+TTAAGTGGATATGATACTGCCACACTGTCATCTCTTAGGTACTCAAGGGTTGTCAAGTAT\n+TCCATCTCCTTGTATGGATCAAAATCATTT\n+>C_II_XVIIIb-95/2\n+GTTCTTGTACAGTTCAGTCATGTATAGGACGGTGTTGTTTAGGCCTCTCACTCTCAGATA\n+GTAGAGTTGGTAAGAACAGTCAAGGAGCACCTCGAGTGCCGCATATTCGAATAAGCGGAC\n+CACATCTGAATTCTGGGCCTCACTGATCCA\n+>C_II_XVIIIb-93/2\n+TAAAATTCGCTTCTTTCGGATGAGATGAACCCGGCACGGCGACATTTCGGACCAACACCA\n+ACACAGTTTCTAAATTCGGTCGTCTATAGGAATCTACAAGCGGAAGTTCCATGTAAAGAA\n+GGATTTGTCCAGGAGTTCTACCCATTATGG\n+>C_II_XVIIIb-91/2\n+ATCAACAACATAGGTACGCGAAACCTGGTAGAAGGTTTGGAGCCCATATTGCGTTCATAA\n+TGTGCTAGTTAGGTTCCAGACTCTTCTACACGTGTTTTTTCTAATTAGATAGACAGGTGA\n+ACTAGCTATAAGCAATCAAGATAGACTATT\n+>C_II_XVIIIb-89/2\n+TGTGTGATTTTACAAGGGTGCGAGCCTGTAGAGGGTTGTGATGGCAATCAACCATTCAGT\n+GCAAGGCGTTTGATCTTCCTGATCTCTTCAATCTACCTGGCTGCATCCAGCTTGCTCAGG\n+AGCTTAGCTGAGGAGCTTGGATGCATTGGG\n+>C_II_XVIIIb-87/2\n+AGAAGTTGTCACAAACTTTGTGAAGCTAACTTATCACCATATCCGGAGAATCATCTGACC\n+TTACCTCTCTCGATACGGCTATTACTTGAATGTCACCTTGTACCATGCAGGCAAAACGAC\n+AGTGTGATCTTGCTGCAGCAAGTTGGATTG\n+>C_II_XVIIIb-85/2\n+GGAAGTGCACTTGTCGGCTAGGTTGTGCAGTGGGGTGGGTCGGGGAGCGTAGGAGAGTTC\n+TGGGAGGATGGTTTGGGGTGACCTTATGGGGGCAGGCTGGGTGTTGCCGTTCAGTACCCC\n+CAGTCAGTGTCATTATCTTGGGATGGCCCA\n+>C_II_XVIIIb-83/2\n+TTAAGGCATGTTGATGCCGTGTATGCTGCCTTGATGCTGCTTGAACTCACTGGGGTTACT\n+CGACTGCGGGATATGTTAACGAATACTGCAGACACGGGATTGAGTCTTGCCTGTCCATCA\n+TCAAGCATTGTCCCGAATACCCCTCGTAGG\n+>C_II_XVIIIb-81/2\n+ATTCAGCAGAGACCGCGTGAAGTATCGCAGTTCCACAAGGCAAGACCAAGGCACTGAGCA\n+CTGCATGGGAGAAGCACGGAAGTGTCCAATCAAATGTCGGCCAGGACGCCCCCGACCAAC\n+AAGCCAGACCAGACAAACAGCCGTCCGCAC\n+>C_II_XVIIIb-79/2\n+AGAAGCACGGGCGTGTCCAATCAAATGCAGGCCAGGACGCCCCCGACCAACAAGCCAGAC\n+CAGACAAACAGCCGTCCGCACCCGAGCAGGCGGCCCAACACAGTGACCCGCCGGCCACAT\n+CCACCGAGTCCTCTCCCGCCCAGGCTGCAG\n+>C_II_XVIIIb-77/2\n+GCAATTTTGTTCAGAGATGATGTTTTCTTGTCTAGTAGATCCAATCACCCATTAGTCTCC\n+TCTAATATGTGTTCGCTGACGCTAGCAGACTATGCCCGGAACAGAAGCTGGTTACCTTTG\n+ACAGGGGGTAGGAAGATACTAGGCGTATCT\n+>C_II_XVIIIb-75/2\n+CATTGCTTCTACACCTGTGGCTCATGTCCAGCTACCTGTCGACTTTGTGCAAATGATGAT\n+GTCTATGATGGAGGCATTATCACAGAAGGTAAGTAAAGTTGACTATCAACTAGATCTAGT\n+CTTAAAACAGACATCTTCTATCCCTATGAT\n+>C_II_XVIIIb-73/2\n+TACAGTCAAGGAACGGTACTTGAGGGAACAACGGTGCCAGGATAGTGTCTCTGTCCTCTC\n+TTTCCCTGATCAGATTAAGACTCTTCCTGGACATGTAATATAGATTGGCGGGAAATGTGA\n+TTATGTTGGGAGATATGATAGAGTTCACTT\n+>C_II_XVIIIb-71/2\n+GTAATAAGAGCAGATATGCCGGTCAGTCTTACATTGACTTTGTCTAGCTTGCTGTTACTT\n+TTTGCCAACTTATCCAAGGCATTGCTTATTGAATTGTTGACATTTCCAAGCTCAATTGAT\n+ATATCGAGATTGCCGGTCACGATGACTTGA\n+>C_II_XVIIIb-69/2\n+CGAGGTCTATATGTTGACTGCCTTATCTCCTGTTATTACAATCCCCGCAGCTGCAAGGGG\n+CCTGCCATCAAGGGAGTTTGTCAGACAGACGCAGCTTAATATCAGCATAGTCCGAATGAT\n+CAGCATCAGAGGTACTGGAATCCTGGTAGA\n+>C_II_XVIIIb-67/2\n+CCCTTTCACCTGCCTTCAGCCATGTAACCCCATCCGACCGAGCCAACACAGGCGTAACTC\n+GGTTCGCCAACAATCCACTCAGAGCCCGAGGTATTAGAAAAAAATACGGGTAGAAGGGAG\n+ACACCTGGAGACCAGGACGAGTCACCAAAG\n+>C_II_XVIIIb-65/2\n+GCAAATACCACTTTGCCAGGGCCTTTATGTGCACATCAGTCTGGAGGCTTGGAGTAGAGT\n+ATGCTCAGGCTCAGGGAAGTAGCATCAATGAAGACATGGCTGCTGAACTAAAACTGACTC\n+CGGCAGCAAGGAGAGGTCTGGCGGCTGCTG\n+>C_II