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Changeset 3:3f05bf162005 (2021-04-19)

Previous changeset 2:2cff76cf35c6 (2021-03-19) Next changeset 4:2e5ae05160e0 (2021-05-17)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"

modified:
merge_metaphlan_tables.xml
tool_data_table_conf.xml.sample

removed:
metaphlan2_macros.xml
repository_dependencies.xml
test-data/community_profile.tabular
test-data/formatted_to_krona.tabular
test-data/heatmap.pdf
test-data/heatmap.png
test-data/heatmap.svg
test-data/input_sequences.fasta
test-data/input_sequences.fastq.gz
test-data/marker_metadata.json
test-data/marker_sequences.fasta
test-data/merged_community_profile.tabular
tool-data/metaphlan2_database.loc.sample
transform_json_to_pkl.py

diff -r 2cff76cf35c6 -r 3f05bf162005 customizemetadata.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/customizemetadata.py Mon Apr 19 20:54:50 2021 +0000

[

b"@@ -0,0 +1,480 @@\n+#!/usr/bin/env python\n+# -*- coding: utf-8 -*-\n+\n+import argparse\n+import bz2\n+import json\n+import pickle\n+import re\n+from pathlib import Path\n+\n+\n+def load_from_json(json_fp):\n+ '''\n+ Read JSON file with marker metadata\n+\n+ :param json_fp: Path to JSON file\n+ '''\n+ with open(json_fp, 'r') as json_f:\n+ data = json.load(json_f)\n+\n+ for m in data['markers']:\n+ data['markers'][m]['ext'] = set(data['markers'][m]['ext'])\n+\n+ for t in data['taxonomy']:\n+ if isinstance(data['taxonomy'][t], list):\n+ data['taxonomy'][t] = tuple(data['taxonomy'][t])\n+ return data\n+\n+\n+def dump_to_json(data, json_fp):\n+ '''\n+ Dump marker metadata to JSON file\n+\n+ :param json_fp: Path to JSON file\n+ '''\n+ for m in data['markers']:\n+ data['markers'][m]['ext'] = list(data['markers'][m]['ext'])\n+\n+ with open(json_fp, 'w') as json_f:\n+ json.dump(data, json_f)\n+\n+\n+def transform_pkl_to_json(pkl_fp, json_fp):\n+ '''\n+ Read Pickle file and drop it to a JSON file\n+\n+ :param pkl_fp: Path to input Pickle file\n+ :param json_fp: Path to output JSON file\n+ '''\n+ # load metadata from Pickle file\n+ with bz2.BZ2File(pkl_fp, 'r') as pkl_f:\n+ in_metadata = pickle.load(pkl_f)\n+\n+ out_metadata = {\n+ 'markers': in_metadata['markers'],\n+ 'taxonomy': in_metadata['taxonomy'],\n+ 'merged_taxon': {}\n+ }\n+ # transform merged_taxons tuple keys to string\n+ for k in in_metadata['merged_taxon']:\n+ n = ' , '.join(k)\n+ out_metadata[n] = in_metadata['merged_taxon'][k]\n+\n+ # dump metadata to JSON file\n+ dump_to_json(out_metadata, json_fp)\n+\n+\n+def transform_json_to_pkl(json_fp, pkl_fp):\n+ '''\n+ Read JSON file and drop it to a Pickle file\n+\n+ :param json_fp: Path to input JSON file\n+ :param pkl_fp: Path to output Pickle file\n+ '''\n+ # load metadata from JSON file\n+ in_metadata = load_from_json(json_fp)\n+\n+ out_metadata = {\n+ 'markers': in_metadata['markers'],\n+ 'taxonomy': in_metadata['taxonomy'],\n+ 'merged_taxon': {}\n+ }\n+ # transform merged_taxons keys to tuple\n+ for k in in_metadata['merged_taxon']:\n+ n = ' , '.split(k)\n+ out_metadata[n] = in_metadata['merged_taxon'][k]\n+\n+ # dump metadata to Pickle file\n+ with bz2.BZ2File(pkl_fp, 'w') as pkl_f:\n+ pickle.dump(out_metadata, pkl_f)\n+\n+\n+def add_marker(in_json_fp, out_json_fp, name, m_length, g_length, gca, k_name, k_id, p_name, p_id, c_name, c_id, o_name, o_id, f_name, f_id, g_name, g_id, s_name, s_id, t_name):\n+ '''\n+ Add marker to JSON file\n+\n+ :param in_json_fp: Path to input JSON file\n+ :param out_json_fp: Path to output JSON file\n+ :param name: Name of new marker\n+ :param m_length: Length of new marker\n+ :param g_length: List with lengths of genomes from which the new marker has been extracted\n+ :param gca: List with GCA of genomes from which the new marker has been extracted\n+ :param k_name: List with Name of Kingdom for genomes from which the new marker has been extracted\n+ :param k_id: List with NCBI id of Kingdom for genomes from which the new marker has been extracted\n+ :param p_name: List with Name of Phylum for genomes from which the new marker has been extracted\n+ :param p_id: List with NCBI id of Phylum for genomes from which the new marker has been extracted\n+ :param c_name: List with Name of Class for genomes from which the new marker has been extracted\n+ :param c_id: List with NCBI id of Class for genomes from which the new marker has been extracted\n+ :param o_name: List with Name of Order for genomes from which the new marker has been extracted\n+ :param o_id: List with NCBI id of Order for genomes from which the new marker has been extracted\n+ :param f_name: List with Name of Family for genomes from which the new marker has been extracted\n+ :param f_id: List with NCBI id of Family for genomes from which th"..b'for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--p_name\', help="Name of Phylum for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--p_id\', help="NCBI id of Phylum for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--c_name\', help="Name of Class for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--c_id\', help="NCBI id of Class for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--o_name\', help="Name of Order for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--o_id\', help="NCBI id of Order for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--f_name\', help="Name of Family for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--f_id\', help="NCBI id of Family for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--g_name\', help="Name of Genus for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--g_id\', help="NCBI id of Genus for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--s_name\', help="Name of Species for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--s_id\', help="NCBI id of Species for genome from which the new marker has been extracted", action="append")\n+ add_marker_parser.add_argument(\'--t_name\', help="Name of Strain for genome from which the new marker has been extracted", action="append")\n+ # remove_markers subcommand\n+ remove_markers_parser = subparsers.add_parser(\'remove_markers\', help=\'Remove markers from JSON file\')\n+ remove_markers_parser.add_argument(\'--in_json\', help="Path to input JSON file")\n+ remove_markers_parser.add_argument(\'--markers\', help="Path to file with markers to remove (1 per line)")\n+ remove_markers_parser.add_argument(\'--out_json\', help="Path to output JSON file")\n+ remove_markers_parser.add_argument(\'--kept_markers\', help="Path to file with kept markers")\n+ # keep_markers subcommand\n+ keep_markers_parser = subparsers.add_parser(\'keep_markers\', help=\'Keep markers from JSON file, others will be removed\')\n+ keep_markers_parser.add_argument(\'--in_json\', help="Path to input JSON file")\n+ keep_markers_parser.add_argument(\'--markers\', help="Path to file with markers to keep (1 per line)")\n+ keep_markers_parser.add_argument(\'--out_json\', help="Path to output JSON file")\n+\n+ args = parser.parse_args()\n+\n+ if args.function == \'transform_pkl_to_json\':\n+ transform_pkl_to_json(Path(args.pkl), Path(args.json))\n+ elif args.function == \'transform_json_to_pkl\':\n+ transform_json_to_pkl(Path(args.json), Path(args.pkl))\n+ elif args.function == \'add_marker\':\n+ add_marker(\n+ args.in_json,\n+ args.out_json,\n+ args.name,\n+ args.m_length,\n+ args.g_length,\n+ args.gca,\n+ args.k_name,\n+ args.k_id,\n+ args.p_name,\n+ args.p_id,\n+ args.c_name,\n+ args.c_id,\n+ args.o_name,\n+ args.o_id,\n+ args.f_name,\n+ args.f_id,\n+ args.g_name,\n+ args.g_id,\n+ args.s_name,\n+ args.s_id,\n+ args.t_name)\n+ elif args.function == \'remove_markers\':\n+ remove_markers(args.in_json, args.markers, args.out_json, args.kept_markers)\n+ elif args.function == \'keep_markers\':\n+ keep_markers(args.in_json, args.markers, args.out_json)\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">3.0.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.01</token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_3174</edam_topic>
+            <edam_topic>topic_0194</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_2478</edam_operation>
+            <edam_operation>operation_0324</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">1101/2020.11.19.388223</citation>
+        </citations>
+    </xml>
+    <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>
+    <xml name="tax_lev">
+        <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
+            <option value="a" selected="true">All taxonomic levels</option>
+            <option value="k">Kingdoms only</option>
+            <option value="p">Phyla only</option>
+            <option value="c">Classes only</option>
+            <option value="o">Orders only</option>
+            <option value="f">Families only</option>
+            <option value="g">Genera only</option>
+            <option value="s">Species only</option>
+        </param>
+    </xml>
+</macros>

diff -r 2cff76cf35c6 -r 3f05bf162005 merge_metaphlan_tables.xml
--- a/merge_metaphlan_tables.xml Fri Mar 19 21:40:18 2021 +0000
+++ b/merge_metaphlan_tables.xml Mon Apr 19 20:54:50 2021 +0000