_XVIIIb-63/2\n+CACCTCGATTTCCGCATATTCGAATAAGCAGACAACATCTGAATTCTGGGCCTCACTGAT\n+CCAATTTCGTGTGTTGTCATACACTATTATAGCATCATTCTTGATAGAGGTATCTTCATC\n+ATAAGAAACCACTGATTGGCCGATCAACTT\n+>C_II_XVIIIb-61/2\n+GTTAGTCCTCTGACTGTCCGATAGTAGAGTTGGTAAGAACAGTCAAGGAGCACCTCGAGT\n+GCCGCATATTCGAAAAAGCGGTCCACATCTGAATTCTGGGCCTCACTGATCCAATTTCGT\n+GTGTTGTCATACACTATTATAGCATCATTC\n+>C_II_XVIIIb-59/2\n+CCTTGTATGTATAAAAATCATTTGTTTCTAATATCTCAATCAAGAGGCGATTAGTTGAGG\n+TCGCCTCTTTTATCTGTTTCTTTTGGTCCTCAGAGAGGAGGTTCCGCCTGAATGAGGCGA\n+GCCAGTTATCTTTCGGATGTGCGATTGCCT\n+>C_II_XVIIIb-57/2\n+CTGGTATGGGCCACTTTATTAAGAAAAACTAAAAAAAGCATTGTAATATAAAGGAAACCA\n+ACACACAAAAGAAAGCACGGGTAGGACATGGCAGGCTCTGGTCCCGAA'..b'CTCAT\n+>C_II_XVIIIb-21/2\n+CACAAGCAAAACAAAACACATCACTAGGGCTCGGAAACAATACCCTTGATCAGATGAGGG\n+CCAATACAAGAGCATGACCTCAAATGAGAATTGGATGCACGTACAGCAGCAGCCTGTATG\n+TCAATTCTGACAGCCTGTCAGATCGAAAAC\n+>C_II_XVIIIb-19/2\n+ACTAGATCTAGTTGATAGTCAAGTTTACTTACCTTCTGTGATAATGCCTCCATCATAGAC\n+ATCATCATTTGCACAAAGCCGACAGGTAGCTGGACATGATCCACAGGTGCAGGAGTATTG\n+TCTTGGTTCTGCCCTGACTGGGGCACATGA\n+>C_II_XVIIIb-17/2\n+GTACATATTCCCTGGATATGAGCCTGAGACCACGGGTCTGGTGCATGAGACTAATAGTTT\n+CGCAGACATTTCGATGAAATCTATATCTGCCAGCTGGTGTGACCCGTCATGGTTAATTAG\n+GCCTACTGCATTCAACCTTGGGTGTATAAT\n+>C_II_XVIIIb-15/2\n+AACTGGCGCCCCACATCCACTAGTATTCACAGACCCGTTGATTTGATAAGAGAGGGATGT\n+TATTGCATTCATAATTATAGATTCGGTGTTTAGTAGCGCTAGCGGAGATTCAAGAGCCAC\n+CTGTTTATATATCCTATCTGTCACATCTTG\n+>C_II_XVIIIb-13/2\n+TGACCTCCAGGATCTGTAGTGTGCACTGTTTAAGTGATGTTCTCTTTTTCCCGTCTGTAG\n+AGAGGTTATAAGGAGTAAATAAGAATACTGTGTCAGCAAGGTCCCCCTCGGCATCCATGT\n+AGATCACAGATCTAATGACTGTGTCAATGT\n+>C_II_XVIIIb-11/2\n+CACCTCATGCCATCGTCGTGTCACGGAAATCCTATCTAGTCCCCTACCGAGGCTGATGAA\n+GTTCTTGGGAGAAAATATTGATGCTGCACTGATCGCAGCAGGGGGACAGCCCGTCCGTCC\n+CTTTTGTGCAGAAAGTTTGGTGAGCACACT\n+>C_II_XVIIIb-9/2\n+ACAATGCCCGGTTCGGGGGATTTAGAATCGTTCCATTACTAGTTGAGATCCTCAAGGATG\n+ATAGAGTTTAAGGGATTAGACCCAGGCAATTGAATCAGCCATAGGACGGCTGGAAGAATG\n+ATATGGCACTGAATATCTTTCGCGATGCCA\n+>C_II_XVIIIb-7/2\n+CTCATGAACCGTTGCTTGAGCTTCATCCAGTACAAGACATCGGTGCTCGGGTGAAAGACC\n+CGTTAACCCGACAACCTGCATCATTTATACAAGAGCTAGATTTGAGTGCTCCAGCAAGGT\n+ATGATGCATTTACGCTTAGCGAGATTTGCC\n+>C_II_XVIIIb-5/2\n+ATCTCCACAGCAATTTTTGCTTGTGTATCCGGGAAGCGCCTGTTGCGGTTCCTTTCGAGC\n+TACTTGGATTGGCACCAGAATTAAGGATGGTAACCTCAAATAAGTTCATGTATGATCCTA\n+GCCCTATATCAGAGAAGGATTTTGCAAGAC\n+>C_II_XVIIIb-3/2\n+TCAGCTTGTATCCGTTCTGCCATTACCTGGCGGGTCCTTAGCTTCTTTGTCAACTTAGCA\n+AAAATTCGCCCATTCACTTTCACCTCCTTCTCTTTAAGTGAATATGATACTGCCACACTG\n+TCATCTCTTAGGTACTCAAGGGTTGTCAAG\n+>C_II_XVIIIb-1/2\n+AAAAGTGAGGGGGCGAACTTTTGCTAAGTTTACACAGAAGCTAAGGAACTGCCAGGTAAT\n+GGCAGAAGGGATTCTAGCTGACCAGATTGCTCCTTTCTTCCAAGGAAATGGGGTCATTCA\n+AGATAGCATATCCTTGACTAAGAGTATGTT\n+>HQ630064-957/2\n+CTGATCCAGTGGCCCTTCGTTACTCACGAAGTATCTGTGCATTTATACGTGACGCCACGC\n+TAACAAGGAAGCGCCGCGCAATTTGCTCACGGTTGGGCGTAGCTCTGTGCTCGAGCGCAC\n+GCGAAAAATTCTCGTCTCATTTCCCCTTAC\n+>HQ630064-665/2\n+TCGAATAGGCCGTGGTTTGCGGCCGTACTCGTAGAAGCACAAAATATCGCCCTACTCGTG\n+TGTCAAAAAGGAAAAGTCTTAATGGGCTGTGAAGTGATCTGGAGATCAAAGCGGCACTCT\n+CTTTGAGAAGTCTCTTCTCGAGACTCTCTC\n+>HQ630064-403/2\n+TACGGTGGGGGTCACAACAATTTAACCAATGAAATGTTTCTTTATTATAAGAGCGGTATA\n+GCAGATTTAATAAAATACCTTTTTTGAAAAAATATTGACCTGTCTCGCGTTGTAGATTCT\n+TCGCATCCGCGTTCCGTCATAATTCCAAGA\n+>HQ630064-343/2\n+CTCCCGTGCATGTATACGTGACGCCACGCTAACAAGGAAGCGCCGCGCAATTTGCTCACG\n+GTTGGGCGTAGCTCTGTCCTCGAGCGCACGTGAAAAATTCTCGTCTCATTTCCCCTTACC\n+ACACCACACCAAACACTGGTAGTAAAACCG\n+>HQ630064-307/2\n+TTTTTCACAGACGGGGACGTTCTCATCTAACTTCGGGGATCCTGGGGATATATTTTATAG\n+CGATGTAGTAGGGGGAGATGGCCCAATATTCGAAGATCCAGAGGACATTTGTACCCGTAG\n+ACCGGAATATGGAGAAAAGCTAAAAGAACA\n+>HQ630064-241/2\n+CATAATCATTTACAAAACGCGGGACCTCGACAATATGCGGGAAAATCTAACAGCAATCTA\n+TCTTGGAGAATACGCTCTTCCGAAAGACCGTGGGAAAAAATTAGAAAATTTACCCACGGA\n+CCCAAGTCCCGCTTTGCCATTTTAGGAAAA\n+>HQ630064-217/2\n+AAATCGCATGTCACACCCCAGCGTCGGAAAAACCGCCCGAGACGAAGTTGCTTCTTCTTT\n+GGGGCCCCCTCTTTTTTAAGCTACAAAATTTGCTTTGAGGCCTTTTCCTTTCTTTCTTTC\n+TTTCGCGTGTGATTGACGGGGGTTTACGTG\n+>HQ630064-199/2\n+CCGTTAGCACTTAAGTAACCGGAGCTTGGCAACACCAAGGCCTCATCCCAACATCCAAAG\n+CACTCGAGCAAACGCAGGAGTAGCAAATCTCGCTATTTCAAAGCTTCAGAATCGTGTAAT\n+ACACCGTCACGCTTGCTATCTTTCTCATCT\n+>HQ630064-111/2\n+GAAACTTGAATAAGAGCTCCCCAACTACGCTGCTAGAACTAGCAAATTTTATGCTCGCCA\n+ACAAGGTGTTGGAGTTCTGCGACCACGGAGAGATGGCCGGCAGAGCACAATATTATATAA\n+GTACTCCATCGATGATCATTACGACCTCCA\n+>HQ630064-105/2\n+TTATTAAATTGTTATTTCCACCACCGCAGAGCAATACCGTGATGTTCTTTACGCCCTCTT\n+CTCCGGTCGTTGTGTTGTCCATACATCTCGTCTTCCCTCAGCGCTGCCCGCAAATGGTTC\n+AACGTATGTCGGTTGGTTGACTATGTCCTA\n+>HQ630064-11/2\n+TGGGCGTAGTTCTGTCCTCGAGCGCACGCGAAAAATTCTCGTCTCATTTCCCCTTACCAC\n+ACCACACCAAACACTGGTAGTAAAATCGCATAATGCACCCCAACGTCGGAAACACAGCCC\n+GAGACGATGTTGCTTCTTCTTTAGGGCCCC\n+>HQ630064-3/2\n+CCACAGTTATTTGCAATAGGACTCGAGTGAGTTTTAAGAAGAGACTTCTCAAAGAGAGAG\n+CCGCTTTGATCTCCAGATCACTTCACAGCCCATTAAGACTTTTCCTTTTTGACACACGAG\n+TAGGGCGATATTTTGTGCTTATCCGAGAAC\n'

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k2.11176.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k2.11176.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,28 @@
+>C_II_XVIIIb-65/2
+GCAAATACCACTTTGCCAGGGCCTTTATGTGCACATCAGTCTGGAGGCTTGGAGTAGAGT
+ATGCTCAGGCTCAGGGAAGTAGCATCAATGAAGACATGGCTGCTGAACTAAAACTGACTC
+CGGCAGCAAGGAGAGGTCTGGCGGCTGCTG
+>C_II_XVIIIb-57/2
+CTGGTATGGGCCACTTTATTAAGAAAAACTAAAAAAAGCATTGTAATATAAAGGAAACCA
+ACACACAAAAGAAAGCACGGGTAGGACATGGCAGGCTCTGGTCCCGAAAGGGCAGAGCAC
+CAGCTTATCCTACCAGAGTCACATCTATCC
+>C_II_XVIIIb-49/2
+GACCCGATTTCCTTGGAAGAACGGTGCAATCTGTTCAGCTAGAATCCCTTCTGCCATTAC
+CTGGCAGTTCCTTAGCTTCTTTGTCAACTTAGCAAAAATTCTCCCATTCACTTTCACCTC
+CTTCTCGTTAAGTGAATAGGATACTGCCAC
+>C_II_XVIIIb-45/2
+GATCTTGGATGTTACAATACTAGGGCCAAGAGTCAAAGATATCAACAAAATAGGTGATGT
+AATTAGCCTAGTACTCAGAGGTAAGGTTTCCCTGGAGGACCTCATCCCACTAAGGACATA
+CCTGAAGCGCAGTACCTGCCCTAAGTATCT
+>C_II_XVIIIb-17/2
+GTACATATTCCCTGGATATGAGCCTGAGACCACGGGTCTGGTGCATGAGACTAATAGTTT
+CGCAGACATTTCGATGAAATCTATATCTGCCAGCTGGTGTGACCCGTCATGGTTAATTAG
+GCCTACTGCATTCAACCTTGGGTGTATAAT
+>C_II_XVIIIb-9/2
+ACAATGCCCGGTTCGGGGGATTTAGAATCGTTCCATTACTAGTTGAGATCCTCAAGGATG
+ATAGAGTTTAAGGGATTAGACCCAGGCAATTGAATCAGCCATAGGACGGCTGGAAGAATG
+ATATGGCACTGAATATCTTTCGCGATGCCA
+>C_II_XVIIIb-1/2
+AAAAGTGAGGGGGCGAACTTTTGCTAAGTTTACACAGAAGCTAAGGAACTGCCAGGTAAT
+GGCAGAAGGGATTCTAGCTGACCAGATTGCTCCTTTCTTCCAAGGAAATGGGGTCATTCA
+AGATAGCATATCCTTGACTAAGAGTATGTT

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k2.11176.max2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k2.11176.max2.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,8 @@
+>C_II_XVIIIb-65/2
+GCAAATACCACTTTGCCAGGGCCTTTATGTGCACATCAGTCTGGAGGCTTGGAGTAGAGT
+ATGCTCAGGCTCAGGGAAGTAGCATCAATGAAGACATGGCTGCTGAACTAAAACTGACTC
+CGGCAGCAAGGAGAGGTCTGGCGGCTGCTG
+>C_II_XVIIIb-57/2
+CTGGTATGGGCCACTTTATTAAGAAAAACTAAAAAAAGCATTGTAATATAAAGGAAACCA
+ACACACAAAAGAAAGCACGGGTAGGACATGGCAGGCTCTGGTCCCGAAAGGGCAGAGCAC
+CAGCTTATCCTACCAGAGTCACATCTATCC

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k2.11176.parents.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k2.11176.parents.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,76 @@
+>C_II_XVIIIb-99/2
+TAGTGTTATCAGTCAGCTCCATGTTCCTTGGAAGATGAAAGCAAGTAAACTGCTCATCTC
+CACTGTCACACTTTGTGCACCCTCCACTGACACTGAGAATCTCTCCTTCCACAAGTTCTA
+TGGTGTCAGGATTAGAGACGCCTAGTATCT
+>C_II_XVIIIb-97/2
+GTCCCTAGCGTCTTCGTCTACTGAGGAAATATTCGCCCATTCACTCTCACCTCCTTCTCT
+TTAAGTGGATATGATACTGCCACACTGTCATCTCTTAGGTACTCAAGGGTTGTCAAGTAT
+TCCATCTCCTTGTATGGATCAAAATCATTT
+>C_II_XVIIIb-93/2
+TAAAATTCGCTTCTTTCGGATGAGATGAACCCGGCACGGCGACATTTCGGACCAACACCA
+ACACAGTTTCTAAATTCGGTCGTCTATAGGAATCTACAAGCGGAAGTTCCATGTAAAGAA
+GGATTTGTCCAGGAGTTCTACCCATTATGG
+>C_II_XVIIIb-87/2
+AGAAGTTGTCACAAACTTTGTGAAGCTAACTTATCACCATATCCGGAGAATCATCTGACC
+TTACCTCTCTCGATACGGCTATTACTTGAATGTCACCTTGTACCATGCAGGCAAAACGAC
+AGTGTGATCTTGCTGCAGCAAGTTGGATTG
+>C_II_XVIIIb-85/2
+GGAAGTGCACTTGTCGGCTAGGTTGTGCAGTGGGGTGGGTCGGGGAGCGTAGGAGAGTTC
+TGGGAGGATGGTTTGGGGTGACCTTATGGGGGCAGGCTGGGTGTTGCCGTTCAGTACCCC
+CAGTCAGTGTCATTATCTTGGGATGGCCCA
+>C_II_XVIIIb-75/2
+CATTGCTTCTACACCTGTGGCTCATGTCCAGCTACCTGTCGACTTTGTGCAAATGATGAT
+GTCTATGATGGAGGCATTATCACAGAAGGTAAGTAAAGTTGACTATCAACTAGATCTAGT
+CTTAAAACAGACATCTTCTATCCCTATGAT
+>C_II_XVIIIb-65/2
+GCAAATACCACTTTGCCAGGGCCTTTATGTGCACATCAGTCTGGAGGCTTGGAGTAGAGT
+ATGCTCAGGCTCAGGGAAGTAGCATCAATGAAGACATGGCTGCTGAACTAAAACTGACTC
+CGGCAGCAAGGAGAGGTCTGGCGGCTGCTG
+>C_II_XVIIIb-57/2
+CTGGTATGGGCCACTTTATTAAGAAAAACTAAAAAAAGCATTGTAATATAAAGGAAACCA
+ACACACAAAAGAAAGCACGGGTAGGACATGGCAGGCTCTGGTCCCGAAAGGGCAGAGCAC
+CAGCTTATCCTACCAGAGTCACATCTATCC
+>C_II_XVIIIb-49/2
+GACCCGATTTCCTTGGAAGAACGGTGCAATCTGTTCAGCTAGAATCCCTTCTGCCATTAC
+CTGGCAGTTCCTTAGCTTCTTTGTCAACTTAGCAAAAATTCTCCCATTCACTTTCACCTC
+CTTCTCGTTAAGTGAATAGGATACTGCCAC
+>C_II_XVIIIb-45/2
+GATCTTGGATGTTACAATACTAGGGCCAAGAGTCAAAGATATCAACAAAATAGGTGATGT
+AATTAGCCTAGTACTCAGAGGTAAGGTTTCCCTGGAGGACCTCATCCCACTAAGGACATA
+CCTGAAGCGCAGTACCTGCCCTAAGTATCT
+>C_II_XVIIIb-43/2
+GGGGCAGCGAATGAGAGAGGATATGGGGCGCCTGTTCATGACCCAGATTATATCGGAGGG
+ATAGGCAGAGAACTCATAGTAGACGACACCAGTGATGTCACATCATTTTATCCTTCCGCA
+TATCAATAACACTTGAATTTTATCCCGGCG
+>C_II_XVIIIb-33/2
+CATAGGGATAGAACATGTATGTTTTAAGACGAGATCTAGTTGATAGTCAACTTTACTTAC