[

@@ -1,55 +1,47 @@
-<tool id="merge_metaphlan_tables" name="Merge" version="@WRAPPER_VERSION@.0">
-
-    <description>MetaPhlAn2 files</description>
-
+<tool id="merge_metaphlan_tables" name="Merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>MetaPhlAn abundance tables</description>
     <macros>
-        <import>metaphlan2_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
-
+    <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
     <version_command>merge_metaphlan_tables.py -v</version_command>
-
-    <command>
-<![CDATA[
-        merge_metaphlan_tables.py
-            #for $element in $input_files
-                '$element'
-            #end for
-            > '$output'
+    <command detect_errors="aggressive"><![CDATA[
+merge_metaphlan_tables.py
+    #for $element in $inputs
+        '$element'
+    #end for
+    > '$output'
]]>
     </command>
-
     <inputs>
-        <param name="input_files" type="data" format="tabular,txt" multiple="True" label="MetaPhlAn2 output file to join" />
+        <param name="inputs" type="data" format="tabular,txt" multiple="true" label="Predicted taxon relative abundance tables generaed by MetaPhlAn" />
     </inputs>
-
     <outputs>
-        <data format="tabular" name="output" label="${tool.name} on ${on_string}: Merged MetaPhlAn2 files" />
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Merged taxon relative abundance tables" />
     </outputs>
-
     <tests>
-        <test>
-            <param name="input_files" value="community_profile.tabular,community_profile.tabular"/>
-            <output name="output">
+        <test expect_num_outputs="1">
+            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
+            <output name="output" ftype="tabular" >
                 <assert_contents>
-                    <has_text text="#SampleID" />
-                    <has_text text="k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron|t__Bacteroides_thetaiotaomicron_unclassified" />
+                    <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
+                    <has_text text="dataset_"/>
+                    <has_text text="NCBI_tax_id"/>
+                    <has_text text="clade_name"/>
                 </assert_contents>
             </output>
         </test>
     </tests>
-
     <help><![CDATA[
-
-**What it does**
+What it does
+============

-MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
+MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
+Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.

-This tool performs a table join on one or more metaphlan output files
-
+This tool performs a table join on one or more tab-separated files with the predicted taxon relative abundances
+that have been generated by MetaPhlAn.
     ]]></help>
-
     <expand macro="citations"/>
</tool>

diff -r 2cff76cf35c6 -r 3f05bf162005 metaphlan2_macros.xml
--- a/metaphlan2_macros.xml Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,40 +0,0 @@
-<?xml version="1.0"?>
-<macros>
-    <token name="@WRAPPER_VERSION@">2.6.0</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">metaphlan2</requirement>
-            <yield/>
-        </requirements>
-    </xml>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" level="fatal"   description="" />
-            <regex match="ERROR"
-                   source="stderr"
-                   level="fatal"
-                   description="" />
-            <regex match="WARNING"
-                   source="stderr"
-                   level="warning"
-                   description="" />
-        </stdio>
-    </xml>
-    <xml name="citations">
-      <citations>
-          <citation type="doi">10.1038/nmeth.3589</citation>
-      </citations>
-    </xml>
-    <xml name="tax_lev">
-      <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
-        <option value="a" selected="true">All taxonomic levels</option>
-        <option value="k">Kingdoms (Bacteria and Archaea) only</option>
-        <option value="p">Phyla only</option>
-        <option value="c">Classes only</option>
-        <option value="o">Orders only</option>
-        <option value="f">Families only</option>
-        <option value="g">Genera only</option>
-        <option value="s">Species only</option>
-      </param>
-    </xml>
-</macros>

diff -r 2cff76cf35c6 -r 3f05bf162005 repository_dependencies.xml
--- a/repository_dependencies.xml Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-<?xml version="1.0" ?>
-<repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases.">
- <repository name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="83f07f40b200"/>
-</repositories>
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-abundances.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances.tabular Mon Apr 19 20:54:50 2021 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-bowtie2out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-bowtie2out.tabular Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,140 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No newline at end of file\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-ignore-marker-bowtie2out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-ignore-marker-bowtie2out.tabular Mon Apr 19 20:54:50 2021 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-legacy-abundances.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-legacy-abundances.tabular Mon Apr 19 20:54:50 2021 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,278 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No newline at end of file\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares-two-inputs.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-two-inputs.sam Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,377 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6\t765\t42\t91M\t*\t0\t0\tCAACGATGGCGCCGCTGTAGAGGGGCAGGCTCACTCGACTACCCCGAAGGCAGAGTTCGGCACCGCGCTTAACCAAGGGGCAACGCCGTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:75G15\tYT:Z:UU\n+HWI-EAS109_102883399:4:86:2354:13206/2\t0\t38303__E2S5B9__HMPREF0305_11721\t628\t42\t100M\t*\t0\t0\tGAGTCGTATCTTCGCTATGGGCAGTTTGTTGATGCAGCCCAAGACTCAGAGAAGATGAGTATTACCGAACTGGTCGATACCGCTATCGAAGAGTCCGATA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:35G64\tYT:Z:UU\n+HWI-EAS109_102883399:3:118:12526:20595/1\t16\t29394__H3NDE2__B8A45_00965\t86\t23\t100M\t*\t0\t0\tAACGTGGGGTGAAAAATCGACCAGCAGGATTACGGACATACAGTTTAGTTTGCTTAGGATCCGCTTTGATTATGTTGACGAATCAATATATTACAGAACA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-30\tXN:i:0\tXM:i:5\tXO:i:0\tXG:i:0\tNM:i:5\tMD:Z:29C4A17T8T2C35\tYT:Z:UU\n+HWI-EAS109_102883399:3:35:14701:14421/1\t16\t478__A0A1B8PMT8__A9Z60_01500\t160\t40\t100M\t*\t0\t0\tACTCGTGATAATACTTCACTGGCATTATCAAGTTCTTTGGTTAAAGAAACTGTGGGTGATACCAAAAAAGACTCAGAGATGTTACTGGGACAACTCTCCA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:41C2G0C54\tYT:Z:UU\n+HWI-EAS109_102883399:4:51:2231:13778/1\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n+HWI-EAS109_102883399:4:65:18885:8678/1\t16\t37637__V7ZTH7__N579_0112775\t469\t42\t100M\t*\t0\t0\tGATTTTGTTGATGATCCGGATTCTACTCGGATGTTTTCTGAGAACTCCGCCTGCCCAAACGGGCATGCTCTGACGATTGATGAGTATGAACCCCGCTCCT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+HWI-EAS109_102883399:3:54:17385:9920/2\t0\t29394__H3NE37__B8A45_05170\t63\t42\t100M\t*\t0\t0\tACAGTATTACAACGATCAAGCCTTATTTAAATACGATTGGAACTTTTTCCAATTAAAATTTCAGCCGTATTTACAGGAATTCAAGTTAATTGAAGAAATG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:100\tYT:Z:UU\n+HWI-EAS109_102883399:4:2:5506:17168/2\t0\t29394__H3NFP2__B8A45_07105\t284\t42\t100M\t*\t0\t0\tGCCTAGCAATTGAGCAAGTTGATGGTAAGTTTATCTTGAAGCTCTATATTTGGGATGGGGCTGAGCATTATTATATGGACATGGATGCTGAGACCGGTGA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-6\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:10C89\tYT:Z:UU\n+HWI-EAS109_102883399:4:95:2036:2688/2\t16\t478__A0A1B8PJ21__A9Z60_08925\t339\t24\t76M\t*\t0\t0\tCATTTGGGCATCTTCGATCTCTATCACGCCTGAGCGTGAACAAGTGATGGATTTTAGTGAGCCATATTTGAATCAT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-18\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:0T8G8T57\tYT:Z:UU\n+HWI-EAS109_102883399:4:51:2231:13778/1\t16\t1747__D4HCY1__CP884_07625\t394\t42\t78M\t*\t0\t0\tGAATACGAGGATAGTCTCGGGGCTGTCGCGGGTGGTGAAGCATTCCACTACGCCGTTCTGCATTTTCGGCTTGATGAC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:78\tYT:Z:UU\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares.biom Mon Apr 19 20:54:50 2021 +0000

[

@@ -0,0 +1,1 @@
+{"id": "MetaPhlAn_Analysis","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by": "MetaPhlAn","date": "2021-04-09T17:17:44.233735","matrix_element_type": "float","shape": [7, 1],"type": null,"matrix_type": "sparse","data": [[0,0,5.98726],[1,0,18.75365],[2,0,9.63281],[3,0,13.4261],[4,0,13.73399],[5,0,22.57968],[6,0,15.88652]],"rows": [{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Corynebacterium_accolens"]}},{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Corynebacterium_pseudodiphtheriticum"]}},{"id": "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Propionibacteriales", "f__Propionibacteriaceae", "g__Cutibacterium", "s__Cutibacterium_acnes"]}},{"id": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Dolosigranulum", "s__Dolosigranulum_pigrum"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_equi"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_lacunata"]}},{"id": "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Moraxella", "s__Moraxella_nonliquefaciens"]}}],"columns": [{"id": "Metaphlan_Analysis", "metadata": null}]}
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares.fasta Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,40514 @@\n+>HWI-EAS109_102883399:3:100:10648:20124/1\n+TTGATATTTCATGTACAGTATAAAATATATATTTGGGTTACTTTGGTATTTTATGTACAGTATATAATCTATATTTGATGTACTTTCATATTTTATGTAC\n+>HWI-EAS109_102883399:3:100:1079:13862/1\n+ATATTGATACTTGCATTAATATCACGGTCATGATTGGCATGGCAACTAGGACAAATCCAATGTCTAACCGCAAGTATCAAGTTTTCTTTTGCCATAATAA\n+>HWI-EAS109_102883399:3:100:10822:2790/1\n+CACACACACATATACACACACACATATACACACACACATACACACACACACAAACACACACACACACAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGA\n+>HWI-EAS109_102883399:3:100:10896:21102/1\n+CTCTTCGTCCTAAGGACCACTGTCTGTGCTGTGTCTTTCAAAGGTCAGAAGAGATTGAACCTTTGTGTTTTTATTTTCCCTGTGTTTGCTTTTTC\n+>HWI-EAS109_102883399:3:100:11210:16352/1\n+GTCTTTTCTTTTTGCTTGCCATTGTGGCTGTAAATTGATACAAAAACTTTTGTGCCTGTATGTTGCACATAAAGCCATAGCCCATTACCATCACTGATTT\n+>HWI-EAS109_102883399:3:100:11502:9110/1\n+TCGCCCAGCAAATTCATCCACCTTGTCAGATGGCACACCCACACGACTTGGGCGAAATTCTACGCACAGTTTAAATAATTTATCCAAACGACCAAAGCCC\n+>HWI-EAS109_102883399:3:100:11549:6243/1\n+TGGAAGCGTTGGGGATTTACGTAGTTTGTTGGATTTGCTTCCCGTCGCTGGTGGTGATGGCACGCTGGACGATCGTTACGCTGAGCTTTCT\n+>HWI-EAS109_102883399:3:100:11778:13384/1\n+AAGTACATCAAATATATATTTTATTCTGTACATAAAATATGAAAGTACACCAGATATATATTCTATAGTGTACATAAAATATCAAAGTACCCAAACTATA\n+>HWI-EAS109_102883399:3:100:12997:10542/1\n+ATAATATATGATACATATTATACATCTTATATATGAAATTATATAATTATAGATAACATAATACACATTTATATGTATTATGAAATATAACAAAGGTACT\n+>HWI-EAS109_102883399:3:100:13379:16343/1\n+TATTATATACTGTACATCAAATATGAAAGTTCCCAAACATTTATAATAATCTGTACAGAAAATATCAAAGTACTCAAACTATAAACTGTACATAAAATAT\n+>HWI-EAS109_102883399:3:100:13680:7440/1\n+AATGTTTATGCCCTATCGCCATGGTGACGGAATTAGGGGTCTCCTGCTCTTCGTCCTAAGGACCACTGTCTGTGCTGTGTCTTTCAAAGGTCAGAAGAGA\n+>HWI-EAS109_102883399:3:100:14551:6350/1\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTG\n+>HWI-EAS109_102883399:3:100:14666:5491/1\n+TCGTATCTTGTCGACGGCTGGGCCTACCTGGTGTTTTACGGGGCGCTGGCGTTTTTGCTGATCGTTTTTGCCAACTATTCCGCCTTCGGGGTGCGG\n+>HWI-EAS109_102883399:3:100:14711:18833/1\n+TATTTAATACGTATATTAACCGTATAATATATTCTATATATGATATATAACATATATTATATATGTCATAAATTATAATATATACTATATGTCATATTGT\n+>HWI-EAS109_102883399:3:100:14778:2943/1\n+CCTTAACTAGTAATTTGAAGAGTTGGCATTTGTAAGGCCAGTATGAATATACCTTCAAAGCAGCAACACAGGTTCCCCATGAGAAAAAGCAAACTTAGGG\n+>HWI-EAS109_102883399:3:100:15216:16187/1\n+TCAATACCAAGACTTTTATTCAGCACCAGCACCAGCACCAGCACCCATGCCATTTTATGCAACAGATTGATGCTAATTTATGCTTAATTTGCCCTATTTT\n+>HWI-EAS109_102883399:3:100:15403:10319/1\n+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATATCGTATGCCGTCTTCTGCTTGAAAAAAA\n+>HWI-EAS109_102883399:3:100:15588:15047/1\n+GTATATAATAATATACAGTGTCATATATATAATATATATAACCTATGTATAATATTGTTTTACATCCTGCATCTTATGTTATATATATTGTATAAAATAT\n+>HWI-EAS109_102883399:3:100:15950:5267/1\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGT\n+>HWI-EAS109_102883399:3:100:16342:18195/1\n+AATACAAAACTTAACACAAGCCCAATCACTGTACCCAAAAAAGCAGTAATCAGCGTATATTTGGCATGACTCATGAGTAAATAAAAATCATCAATAAACG\n+>HWI-EAS109_102883399:3:100:16772:11935/1\n+TATATATTATATATAATACGTTGTATGTATAATACCTATATTAAATATATATTATATGACTATGTTATTAATTACATGTCACATGTGTTATATATTATAT\n+>HWI-EAS109_102883399:3:100:17086:13140/1\n+GTGTATATTTCTTATTATTTCATACTAAGGTACCAGCAGGAAATTGACTGAGAAAGCAGAACCCCCGAGGTTCAAAAGTAGAGATGTAGAGGTGGTCAAG\n+>HWI-EAS109_102883399:3:100:17665:4571/1\n+GAGGTAAATCCAATATAGAGATCGCGCAAGAAATGCACTACTCAGAATCAGCAACGAAAAAACGAGTATCTAAGCTCATTCATCGGTTTGGTGCTAGCTC\n+>HWI-EAS109_102883399:3:100:17797:18754/1\n+ATAAAAACACAAAGGTTCAATCTCTTCTGACCTTTGAAAGACACAGCACAGACAGTGGTCCTTAGGACGAAGAGCAGGAGACCCCTAATTCCGTCACCAT\n+>HWI-EAS109_102883399:3:100:18441:1058/1\n+