+CTTCTGTGATAATGCCTCCATCATAGACATCATCATTTGCACAAAGTCGACAGGTAGCTG
+GACATGATCCACAGGTGCAGGAGCATTGTC
+>C_II_XVIIIb-29/2
+CTCAGTTGCACAAACTCGACAGGTAGCTGCATATGATCCACAGGTGCAGGAGTATTGTCT
+TGGTTCTGCCCTGACTGGGGCACATGAGGGGTTGCACCAGCTGATGGTTGTGACTCCTTC
+CATAGTCCATGATATGCTGTGTTCGCGTCT
+>C_II_XVIIIb-19/2
+ACTAGATCTAGTTGATAGTCAAGTTTACTTACCTTCTGTGATAATGCCTCCATCATAGAC
+ATCATCATTTGCACAAAGCCGACAGGTAGCTGGACATGATCCACAGGTGCAGGAGTATTG
+TCTTGGTTCTGCCCTGACTGGGGCACATGA
+>C_II_XVIIIb-17/2
+GTACATATTCCCTGGATATGAGCCTGAGACCACGGGTCTGGTGCATGAGACTAATAGTTT
+CGCAGACATTTCGATGAAATCTATATCTGCCAGCTGGTGTGACCCGTCATGGTTAATTAG
+GCCTACTGCATTCAACCTTGGGTGTATAAT
+>C_II_XVIIIb-9/2
+ACAATGCCCGGTTCGGGGGATTTAGAATCGTTCCATTACTAGTTGAGATCCTCAAGGATG
+ATAGAGTTTAAGGGATTAGACCCAGGCAATTGAATCAGCCATAGGACGGCTGGAAGAATG
+ATATGGCACTGAATATCTTTCGCGATGCCA
+>C_II_XVIIIb-5/2
+ATCTCCACAGCAATTTTTGCTTGTGTATCCGGGAAGCGCCTGTTGCGGTTCCTTTCGAGC
+TACTTGGATTGGCACCAGAATTAAGGATGGTAACCTCAAATAAGTTCATGTATGATCCTA
+GCCCTATATCAGAGAAGGATTTTGCAAGAC
+>C_II_XVIIIb-3/2
+TCAGCTTGTATCCGTTCTGCCATTACCTGGCGGGTCCTTAGCTTCTTTGTCAACTTAGCA
+AAAATTCGCCCATTCACTTTCACCTCCTTCTCTTTAAGTGAATATGATACTGCCACACTG
+TCATCTCTTAGGTACTCAAGGGTTGTCAAG
+>C_II_XVIIIb-1/2
+AAAAGTGAGGGGGCGAACTTTTGCTAAGTTTACACAGAAGCTAAGGAACTGCCAGGTAAT
+GGCAGAAGGGATTCTAGCTGACCAGATTGCTCCTTTCTTCCAAGGAAATGGGGTCATTCA
+AGATAGCATATCCTTGACTAAGAGTATGTT

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/out2.k2.exclude_both.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/out2.k2.exclude_both.fa Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,176 @@
+>C_II_XVIIIb-101/2
+GGGACCGCGTGCTAGCCCATAGCAAATGCCTCTCCACAGGTTGCTAAGATACTCTGGAGC
+CAAACCGCGCACCTGCGGAGCGTGAAAGTCATCATTCAAGCTGGCACCCAGCGCGCTGTC
+GCAGTGACCGCTGATCATGAAGTCACCTCT
+>C_II_XVIIIb-95/2
+GTTCTTGTACAGTTCAGTCATGTATAGGACGGTGTTGTTTAGGCCTCTCACTCTCAGATA
+GTAGAGTTGGTAAGAACAGTCAAGGAGCACCTCGAGTGCCGCATATTCGAATAAGCGGAC
+CACATCTGAATTCTGGGCCTCACTGATCCA
+>C_II_XVIIIb-91/2
+ATCAACAACATAGGTACGCGAAACCTGGTAGAAGGTTTGGAGCCCATATTGCGTTCATAA
+TGTGCTAGTTAGGTTCCAGACTCTTCTACACGTGTTTTTTCTAATTAGATAGACAGGTGA
+ACTAGCTATAAGCAATCAAGATAGACTATT
+>C_II_XVIIIb-89/2
+TGTGTGATTTTACAAGGGTGCGAGCCTGTAGAGGGTTGTGATGGCAATCAACCATTCAGT
+GCAAGGCGTTTGATCTTCCTGATCTCTTCAATCTACCTGGCTGCATCCAGCTTGCTCAGG
+AGCTTAGCTGAGGAGCTTGGATGCATTGGG
+>C_II_XVIIIb-83/2
+TTAAGGCATGTTGATGCCGTGTATGCTGCCTTGATGCTGCTTGAACTCACTGGGGTTACT
+CGACTGCGGGATATGTTAACGAATACTGCAGACACGGGATTGAGTCTTGCCTGTCCATCA
+TCAAGCATTGTCCCGAATACCCCTCGTAGG
+>C_II_XVIIIb-81/2
+ATTCAGCAGAGACCGCGTGAAGTATCGCAGTTCCACAAGGCAAGACCAAGGCACTGAGCA
+CTGCATGGGAGAAGCACGGAAGTGTCCAATCAAATGTCGGCCAGGACGCCCCCGACCAAC
+AAGCCAGACCAGACAAACAGCCGTCCGCAC
+>C_II_XVIIIb-79/2
+AGAAGCACGGGCGTGTCCAATCAAATGCAGGCCAGGACGCCCCCGACCAACAAGCCAGAC
+CAGACAAACAGCCGTCCGCACCCGAGCAGGCGGCCCAACACAGTGACCCGCCGGCCACAT
+CCACCGAGTCCTCTCCCGCCCAGGCTGCAG
+>C_II_XVIIIb-77/2
+GCAATTTTGTTCAGAGATGATGTTTTCTTGTCTAGTAGATCCAATCACCCATTAGTCTCC
+TCTAATATGTGTTCGCTGACGCTAGCAGACTATGCCCGGAACAGAAGCTGGTTACCTTTG
+ACAGGGGGTAGGAAGATACTAGGCGTATCT
+>C_II_XVIIIb-73/2