CTGTGTCTTTCAAAGGTCAGAAGAGATTGAACCTTTGTGGTTTTATTTTCCCTGAGTTTGCTTTTTCTCATGGGGAACCGGTGTTGCTGCTTTG\n+>HWI-EAS109_102883399:3:100:19075:9045/1\n+ATATATTATAATTTATATAATGATAAAATTTTTTATAGAATATAAATAATTATATATGATTATATAATTCTACATATTACAAATGAAAATATGTAGAATT\n+>HWI-EAS109_102883399:3:100:19100:11382/1\n+TAATATGGCTGCAGAAACCCCCCAAGAGCGTTCAGTGCCCCCGCATGAACAATGTTCCCC\n+>HWI-EAS109_102883399:3:100:2227:10884/1\n+AATGACAGCTGGCATGAGCTTGGCATTGAGCCTGTCGGTCATTTGGTAATCCACGGGTATCGTATCCACCGCTTGCCCATTAATAGACAGCGCG\n+>HWI-EAS109_102883399:3:100:2800:14548/1\n+GCAAGAGTATTCAATGCAGAGATACACGTTGTCGTTGTTTGCATAT'..b'GAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG\n+>HWI-EAS109_102883399:4:96:5093:3048/1\n+CGGGAGAGCGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGA\n+>HWI-EAS109_102883399:4:97:1937:11653/1\n+CAGCTCCCCCTATGCCTCCGTTTCTAGGAAATGTTGCGCCTGCAGCAGAAACTCCGGGCT\n+>HWI-EAS109_102883399:4:9:4334:5972/1\n+GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAAA\n+>HWI-EAS109_102883399:3:104:6463:17673/1\n+CACACACATTATTACGCTGCGCTTCTTACAACAAGTTATCAGATGGGGAATAGGGCACCCACAAATATAAATATACATTATGTATATAATCATATATAGT\n+>HWI-EAS109_102883399:3:105:3530:10413/1\n+ATATATAATATTGTTTTACATCCTGTATCTTATATTAGATATATCATAGGTAACATAATAATGGATAATTCATAATTATAATATTTATACAATACGACAC\n+>HWI-EAS109_102883399:3:120:6816:3534/1\n+GCCTTGACGACGTCTTATCCGCTGGCGATTGTTGCTCGCGTATTGATCGGCGCCGGTGATGCCTCGGCGTTCTTGG\n+>HWI-EAS109_102883399:3:14:13657:17008/1\n+TAATTACATGTCACATATGTTATATATTATATATTTTACATAGAATGTACTGGTTACATACAATATATAGTATGTTACCTGTAATGTATAATTTATTACA\n+>HWI-EAS109_102883399:3:1:6565:9569/1\n+TATTATGCATAATTTATAATATACAATATGTGGAATGTGATATATATAACATATAATATATGATATATGATATACAGTATATGATATATAACATACAATA\n+>HWI-EAS109_102883399:3:24:10907:13582/1\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGT\n+>HWI-EAS109_102883399:3:43:5734:14285/1\n+AGGCGTTTGGTTTCATCAAGGCTTGCTCCTGCCTTTGGGGTTGCTATGACCACAAAAAAGCCATCACCATAGCCCAAACTGTCATAACTGCTGTATGCT\n+>HWI-EAS109_102883399:3:46:16209:7151/1\n+ATCTTATATCATACATTATATGTTATATATATCACATTCTACATATTGTATATTATAAATTGTACACAATATATTGCATTCTTTATTTTACATGTAATCA\n+>HWI-EAS109_102883399:3:57:11738:2514/1\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATATCGT\n+>HWI-EAS109_102883399:3:59:12370:16325/1\n+CTAAGATGATTTGACCGCCTTGTCAGTAGGAGTTTGGGTTTTGGTTCGTCTGTAATAACTAAAAGCACACATGCCTGTGGTAAAGGGTTTGAAGCTAACA\n+>HWI-EAS109_102883399:3:62:12328:3801/1\n+ATATTATATATCATATATGATATAGTACCTTTGTTATATATCATAATACATATAAATGTGTATTATGTTATCTATAATTATATAATTTCATATATAAGAT\n+>HWI-EAS109_102883399:3:64:10378:11274/1\n+CGTTGTACTTTAAGCTGGCCTTGCTCATCGGACATATACAGATAAAACGGATCATCCTGGTTGCGCGTATCCCACCACTGTTTTCGGGTTTCCTTAGTGG\n+>HWI-EAS109_102883399:3:69:7124:5695/1\n+TTGAGAAAACTCTTCCGGCATCCTAGGGGAACAGAGGTACGATTTTTCGAGACAGTCGAGGGAGAAGCCACCCCAGATTTTAGGATTGGATCTTTATTCA\n+>HWI-EAS109_102883399:3:75:4419:11351/1\n+TGCGGATTCATCGGGTTGGGCCGCCTGGGCGGGGCTCACCCCCACACTGCTGACGAGCGC\n+>HWI-EAS109_102883399:3:78:3607:5515/1\n+GAAAAATTAAAGGCAGTCTGTCCTGCTTTTTATGGGCAAATCTACTCATGTATTGCCACAGGTATGGGATTGATGTCTTGACTGTTTTGG\n+>HWI-EAS109_102883399:3:86:19018:14133/1\n+ACAAAATCTTACCTTTGTCTTCCTTGGACGTGCCTGGGCACCACTTCTGCCAACCTGTGAAGCCATCCTGCCCTGACAGAGATCGGAAGAGCGGT\n+>HWI-EAS109_102883399:4:114:5270:19170/1\n+TGTACCTTCATATTTTATGTACAGTATACAATATACATTCTGGGTACTTTGATATTGTATGTACAGTATGCTATATATTCTGGTTACTTTGATATATTAT\n+>HWI-EAS109_102883399:4:26:13028:14044/1\n+TGAGTGGGATTAAGGCGGTCAAGGTCTAAGGAGTTGAATAAAATTGGCAGGCAACATAAGCGGTCATTCATGGCGACAGGCTGTGAATAAAAGGG\n+>HWI-EAS109_102883399:4:29:1227:15411/1\n+ACGTATCGGTTGTATGGAAATAGACTTCTGTATGATAGATGTAGGTGTCTGTGTTATACAAATAAATACACATCGCTCTATAAAGAAGGGATCGTC\n+>HWI-EAS109_102883399:4:29:16361:20631/1\n+ATCAGTACGATGTCATCAGATGGGCGGACAACAAACCCAAAACTCTCTTCATTGATGTTGCCCGTTACTCGATAATAGAGGTTGATTTTGT\n+>HWI-EAS109_102883399:4:2:16905:14371/1\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTG\n+>HWI-EAS109_102883399:4:51:2231:13778/1\n+GTCATCAAGCCGAAAATGCAGAACGGCGTAGTGGAATGCTTCACCACCCGCGACAGCCCCGAGACTATCCTCGTATTC\n+>HWI-EAS109_102883399:4:70:16446:12691/1\n+TATATAGTGCCAAATGAGAGAGTCCAACCAAGCGAAAAGGGAGTAGGACATTCTCACCATCTAAGCTGTGGCGGTGAGCATTGTCCGCATCGGT\n+>HWI-EAS109_102883399:4:70:1686:3360/1\n+CATGTGAAGGCTTTTATGGGCATGTTGGATCGATATTCGGTTGATGTGGCGTCTGGTGGCCGTGGTGGGGGTTCTGCTGTGGCGATGATTGACCGG\n+>HWI-EAS109_102883399:4:71:12108:17024/1\n+GGGTGTTATTTGGTGATGATACTTGATTGTTAAATCAATGTCATTGTTAACATCAAGAAGGCAAAAATTGGCAACGGTTATTCTTATATTCTTATTTATA\n+>HWI-EAS109_102883399:4:90:13950:7907/1\n+AAATATGAAAGTACATCAAATATAGATTATATACTGTACATTAAATACCCAAGTACCCCAAATATACATTTTGTACTGTACATGAAATATCAAAGTTCAC\n+>HWI-EAS109_102883399:4:98:17563:4110/1\n+TATATTATAATATTATGTATGTTAGTTATATTGGGTGATATGTAATATATATTATGTAATATGAAATAATATAATATATATTATATTATGATATTTTATG\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares.fasta.gz

Binary file test-data/SRS014464-Anterior_nares.fasta.gz has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/SRS014464-Anterior_nares.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares.sam Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,235 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diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/community_profile.tabular
--- a/test-data/community_profile.tabular Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/formatted_to_krona.tabular
--- a/test-data/formatted_to_krona.tabular Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-68.05418 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_stercoris
-31.94582 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_thetaiotaomicron
-68.05418 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_stercoris Bacteroides_stercoris_unclassified
-31.94582 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides Bacteroides_thetaiotaomicron Bacteroides_thetaiotaomicron_unclassified

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/heatmap.pdf

Binary file test-data/heatmap.pdf has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/heatmap.png

Binary file test-data/heatmap.png has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/heatmap.svg
--- a/test-data/heatmap.svg Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/input_sequences.fasta
--- a/test-data/input_sequences.fasta Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2260 +0,0 @@\n->r2|637000026.fna|5753889|5754040|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln383_#0/1\n-CTCCGTCCGCTGGTAGAACGTCTGGTAGAAGCTCAAAAAGCATTGGCAACCAAATACCTTTCCGAAGCCAAACGACTGATTGCCTCCAACGACAAGAAGGAAGTGGAAGAAGGATTCCTTGCCCTTTATCGTAGCCACAAGTGTCTTCCGA\n->r3|637000026.fna|1749333|1749484|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln165_#0/1\n-AAGTAAAAGTCTACACACAGGAAGGAACGATAATGGAAAGTACGATTGAAGTAAATCGTCCGATGGAGATAGCAGGATGGAAAATTTATCAGCTTAGTTATGATGAGTCGAAAGGTCGCTGGAGCGATATCAGTGTCTTTGAGCTGGTTCG\n->r8|637000026.fna|2991814|2991965|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln402_#0/1\n-AGAAAGTTTTGATCAAAGCATGGGATGCTGAAAACGGACCGGTAATTATCGACTCAGGAGAAAGTACCTACAACACAACCGCCAAAAAGTTCAGCCTCAAATATACGATCGGTAACACGCTATATGAAGAGCAACTGACCAAAGAAAAAGA\n->r24|641736196.fna|214158|214309|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln388_#0/1\n-CAGATACGAGTACCAATTGGCCGTCAACGACTATTGGAAGGAAGTCGGCGGATTGCAGATGCTGCCCGGAACCAACCGCTCCAGCGACCGCTTTGTACGCGCGTCATTCTACATTCATGCCATTCCGCAGACAGCAGACGCGGCGATTGCA\n->r32|637000026.fna|4140951|4141102|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln422_#0/1\n-TATTCTCAGGGGACTAATTGGTGATATAGTGCTCGATTATGATAGAGGTGAAGGAATTATGTCCTTTAAGACTCAAAAGGTAGGTTATATATCAGGATATTATTTGGGATGTACTACATATTGTTATGCCATGGGATTTTATCCTACATAT\n->r55|637000026.fna|6212867|6213018|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln342_#0/1\n-CAGGCGTCGGGTGAGCTGGACTTTGAAGAGTTGTGCGAAGCGATCACCAGTCGTTCTACTTGTACGGAAACGGATGTACGTGCGGCTATTTCGGGTATTCTTTACGAAGTGAAGCGTGCGTTGAAGGCAGGAAGAATTGCGAGACTGGGTG\n->r94|641736196.fna|124792|124943|_from_ |NZ_ABFZ02000020_Bacteroides_stercoris_ATCC_43183,|_ln396_#0/1\n-AATCAGTTTCATACGCTATCAATATCCGGGGTCAATAGTTTCCATTTGTTGCTCGCTTGACACGCTTTCAAAGCTAACATCTTCCGCATCAATCAACTGTTTGTTTGCGTAATTGTCGGTCAATATTTCACGCTGTGAAGTTTCGTCACCC\n->r115|641736196.fna|175677|175828|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln360_#0/1\n-CTGTCAGATACGTGAAAGATTACATTCGATACGTGAGTATGTAATGAAATATCCTGAGTTTGACGATAGAAACGATATTGACCCGTCAATGCGAATGTTCTATATCCAGTCTGTTGAAGCACAAGCAAAAAATCGAAGTTATTCAGATGCA\n->r121|641736196.fna|7934|8085|_from_ |NZ_ABFZ02000017_Bacteroides_stercoris_ATCC_43183,|_ln383_#0/1\n-TGAGCGGTTCGGTCTATACCCTTATGAATAAAATCTTCAGGGATTCAAAAGAACCGCTGTATGGCCGTGCTGACAATATCATGAAGTTAGCTCCTTTTACTACTTCCGTATTGAAAGAAATCATATCGGATCATAAGGCCGACTATACTAA\n->r145|637000026.fna|1378791|1378942|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln396_#0/1\n-TCCGTCTGATTCGTAGTGTACCAGCATATCCGCCATGACATCGCTCACTGTAGCGCTGAAATCTTTCAGAAGTTTATGGCTGCCCACCCAGTAAGTCTTGCCTTGATAAGACACCTTTATACCTTTGCCTGTGATGCTCTCAAAACTGCTC\n->r158|637000026.fna|3242194|3242345|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln388_#0/1\n-GGACAGCAGTATCAAACGGTTAAAATACGTGAGATACGCAGATGACTTTCTGATTGGAATTACCGGTAATCTTGAAGACTGCAAAACAGTAAAAGAGGATATTAAGAATTATTTGAATGAAGCTCTTAAACTGGAACTGTCAGACGAAAAG\n->r160|637000026.fna|3948359|3948510|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln347_#0/1\n-CGGAAGTGACTCATACATATCAGGTGGTTCTTCCAGTTATAAGAACCTGTCTGCAAGTGAAATGAAGAACACATCTTCATTCACAAACTGGAATTTCAGTACGGTTTGGGAAATGGGAAGTGAATACCCGACATTACAGGGCTTATTAAAA\n->r187|637000026.fna|5220534|5220685|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln396_#0/1\n-GTTACCTTGATCAATGGATTTGCATATTCCAGCAACCACGAGATAGAGGCGTGTCCTGCTTCATGCAAGGCAATCGAGCGTCTTTCCGCTTCTGTGGTAATCTTGGTCTTCTTTTCCAGACCACCGATGATACGGTCTACCGCATCCAGAA\n->r192|637000026.fna|2858128|2858279|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln325_#0/1\n-ACGTGGACGGTTACGCACTGCCGGAAAAAATCAGGAACGCATTCCTGGGATTGGAGGAAAAGGAGAAAACACTCATCAGTTACTTCACCCAGCACAATGAACAGTATGCAAAGAAGGTCGGCAAGACTGCCACGCAAAAGACCTATTCCCG\n->r218|641736196.fna|272465|272616|_from_ |NZ_ABFZ02000022_Bacteroides_stercoris_ATCC_43183,|_ln348_#0/1\n-ATTTCTTCGTCGGTTTCCGTATGGAAGAAGTACACCACGGCCAACTAGGTGAAGTGACGGATGTGGACACCTCTACCATCAACACTCTGTTCGTGGTAGATTATAAAGGAGAAGAATTGCTGATTCCGGCACAGGAAGATTTCATTATGGA\n->r222|637000026.fna|2630231|2630382|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_'..b'CGGACTTTCGGTATCTATCTATATGTCTGAGGTCGCCAATCCGAAGGTGCGCAACTGGCTGAAACCGATCATTGAA\n->r12070|641736196.fna|375596|375747|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln407_#0/1\n-GAATGTTTTTCCATGAATATTTATGTTTTCTGACCGGGAGTCTTTCATGGAATTAATCAATAAATCATACATATGTTCCATTGCTCCCTTAGAAGGAGCTTTGATGTAGCTAACGGTTAAACTGCTGACACCATGTCCTCGAAGTTGCAAT\n->r12072|637000026.fna|2532372|2532523|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln392_#0/1\n-GGCTCCGGGATTGATGTGCAGCATGTCCAACGTTTTGTCGTATTTCACCTTTAATATATGGGAGTGTCCGCTGATGAAAAGTTTCGGCGGACGGGCCATCAAACTGCCGATAACCGAAGGGTCGTACTTGCCCGGATACCCGCCGATATGC\n->r12073|637000026.fna|6194446|6194597|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln420_#0/1\n-CTGAATATTATAGTCATATCCCTTCACCGGTTCTTCCAGCTCTTTGAATATCACAAAGGCGCGTTGCCCGTCTTTATTCTTGTCACTGATCCATCCGTTTCCATTGCTCGGGAACATTGTTTTTCCATCATCCAGAGTGAAATAGAAATCC\n->r12077|641736196.fna|245225|245376|_from_ |NZ_ABFZ02000016_Bacteroides_stercoris_ATCC_43183,|_ln342_#0/1\n-ATGCAGTGTCGCCCACCATGTCCATGTCGCTCTCACGGTCGAAAAGCAATGTATAATAATTCTGTTTGGTAAACAGGTAGTCGTGCTTCCAGAAGCGTTCCTCTATCTTCGAAGGAGTGTCCCGGTTGTAATAAGGCAAAGGAAACTCCGT\n->r12078|641736196.fna|76492|76643|_from_ |NZ_ABFZ02000017_Bacteroides_stercoris_ATCC_43183,|_ln385_#0/1\n-GATCCTTTCAGTTCGTACCACTCGTCATCCGGCAATCCGTTTCCGTTTATATCTTGCATGACCCATACGATACCCGGTTCGGAACTGCCGTCAAAGGCGTTCCCCTGAACACAGAAATCATATTGGTTACCCGAATTGGGAATACTGTGGT\n->r12088|641736196.fna|108362|108513|_from_ |NZ_ABFZ02000016_Bacteroides_stercoris_ATCC_43183,|_ln368_#0/1\n-AGGTTTCCACACTTCCTCGCCAAAATAGTTGTGAGGACCACCGAAGCGGCAGTCCAATATTCCGGCAAGCGCCGCTTCCGGATAGCCGGAATTGGGACTGGCATGCTTGCTGCCGTATTTCCCCACAAAAAGCAGCAACGGGAATCTGCCG\n->r12120|637000026.fna|4257090|4257241|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln262_#0/1\n-ACGGGCTTCTTCGCCAATGCTCTTCCCATAAAGATAAGACATTTCGGGATTCCATGTTGCAGAAAGGCAAGTCAATGCAGGATAGGCTATACAGGAATCGTTTGTCCATCCTGCCTGATCCCACTCATCCCATAATACTTCGGGACGGATG\n->r12152|637000026.fna|2685134|2685285|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln353_#0/1\n-CACTCAAATCATCAATCAAGCTGACTTTCTTTAATGTATCCTTCTTAGCATCATAATATTTCATCTCCAGATTATTAGCAATCGAGAAACTAACCGTTCCCGAACCCTCACGTGAAGGGACTCCAAAAGGCTGTCCCGTATAGGGTGAATA\n->r12163|637000026.fna|5651468|5651619|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln367_#0/1\n-AATGAACAACACCATTAAAAACGGTTGGCTATTCGACTGTGATGATGAGAGCTTCGAGCAAGTAAGCAAGCGCATTGAAGATGCTGTATATGTATATAATCATGTGCGGCCTCATCAAGGGATAAACATGAGGACACCTATGGAAGTGGTC\n->r12201|641736196.fna|253613|253764|_from_ |NZ_ABFZ02000023_Bacteroides_stercoris_ATCC_43183,|_ln348_#0/1\n-CCACTCCGGAAGGTATTATTGGCAATGAAGACTGCGGGCAGATGTCGGCATGGTATATTCTTTCAAGTATGGGACTTTATTCGGTTTGTCCTGGTAGCAACGAATATGTTCTTACTACTCCCTTGTTCGAGAAAGTTGTAGTGCATTTGGC\n->r12208|637000026.fna|1887139|1887290|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln435_#0/1\n-ACATCGCGGTTGCTTTTCGCTACCCGTACCTTTCCGCGTCTCTTTCCCCAGTCCAGAATCGGAATCTGAACGCCTACCTGCACAATCTGATTATCCTGCAAGTTCCTGTAGACACTGGAAAGTTCACGACTCTCTCCCGTATATCCTACAC\n->r12218|641736196.fna|422226|422377|_from_ |NZ_ABFZ02000018_Bacteroides_stercoris_ATCC_43183,|_ln296_#0/1\n-GTCCAATTGCGCACGTGCCAGCCGGGTGGCATTAACCAGTTTTGTACCGTTGAAGAGTGTCCAACTGAGGCTTGGCGCTATTTCAAACGTCATACTGTTCCGTTTGGTGAAATCTTTCAGGTCATGGGAAGAATATCCTACGGAACCTTTT\n->r12223|637000026.fna|4646221|4646372|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln436_#0/1\n-CGGTACTGCTTTTAGAAAGGAACGGATACGGGGTTGAGTCCATTTCTTTTTGTCATAGAAGAACATCCAGGTCATTTGTAACCATTGGGCTGCTGAGTCTACCTGATGAATCGACTCGTAAATCTTGCTTGAAACATTGGCTAAAAAATCC\n->r12228|641736196.fna|168782|168933|_from_ |NZ_ABFZ02000023_Bacteroides_stercoris_ATCC_43183,|_ln401_#0/1\n-GGTCTCTACCATTTCCGAAATGTTACCTTTCTCTACACGGAACATTTTATAATCACTGCCCACCTTATGCAGAATACGATCCAAATGTTCACGATTGGTATCTGTTATAAAGATCTGTCCAAAGTTATCACCTGCCACCAGTTTAATTATC\n->r12236|637000026.fna|5656063|5656214|_from_ |NC_004663_Bacteroides_thetaiotaomicron_VPI-5482,_c|_ln344_#0/1\n-TTCAGTGAGACAGATGTGCGGACCATGTTTCAGTACTATAAAGACGCCGGACAACTGCCGGCAGATACAGACATAGATGCACTGATTCGGGAAATAAAACCGTGGTATGACAATTATTGCTTTGCCAAAGAAAGTCTGGAACGTGATCCGA\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/input_sequences.fastq.gz