+TACAGTCAAGGAACGGTACTTGAGGGAACAACGGTGCCAGGATAGTGTCTCTGTCCTCTC
+TTTCCCTGATCAGATTAAGACTCTTCCTGGACATGTAATATAGATTGGCGGGAAATGTGA
+TTATGTTGGGAGATATGATAGAGTTCACTT
+>C_II_XVIIIb-71/2
+GTAATAAGAGCAGATATGCCGGTCAGTCTTACATTGACTTTGTCTAGCTTGCTGTTACTT
+TTTGCCAACTTATCCAAGGCATTGCTTATTGAATTGTTGACATTTCCAAGCTCAATTGAT
+ATATCGAGATTGCCGGTCACGATGACTTGA
+>C_II_XVIIIb-69/2
+CGAGGTCTATATGTTGACTGCCTTATCTCCTGTTATTACAATCCCCGCAGCTGCAAGGGG
+CCTGCCATCAAGGGAGTTTGTCAGACAGACGCAGCTTAATATCAGCATAGTCCGAATGAT
+CAGCATCAGAGGTACTGGAATCCTGGTAGA
+>C_II_XVIIIb-67/2
+CCCTTTCACCTGCCTTCAGCCATGTAACCCCATCCGACCGAGCCAACACAGGCGTAACTC
+GGTTCGCCAACAATCCACTCAGAGCCCGAGGTATTAGAAAAAAATACGGGTAGAAGGGAG
+ACACCTGGAGACCAGGACGAGTCACCAAAG
+>C_II_XVIIIb-63/2
+CACCTCGATTTCCGCATATTCGAATAAGCAGACAACATCTGAATTCTGGGCCTCACTGAT
+CCAATTTCGTGTGTTGTCATACACTATTATAGCATCATTCTTGATAGAGGTATCTTCATC
+ATAAGAAACCACTGATTGGCCGATCAACTT
+>C_II_XVIIIb-61/2
+GTTAGTCCTCTGACTGTCCGATAGTAGAGTTGGTAAGAACAGTCAAGGAGCACCTCGAGT
+GCCGCATATTCGAAAAAGCGGTCCACATCTGAATTCTGGGCCTCACTGATCCAATTTCGT
+GTGTTGTCATACACTATTATAGCATCATTC
+>C_II_XVIIIb-59/2
+CCTTGTATGTATAAAAATCATTTGTTTCTAATATCTCAATCAAGAGGCGATTAGTTGAGG
+TCGCCTCTTTTATCTGTTTCTTTTGGTCCTCAGAGAGGAGGTTCCGCCTGAATGAGGCGA
+GCCAGTTATCTTTCGGATGTGCGATTGCCT
+>C_II_XVIIIb-55/2
+ATGCAGTGGGCGGGAGGTGATTAATGCACGGGCCGTTTCCTTCTCCACTGCCATATCAGG
+CCCACCTGCAGTAGCAGATTTAACTAGGTCTGAAGGCTGCTGTACCGGTTGTGAGAGTTT
+ATTGAGTGTCATTTCACCCCCTTGTGTCAC
+>C_II_XVIIIb-53/2
+CTCTGAGACTTTAGTGCCCAGAACGTCACAACCTAAAGGAGTTGCACTCACACTGCAGGA
+CTTCCGACTTTGGGTGTCATCTAAGTTGATAGAACGCAGAGTAGAAAAGAATACCCTCCC
+TGTCGCAGATACCCGAAGCACACCAAGTGC
+>C_II_XVIIIb-51/2
+TTAAGGATGGTAACCTCAATTAAGTTCATGTATAATCCTAGCCCTATATCAGAGAAGGAT
+TTTGCAAGACTCGACTTAGCTATCTTCAAGAGTTATGAGCTTAATTTGGAGTCATATTCC
+ACACTGGAGCTGATGAACATTCTTTCAATC
+>C_II_XVIIIb-47/2
+TCGCACTCAATATCTTTCGCGATGCCCGGTGTTAAACTGAATAACAACACAAGCCCAGAT
+CCCGTGCTGCCGGGTAGCCACAATCTAACAACACTGACATGATTAGTCTGAGTCCTGTTT
+TTGGCCACTTTAGTAAGAAAAAATAAAAAA
+>C_II_XVIIIb-41/2
+GTCCTTCTCCACTGCCATATCAGGCCCACCTGCAGTAGCAGATTTAACTAGCTCTGAAGG
+GTGCTGTACCGGTTGTGAGAGTTTATTGAGTGTCATTTCACCCCCTTGTGTCACATAAGG
+AGATGGGTCTCCAGGGCCCGAAATTAAAAC
+>C_II_XVIIIb-39/2
+AAGGCCGCGTGTCAAGGCCGCTACAATATGCGGGAAGGTCATTGGGCAGCTTCATGCCGA
+TTCAGCGGAGATCTCACACGATGTCATGGTGAGAGAGTGCAAGAGTTTATCTGCCCTCGA
+ATTTGAGCCATGCATAGAGTATGACCCCGT
+>C_II_XVIIIb-37/2
+GATAGGTAAGGTCTGATGATTCTGCGGATCTGGTGTTAACTCAGCTGCACCAAGCTAGGG
+ATAACTTCTTTAAGGAATTAATTCATGTCAATCATCTGATTGGTCATAACTTGAAAGATC
+GTGAAACCATCAGGTCAGACACATTCTTCA
+>C_II_XVIIIb-35/2
+CTGAGTGGTTCGTTAGCATCTTCGCTAACAGCAATCCGAAGACACAATACCGCAAAATTC
+CATCTATCCTCTGGATCATCACTGTTAAGAGTAAATACTGGGACTTCAACTTTTAAAGTG
+CTCCCTTTCTCTCCTCCTCCGTGAGTTCCG
+>C_II_XVIIIb-31/2
+GTGCATCAATACTCGAATGAGTAAGGGTACAGCCAATGCTTTCTCCTCTGTCTCATTGTC
+CTCCGTATGCACTCCGGATAATAAAGGGTTTGAACAAGTCTCAAATAAGACCTTTTGTGT
+ATGCTTCTTGAGGACAATATTTGGGCTTGC
+>C_II_XVIIIb-27/2
+TATAGGAATCTACAAGCGGAAGTGTAATGTAAATAAGGATTTGTCCAGGAGTTCTACCCA
+TTATGGAGAGAGAATGCAGAAGAAAGCGACCTGACTTCAGATAGAGCAGTGGGATATATC
+ACATCTGTAGTGCCCCACAGGTCTGTAGCA