Binary file test-data/input_sequences.fastq.gz has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/marker.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/marker.txt Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,1 @@
+13076__A0A2I1PE66__CYJ72_10760
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/marker_metadata.json
--- a/test-data/marker_metadata.json Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,1 +0,0 @@\n-{"taxonomy": {"k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Micromonosporaceae|g__Salinispora|s__Salinispora_pacifica|t__GCF_000374725": 5438612, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Mononegavirales|f__Rhabdoviridae|g__Nucleorhabdovirus|s__Maize_mosaic_virus|t__PRJNA14920": 12133, "k__Archaea|p__Euryarchaeota|c__Halobacteria|o__Halobacteriales|f__Halobacteriaceae|g__Halorubrum|s__Halorubrum_sp_T3|t__GCF_000296615": 3168011, "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__GCF_000145075": 2614131, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__GCF_000485655": 5022965, "k__Bacteria|p__Chlamydiae|c__Chlamydiia|o__Chlamydiales|f__Chlamydiaceae|g__Chlamydia|s__Chlamydia_trachomatis|t__GCF_000304515": 1042736, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Leuconostocaceae|g__Weissella|s__Weissella_koreensis|t__GCF_000277645": 1728940, "k__Bacteria|p__Spirochaetes|c__Spirochaetia|o__Spirochaetales|f__Leptospiraceae|g__Leptospira|s__Leptospira_interrogans|t__GCF_000244635": 4459519, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Buchnera|s__Buchnera_aphidicola|t__GCF_000007365": 641454, "k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_sp|t__GCF_000209835": 3545606, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii|t__GCF_000302035": 3973165, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mitis_oralis_pneumoniae|t__GCF_000495335": 2144825, "k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rickettsiales|f__Rickettsiaceae|g__Rickettsia|s__Rickettsia_parkeri|t__GCF_000284195": 1300386, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__GCF_000316745": 5198097, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__GCF_000355055": 5070534, "k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Candidatus_Arthromitus|s__Candidatus_Arthromitus_sp_SFB_2|t__GCF_000252685": 1135256, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Caudovirales|f__Siphoviridae|g__Siphoviridae_noname|s__Lactobacillus_phage_J_1|t__PRJNA227005": 40931, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio_cholerae|t__GCF_000305055": 3943387, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Caudovirales|f__Siphoviridae|g__Siphoviridae_noname|s__Bacillus_phage_Fah|t__PRJNA16382": 37974, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_johnsonii|t__GCF_000162055": 3690010, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella_pneumoniae|t__GCF_000409125": 5671251, "k__Viruses|p__Viruses_noname|c__Viruses_noname|o__Viruses_noname|f__Viruses_noname|g__Viruses_noname|s__Geobacillus_virus_E2|t__PRJNA19797": 40863, "k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinobacteria_noname|f__Actinobacteria_noname|g__Actinobacteria_noname|s__actinobacterium_SCGC_AAA278_O22|t__GCF_000372185": 1138490, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Alteromonadales|f__Pseudoalteromonadaceae|g__Pseudoalteromonas|s__Pseudoalteromonas_sp_BSi20429|t__GCF_000238895": 4495777, "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae|t__GCF_000427035": 2138694, "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__P'..b'teria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974163|ref|NZ_KE340313.1|:332123-333478": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1356, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|384096987|ref|NZ_JH636042.1|:382588-383040": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 453, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974745|ref|NZ_KE340318.1|:c38550-38392": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 159, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|512436172|ref|NZ_KE159460.1|:c349752-348871": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 882, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|514974549|ref|NZ_KE340315.1|:c186066-185032": {"ext": ["GCF_000374365"], "score": 1.0, "clade": "s__Bacteroides_stercoris", "len": 1035, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|384096980|ref|NZ_JH636035.1|:50682-52622": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 1941, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955876|ref|NZ_DS499677.1|:c358511-356622": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1890, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|223955871|ref|NZ_DS499672.1|:29963-30130": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 168, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|514973000|ref|NZ_KE340309.1|:c227121-226093": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 1029, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|512436172|ref|NZ_KE159460.1|:c266283-265069": {"ext": ["GCF_000159875"], "score": 1.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 1215, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|298384780|ref|NZ_GG774704.1|:496496-497020": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 525, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955871|ref|NZ_DS499672.1|:193538-194158": {"ext": [], "score": 0.0, "clade": "s__Bacteroides_stercoris", "len": 621, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}, "gi|298385318|ref|NZ_GG774705.1|:324177-324773": {"ext": ["GCF_000162515", "GCF_000159875"], "score": 2.0, "clade": "s__Bacteroides_thetaiotaomicron", "len": 597, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_thetaiotaomicron"}, "gi|223955873|ref|NZ_DS499674.1|:c270435-267715": {"ext": ["GCF_000243215"], "score": 1.0, "clade": "s__Bacteroides_stercoris", "len": 2721, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_stercoris"}}}\n\\ No newline at end of file\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/marker_sequence.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/marker_sequence.fasta Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,2 @@
+>13076__A0A2I1PE66__CYJ72_10760 UniRef90_A0A2I1PE66;k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis;GCA_002847845
+ATGCTTGAAATGTATATCCAAGGTGTCTCTACAAGGAAAGTTTCGAAAGTTATTGAAAATTTATGTGGGAAAACCTATTCTAAATCATTTGTCTCTTCTCTTACGAAACAACTGGATGAAGAGGTTCGACAATGGCGTCATCACGATTTAAGTCCTGTCCAATACGCTTACCTAGTGGTGGATGTTATTTATATAAAAGTAAGAGAAAATCATAAGGTTGTATCCAAAGCGTGCCATATCGCTATTGGGATTAGTGAAGAAGGAAAACGAAGACTCCTTGGTTTTGACATCAGTGATGGCGAAAGTGATTACTCTTGGTCTCGTTTCTTTAACCACTTAAAAGAAAGAGGCCTAAATGGCCTTAAAATGGTCATATCTGATGCACACACGGGTCTAGTAAAAGCAATTAAGGAAAACTTCCTGAATGTTTCTTGGCAAAGATGTCAGGTTCACTTCTTAATGTATTTGGCAATAGGGAATTGCGTTAAACGGCAATTAATTTTGTATGCCACTTGCCATCACTATCTACTCATGAATTAA
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/marker_sequences.fasta