+>C_II_XVIIIb-25/2
+CAAAGACGTGGGGCATCTTATGAACTAACGTTACTAGCTTGGCGACTGCGGATCTTGTTC
+TTGCTGCTACAATCAGATGCCTTTGGACCTGTTTTATATGGAGCCATGCAAACTTGGCTC
+TGGACCACTTTGAGGGAAACCAGAATGCCG
+>C_II_XVIIIb-23/2
+ATGACCAGCATTATATCCGAGGGCTAGGCCGAGAACTCATAGTAAACGACACCAGTGATG
+TCACATCATTTTATCCTTCCGCATATCAAGAACACTTGAATTTTATCCCGGCGCCTTCTA
+CAGGGTCTGGTTGCACTCGGATACCCTCAT
+>C_II_XVIIIb-21/2
+CACAAGCAAAACAAAACACATCACTAGGGCTCGGAAACAATACCCTTGATCAGATGAGGG
+CCAATACAAGAGCATGACCTCAAATGAGAATTGGATGCACGTACAGCAGCAGCCTGTATG
+TCAATTCTGACAGCCTGTCAGATCGAAAAC
+>C_II_XVIIIb-15/2
+AACTGGCGCCCCACATCCACTAGTATTCACAGACCCGTTGATTTGATAAGAGAGGGATGT
+TATTGCATTCATAATTATAGATTCGGTGTTTAGTAGCGCTAGCGGAGATTCAAGAGCCAC
+CTGTTTATATATCCTATCTGTCACATCTTG
+>C_II_XVIIIb-13/2
+TGACCTCCAGGATCTGTAGTGTGCACTGTTTAAGTGATGTTCTCTTTTTCCCGTCTGTAG
+AGAGGTTATAAGGAGTAAATAAGAATACTGTGTCAGCAAGGTCCCCCTCGGCATCCATGT
+AGATCACAGATCTAATGACTGTGTCAATGT
+>C_II_XVIIIb-11/2
+CACCTCATGCCATCGTCGTGTCACGGAAATCCTATCTAGTCCCCTACCGAGGCTGATGAA
+GTTCTTGGGAGAAAATATTGATGCTGCACTGATCGCAGCAGGGGGACAGCCCGTCCGTCC
+CTTTTGTGCAGAAAGTTTGGTGAGCACACT
+>C_II_XVIIIb-7/2
+CTCATGAACCGTTGCTTGAGCTTCATCCAGTACAAGACATCGGTGCTCGGGTGAAAGACC
+CGTTAACCCGACAACCTGCATCATTTATACAAGAGCTAGATTTGAGTGCTCCAGCAAGGT
+ATGATGCATTTACGCTTAGCGAGATTTGCC
+>HQ630064-957/2
+CTGATCCAGTGGCCCTTCGTTACTCACGAAGTATCTGTGCATTTATACGTGACGCCACGC
+TAACAAGGAAGCGCCGCGCAATTTGCTCACGGTTGGGCGTAGCTCTGTGCTCGAGCGCAC
+GCGAAAAATTCTCGTCTCATTTCCCCTTAC
+>HQ630064-665/2
+TCGAATAGGCCGTGGTTTGCGGCCGTACTCGTAGAAGCACAAAATATCGCCCTACTCGTG
+TGTCAAAAAGGAAAAGTCTTAATGGGCTGTGAAGTGATCTGGAGATCAAAGCGGCACTCT
+CTTTGAGAAGTCTCTTCTCGAGACTCTCTC
+>HQ630064-403/2
+TACGGTGGGGGTCACAACAATTTAACCAATGAAATGTTTCTTTATTATAAGAGCGGTATA
+GCAGATTTAATAAAATACCTTTTTTGAAAAAATATTGACCTGTCTCGCGTTGTAGATTCT
+TCGCATCCGCGTTCCGTCATAATTCCAAGA
+>HQ630064-343/2
+CTCCCGTGCATGTATACGTGACGCCACGCTAACAAGGAAGCGCCGCGCAATTTGCTCACG
+GTTGGGCGTAGCTCTGTCCTCGAGCGCACGTGAAAAATTCTCGTCTCATTTCCCCTTACC
+ACACCACACCAAACACTGGTAGTAAAACCG
+>HQ630064-307/2
+TTTTTCACAGACGGGGACGTTCTCATCTAACTTCGGGGATCCTGGGGATATATTTTATAG
+CGATGTAGTAGGGGGAGATGGCCCAATATTCGAAGATCCAGAGGACATTTGTACCCGTAG
+ACCGGAATATGGAGAAAAGCTAAAAGAACA
+>HQ630064-241/2
+CATAATCATTTACAAAACGCGGGACCTCGACAATATGCGGGAAAATCTAACAGCAATCTA
+TCTTGGAGAATACGCTCTTCCGAAAGACCGTGGGAAAAAATTAGAAAATTTACCCACGGA
+CCCAAGTCCCGCTTTGCCATTTTAGGAAAA
+>HQ630064-217/2
+AAATCGCATGTCACACCCCAGCGTCGGAAAAACCGCCCGAGACGAAGTTGCTTCTTCTTT
+GGGGCCCCCTCTTTTTTAAGCTACAAAATTTGCTTTGAGGCCTTTTCCTTTCTTTCTTTC
+TTTCGCGTGTGATTGACGGGGGTTTACGTG
+>HQ630064-199/2
+CCGTTAGCACTTAAGTAACCGGAGCTTGGCAACACCAAGGCCTCATCCCAACATCCAAAG
+CACTCGAGCAAACGCAGGAGTAGCAAATCTCGCTATTTCAAAGCTTCAGAATCGTGTAAT
+ACACCGTCACGCTTGCTATCTTTCTCATCT
+>HQ630064-111/2
+GAAACTTGAATAAGAGCTCCCCAACTACGCTGCTAGAACTAGCAAATTTTATGCTCGCCA
+ACAAGGTGTTGGAGTTCTGCGACCACGGAGAGATGGCCGGCAGAGCACAATATTATATAA
+GTACTCCATCGATGATCATTACGACCTCCA
+>HQ630064-105/2
+TTATTAAATTGTTATTTCCACCACCGCAGAGCAATACCGTGATGTTCTTTACGCCCTCTT
+CTCCGGTCGTTGTGTTGTCCATACATCTCGTCTTCCCTCAGCGCTGCCCGCAAATGGTTC
+AACGTATGTCGGTTGGTTGACTATGTCCTA
+>HQ630064-11/2