--- a/test-data/marker_sequences.fasta Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,7704 +0,0 @@\n->gi|223955874|ref|NZ_DS499675.1|:82124-83086\n-ATGAAAAAATCGATACTGTTAATGGGCCTTGCAGCTCTCATAGCAAGCTGTTCGGACGAT\n-GACCGGAACAACGATACTGATAATCAGCATCTTGTCAGTCCCTCAATGGCTGTGAGCATC\n-AGCAACACCGACGGCCGCCAAAGCCCGTTTACCGGCATTCTTACAATTATGCCATGCGAT\n-GCAAACAGTTCCATATACTATGGAAATTATGTAAAAGGGAAACTGTCTCCTTTCTACGGC\n-TATTACCGGGTAAAGGACGGAAGTTTCCATGACAATTCCATCAATAGGGAGATTTCTCTG\n-CCGATAGGCACTTACAATATGATTTATTGGGGAACACCCCAATACCAAACTCCCATTTAT\n-GCCCACCCTGCCATAAAAGAGGCGGCTCACAGCATAGGTGCCGATATGTCCAAACAGTCT\n-CTCGGCTTGTTCAGAATATCAGCCGATACCATTTACTATCCCGTATTCGACCTGGTGTAC\n-GCCACACAGCCGGTAAACATCGGAAGCGAAAGCCTCAGTGGCTCTTTAAAACGAGTGGTA\n-GCCGGAATAAAGGTTGTCCTGAAGGACAAAGACAATGCCGTACTAAGTTCCAGTATAGAC\n-AGTGTGTCCGTACGCATCACCAACATTTACAGCGAACTCAACTATTATACGGGAAAACCG\n-CAAGGTACACCACGTACAATCGCGTTCCCTCTGATTCGTTCGAACGATGGTACTCAGATG\n-AGCAACAGCACCGTTATGCTGTTCCCGTCCGCCGGAAAACCGGAATTCCAACTAGCAATC\n-ATTCTTAAAAACGGTAATGTGAAAAGCTTCAGACAAGCATTGAGCAGCCCGCTCGATGCC\n-AATGCCAAACTGACATTAACGTTAAGTCTGGGTGATATTTTCTCTGAAGAATCCTCCGGT\n-GACTTTACCATCGATGACTGGAACGAGAAAAACGAGAATATTGATATACCGATAATAGAG\n-TAG\n->gi|29345410|ref|NC_004663.1|:2392014-2392814\n-ATGAAAATTACAATTATAGGAGCCGGAAACATAGGGAGCGCAGTTGCTGCCTGTCTGGCA\n-AAAGGACATCTCTACAACGAAAAAGATATTATCATTTCTACCCCTCATACAGACAAGCTA\n-GAAAATCTGCACAAACAATTTCCTGCGATACGCATAATGACAGAGAATCAGTATGCCATA\n-TCGGAAGCCGACATTATTATTCTGGCTGTCAAACCATGTATAGTAGACGAAGTATTATCT\n-CCGTTACGATTCTCACGCACCCAAATCCTGGTTTCACTGGTAACCGGAATATCCATTTCT\n-CACCTGGCACATTTATCGGAAACCGAAATGCCTATATTCCGGGTTGTTCCAAACATCGCC\n-ATTACGGAACATTCGAGCCTGACCCTGATAACTTCACGCAAAGCCGGCAAAGAACACCAG\n-CAACTCATAAAACAGACATTTGAAGAAGGAGGAAAGTGTTTGTTCGCAGAAGAGAAACAG\n-CTGGATATCATTTCTGCATTAACTTCCAGTGGAATCGCTTTCGCATTAAAATATATTCAT\n-GCAGCCATGCAAGCCGGCATAGAATTGGGTATCTCCGCTGAAGATGCAATGCGAATGACG\n-GCATATAGCATGGAAGGAGCTACAGAACTGATTTTAAATCACGACACCCACCCGCTGTTA\n-GAAATAGAAAAAGCAGCTACTCCCGGTGGAGCCACCATTAAAGGATTGAATGAACTGGAG\n-CACAGGGGATTTACTTCCGCCGTTATTCATGCCATAAAAAGTAGCGCCACAGTATCGACC\n-GATAAAGAGACTGAAGAATAG\n->gi|298385318|ref|NZ_GG774705.1|:275923-276495\n-ATGATAAATTCAATTAATATACAAATCAGAGAGACCAATACAGATGATTTCGACAGCATA\n-ATGACTGTTGAAAAACAAGCGTTTGGCTATGACAAAGAAGCACAGTTGGTAGCCGATCTG\n-CTGGCTGACAAAACTGCAAAACCAATGGTTTCGTTGCTCGCTTTCTACAAAGGTGAGGCT\n-GTCGGACACATTCTCTTCACCAGAGCCTATTTTGATGGTCAGGGAGCACAACAGATGATG\n-CACATTCTTGCACCTTTAGCTGTCAAGCCGGAATATCAACGGCAGGGTATAGGCGGAATG\n-CTGATACGGGCAGGTATAGAGAGGTTGCAGGAAAAAGGTTCGTGCCTTGTGTTTGTATTG\n-GGGCATAAAGAATATTATCCAAAATATGGTTTTATACCGGATGCAGCCAGGCTGGGTTAT\n-CCTGCTCCTTACCCGATACTGGAACAGTTCTCGGATTATTGGATGGTTCAGGCAATCAGT\n-CCGAAGGGATTTGATGTGGATAAAGGAAAGATCAGGTGTTCGGATGAGTTGAACAAACCT\n-GAACATTGGAGAGATGATGAATCGGACAGATAG\n->gi|514973850|ref|NZ_KE340312.1|:c10221-7987\n-ATGAAACATTTGTCTGTTATTATATCTGTATTATTTTCAATACTTTGTATCGGATGCTCT\n-AAGGAGGATTTTAACGATGGAAAAACCAATGATGTTCAGAACAAGCATTCTCTCCGGCTT\n-TTGGTCTACACACCGACTTCAGAAACTGTTCTTAGTACGGACCTGCCGGGAAACATAGAG\n-GCTTATCTGTTCAAAGAGGGAGTTCTGTCCGACGTTTACAAAAATCTGACAGTGGATAAG\n-AACGGATACACTACAATCAGCTCGTTAGCCGAAGGAGAGCAAATCTATTTCTTTGTAAAC\n-ACCGGTAATCTGCTGGATGGGATTACACAGGAAATAGGCCGATTGAAAGAGAACGAACTG\n-CTTGCCACTACAATACTCTCTGCCTCTCCTCAAGCAGATGGAGAGAAACCGGTGATGACC\n-GGAAAGGCAGACTTAACCGGAAGCCAGGAGAGTACCACCCAAGTATTGCTTACACGGGCC\n-ATTGCCAGAGTAGACTTAAACATAGCTGACGATGCCGACATACAAATCAATAGGATAAGT\n-ATGGATAACATACATTGTGAAGCATTCCTGCTTCCGCAAAATCCGGTCAGTTCGCCGTCC\n-GGTGCAGCATTGGCAAAAATAGACACTACATTCAATACCCCGTTGAAGCCGGGTGAATAT\n-GCCGGATTGGTCCACCTGTATGAACAAGTGGGGGACGGTATTCCTGTGGAGCTGCATGGC\n-ACCCTTGAAGGCGATCCTGTCACACTTTCACTGGCACTGCCTAACACAATCCATAGAAAC\n-CACATTTATAAAATAAAGTTATTTAGCGGAGACAGTTCTAATTTGCAGGCAAGCATATCC\n-GTGGAAAATGAAAGTTGGGAAGTCGAAGAAACTATCACGGCAAAACCTTCTACCAATATT\n-CTGGTTAATAGTGAACTTTCTACTTTGGCTGAAGGGGCGTATATAAGTGCAACAAAAGAT\n-ACGGTTTACCTCCCAAGCAAGGAGTCAACGTCAATACTTGTATTGGATAAGGTGCCGGAA\n-GATGCGGAATTCACAATTGATGGGACAACAGCCTCCATTACTCCGTATACGGAAACTCGT\n-GCCGACCTTCAAGGGAAAAAGTTCTTGGTACGCAATTCTTGGAAAAAGCCGGGTACTAAG\n-ACGGAATATATGTACCTGAATATGCACAGCAAGAGGCACCCGGACTACTACAGTGGCCGG\n-TTGGTAATTGTTCAGTCCAATGCAACGACCTTCAAGGGAGAATTGTATAATCATCTTACA\n-AACACTCCTCCCTATAACATTCATTTCAATAAATATGTCGACAGTGCTTTAGGCCAGATA\n-GAGGTACCT'..b'CGCTTTTCCTATAGGGGGAATTGGTGCAGGTATGTATTGT\n-CTGGAAGGAACAGGCTATATATCTCATATGTCAGTATGGCATCGACCGGAAGTTTTTCAT\n-GAACCGGGAATGTTTGCTGCTCTGTATGTGAAGGGGGTATGTAATGGGGCTAAGGTACTT\n-GAAGGACCTGTATCTGATTGGAGAAAATTTGGAATGCCCAATTACGGTACAGGAGGCAGT\n-ATGGGATCAATATTAGGACTTCCCCGTTTTGATACGGTTGAATTTGAAGCACGTTTTCCG\n-TTTGCCAAAGTTTCATTAACAGATAAAGATATCCCCGTTAAGGTAACCATTTTGGGGTGG\n-AGTCCTTTTATTCCGGGTGATCCGGATAATTCCAGTTTACCGGTAGGAGGATTGGAATAT\n-AGTTTAGAGAATACTAGCAAAGAGGTTCAGGAAACTATTTTCTCCTACCATGCTCGTAAC\n-TTTCTGAGTTCGGGTAAAGGATTGGATGCTATAAAAACGATGCCTCATGGGTTTATCCTT\n-TCACAGTCAGGTACAGAAACGGAGCCTCATTTGCAGGGTGATTTTGCTATCTTTACGGAT\n-CAGGATTCTTTAAAGATCAATTATTGTTGGTTTCGTGGAGGATGGTTTGATAGTCTTACG\n-ATGGTTTGGAACGCTATTGAGACAGGTTTAATGCCACAATCTCCAGCAATAGAGAAAGGT\n-GCACCAGGAGCTTCTATGTTTGTCCCGGTAACATTGATGCCAGGGGAAAAGAAAACAATC\n-AGAATTTATACGGCGTGGTATGTTCCTAACTCGACTTTAAGGCTTGGAAAGGAACCGGAA\n-GACTGGAATGACAATAATGTCGACTCCGCAAGACTAGCTGTAGAAAAGGCAGATAAGGGT\n-AATTATAAACCTTGGTATAGTAGCCGCTTTACAGGAGTGAATGAGGTTATTGATTATTTT\n-CTGTCTCATTATAAGATTTTGCGCAATCAGACGGAAAGGTTCACAGACTCTTTTTATCGT\n-TCTACCTTACCGCCTGAAGTGATTGAAGCTGTTTCTGCTAACTTAAGTATTTTAAAGTCT\n-CCAACGGTGATGCGGCAATATGATGGACGCTTATGGACTTGGGAAGGATGTGCCGATAAT\n-TGGGGCTCGTGTCATGGCTCATGTACTCATGTCTGGAATTATGCACAAGCTATTCCACAC\n-TTATTTCCTTCCTTGGAACGTTCGTTAAGGCATACTGAATTTGAAGAAGGGCAAGATTTG\n-AAAGGCCATCAAGTGTTTCGTGCCAATTTACCGATTCGTCCTACTCGGCACGACTTTCAC\n-TCAGCTGCTGACGGGCAATTGGGAGGTATAATGAAAGTATATCGTGAGTGGCGAATTTCA\n-GGCGATAATGAGTTCCTTATCTCTATGTATCCAAAAGTAAAAAAGAGTTTGGACTACTGT\n-ATCTCAACTTGGGATCCTCGTAGGGTAGGAAGTATTGAAGAACCACACCATAATACTTAT\n-GATATTGAGTTCTGGGGGCCGGATGGTATGCATAATAGTTTCTATTATGGAGCTTTATCA\n-GCTTTCATTCGTATGAGTGAGTTTCTTGATAAAGACGTTACTGAATATAAGAAACTATTG\n-AAAAAAGGACGAAAATTTACTGAAACAGGCTTGTTTAATGGTGAGTATTTTATCCAAAAG\n-ATAGAGTGGAGGGGATTGAATGCAAAAGATCCGACTGTTGCACAAAGTTTCCATAGTTCT\n-TATTCTCCCGAAGCGAAAGAAATACTGGAGAAGGAAGGTCCTAAATATCAGTATGGGAAC\n-GGTTGTCTGTCTGATGGAGTTTTGGGGTCGTGGCTCTCCCGAATGTGTGGGATGGAAGAA\n-ACTCTGAATACAGAAAAAGTGAAAAGCCATTTATTATCAGTACATCGATATAATTTTAAA\n-AAAGATCTGACTGATCACGCCAATCCTCAACGTTCCCCTTACGCTTTAGGCAAAGAAGGA\n-GGCTTATTATTAGGAAGTTGGCCTAAAGGGAGCAAGTTGTCATTGCCTTTTGTCTATAGT\n-AATGAAGTCTGGACAGGAATAGAATATCAAGTAGCTTCACATTTGATGCTACAGGGAGAG\n-GTAGAAAAAGGCCTTGAGATCGTGCGTGCCTGTAGACAACGTTATGATGGAAGTGTCCGT\n-AACCCTTTTAATGAGTATGAGTGTGGACATTGGTACGGACGAGCGTTATCTAGTTATGGC\n-TTACTTCAAGGATTGACAGGAGTCCGATATGATGCTGTAGATAAAACACTGTATATTAAT\n-TCAAAAATAGGAGACTTTATTAGCTTTATCAGTACGGAGTCTGGATTTGGTAATGTAGAA\n-CTTCGTTCCGGAAAACCTTTTGTAAAAGTAGTATCCGGTCATATAGAGGTCGACAGATTT\n-ATCGTATCAGGGAAAGTAGTTGAATAA\n->gi|298386634|ref|NZ_GG774708.1|:c143839-142661\n-ATGGAGCAAAAGAAAATCGTGCTATTCATCCTGATCATTCATCTGGCAGCATTTCTAGCA\n-GGATGCAGCGGAAACAAAAATAGCGGAAATAATGACTCCTCTGATCTATGGAATAAGTTA\n-TCGAGCTACTTCCGCACGCCCGCAGAATACGAAAATGTATATGGGAATTTTCGCTCTCCT\n-TTATTATATTATAATGGGGATACAGTCAGAACCGTTGAAGACTGGCAAAGACGACGAACT\n-GAAATCAAGGACAGATGGATGAGCCTGTTAGGACAATGGCCGCCTGTCATTACCGGACAA\n-ACATTTGAAATTCTGGATACTCTCCACCGTGAAAACTTCATGCAATACCGTGTCCGCTTC\n-TACTGGACTCCCAACGAACAGACTGAAGGTTATTTGCTGGTTCCGGACAAAGAAGGCAAA\n-AAGCCTGCCGTTATCACTACCTTTTATGAACCCGAAACGGCTATCGGATTGGGTGGAAAA\n-CCTTATAGAGACTTTGCATATCAATTGACGAAAAGAGGATTTGTCACATTATCAATAGGA\n-ACAACGAAGACCACAGAGAATCAGACATATTCCATTTATTACCCCAGCATTGAAAATGCA\n-ACTCTCCAACCACTTTCAGCATTAGCTTATGCAGCCGCAAATGCATGGGAAGTATTAGCC\n-AAAGTACAGGACGTCGATTCTACAAGAATAGGCATCACAGGGCATTCTTATGGTGGGAAG\n-TGGGCAATGTTTGCCTCATGCCTATACGAAAAGTTCGCTTGTGCGGCATGGGGAGACCCC\n-GGAATTGTATTCGACGAAACAAAAGAGGGATATATCAATTACTGGGAACCCTGGTATTTG\n-GGATATTATCCGCCACCATGGGAAAATACATGGAGTAAAAATGGGCATGATTATGCTAAA\n-GGCATTTATCCGAAGCTCCGCAAAGAAGGATATGATTTGCATGAATTGCATGCGCTGATG\n-GCACCTCGCCCATTTCTTGTTTCCGGAGGATACTCTGACGGAACAGACCGGTGGATAGCG\n-CTAAACCATACAATAGCGGTCAACCGGCTCTTAGGATACCGCAATAATGTCGCGATGAGC\n-AACAGAGTCAATCATGACCCAACCCCTGAATCAAACGAAATTATATATGATTTTTTTAAA\n-TGGTACTTGCATTCAGCAAATAAATCTACCAAAGAGTAG\n->gi|223955875|ref|NZ_DS499676.1|:c386522-386337\n-TTGGCTTTTAGTTCTGTCCAGTTTTCTTATATTTTTGTAGAAAAAGTATGGGACAGGTAT\n-ATAAAAACAGCCTGGGTTTACGTATTCAACGTAATCCCAGGCTGTTTTTACGGGTATTTG\n-CGGGGGCTTGTTTACCGATTGTTTTTTATTCCGCCAAAGTCGCCCTTCTACTTCAGTCCG\n-AAATAA\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/merged_community_profile.tabular
--- a/test-data/merged_community_profile.tabular Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db-with-one-marker.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db-with-one-marker.fasta Mon Apr 19 20:54:50 2021 +0000