+TGGGCGTAGTTCTGTCCTCGAGCGCACGCGAAAAATTCTCGTCTCATTTCCCCTTACCAC
+ACCACACCAAACACTGGTAGTAAAATCGCATAATGCACCCCAACGTCGGAAACACAGCCC
+GAGACGATGTTGCTTCTTCTTTAGGGCCCC
+>HQ630064-3/2
+CCACAGTTATTTGCAATAGGACTCGAGTGAGTTTTAAGAAGAGACTTCTCAAAGAGAGAG
+CCGCTTTGATCTCCAGATCACTTCACAGCCCATTAAGACTTTTCCTTTTTGACACACGAG
+TAGGGCGATATTTTGTGCTTATCCGAGAAC

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/read1.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/read1.fastq Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,16 @@
+@SRR5680996.16159603/1
+TGGGTCAAGCCTTGGACCCCAAACTCTTCGAAACTGACGGTCGTGGTTGCC
++
+@CCFDFFFHHHHHJJIJJJJJJJJJJJIJJJJIJIIGIIIIIIGIIGHIJJ
+@SRR5680996.2860859/1
+GACTGCTGGCTTTTGTGGACTCTGGATTCCAGGCTTTGCAACCCTAGCGGC
++
+@<@DDDFFHHFFFHEFHIIGIIIIIEIIIIGHIHGGIIIIIIIGEIIIIII
+@SRR5680996.18976829/1
+TAGAGAACAGGGCCCACCAGTCGTACTGGCTCCCCCAAAGGTCCCGACTGT
++
+CCCFFFFFHHHHHJJJJJJJIJJJIJJJJJIJJJJJEHJGIDGIJIJJIJC
+@SRR5680996.16094632/1
+GCAATTGTGATAAAAACTGCATGGTACTGGTATAGAGACAGACCAGTAAAC
++
+CCCFFFFFHHHHGJJJJJJJJJJJHHHIJJHHIJJJJJJJJIIGHIHJJJJ
\ No newline at end of file

diff -r 000000000000 -r 519e0835abd7 test-data/extract_kraken_reads/read2.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extract_kraken_reads/read2.fastq Wed Mar 15 18:18:27 2023 +0000

@@ -0,0 +1,16 @@
+@SRR5680996.16159603/2
+CAATCTCTGGATAGATCTTGGGGGGTGCTGATGGGCTGGACTTTCCGGCTG
++
+CCCFFFFFHHFHFIIIJJJIJIIJD<BDDDDDDDDDDDDDDDDDDDDDDDD
+@SRR5680996.2860859/2
+CTTTCAGACATGTGGGCCATCCACTAGCAACAGGATCTAATTTTTTTGACA
++
+;==D??:B:D??AE<<1;AA<ACF+CEGC@@E?8D3?FDG><F>BF:FFE=
+@SRR5680996.18976829/2
+AGACTGACCAGACAGTCCTCTGTTCCTAGGGGCGGTAGGGAAGCCGAGGTA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJ@EHHHHFFFFDCDD;@
+@SRR5680996.16094632/2
+ACTGGATGGTTTTAGGTCCCTTGTCGAAGATCAAGTGACCATAGGTGTGTG
++
+@CCFFDFFHDFHHIJJIJJJJJIIJJJJJIIJJJGFIIIJHIHIJDGFHFD
\ No newline at end of file

diff -r 000000000000 -r 519e0835abd7 test-data/mpa_output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output.tabular Wed Mar 15 18:18:27 2023 +0000

diff -r 000000000000 -r 519e0835abd7 test-data/mpa_output_intermediate.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_intermediate.tabular Wed Mar 15 18:18:27 2023 +0000

diff -r 000000000000 -r 519e0835abd7 test-data/mpa_output_percentages.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpa_output_percentages.tabular Wed Mar 15 18:18:27 2023 +0000

diff -r 000000000000 -r 519e0835abd7 test-data/only_combined_count.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_combined_count.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/output.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/output_intermediate.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_intermediate.tabular Wed Mar 15 18:18:27 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 519e0835abd7 test-data/sample.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.tabular Wed Mar 15 18:18:27 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'