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db-with-one-marker.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db-with-one-marker.json Mon Apr 19 20:54:50 2021 +0000

[

@@ -0,0 +1,1 @@
+{"markers": {"13076__A0A2I1PE66__CYJ72_10760": {"clade": "s__Globicatella_sanguinis", "ext": [], "len": 540, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"}}, "taxonomy": {"k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis|t__GCA_002847845": ["2|1239|91061|186826|186827|13075|13076", 2411251]}, "merged_taxon": {}}
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db-without-one-marker.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db-without-one-marker.fasta Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,180 @@\n+>1747__A0A1N4YDI5__CP875_06750 UniRef90_A0A1N4YDI5;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_003384555\n+ATGTCCCGTGAGTACGGTGGACGCGTGGCTGACACGAAAACCTCCCGTCATTCCTGGCTACGCATCACTTCCGGTCTCGTCGGGCTGATCCTGACCCTGCCGGTACTGACGTGGTCAGTGGCCGCGATCCTCCCCTCACACAATGCCCTCACCTTCATCTCCTCCGTTCTGGTGGGATCGTTGGCTGTACCGGCTCTGGTCATCGCCGTCATCGCCTTCGTCCTCGCTCTTCTGGGACGAGGTGGTCTGCGAGTGGTGGCCGTTCTCTTCTCGGTGATGGCCCTCATCGTGCCAGTGGCGGCAACGGCGACGACGGCGTGGATCACGGACCGCGCCGGTGGACGTATCAACGTCGTCTCGGCATCTGCGGTGTCGTCGATGTCCGACCACCCTGACGAAACGGTCCGGTATGGATCCGGCCCTGACGAGACGGCCCAGATCTACCGTCCCCATAACCACAATGCCCCGGTACTTGTCGACATTCATGGTGGAGGATGGAGCACCGACGCCACCATGCCCGCCACGTTGAGATGGTTTTCCGACCATGGCTGGTTAGTCATTCGTCCCTCGTACACCCTGGCCACCCAGGGCCACCCCACCTGGAATACTGCACCAAAACAGGTAGCATGTGCCTGGGCCTGGAGCCTGTCCCACGTGAAAGAACTCGGTGGCGACCCTTCACAGGTATCGATCATGGGTGATTCCGCTGGTGGTGGAATGGCCATTAATCTCGCCTACGGCGCCGTCAGCGGAAAGTTGAAGAGTTCCTGCGGCTCAATACGGGCCCCGAAGTCAGTCCTCGCCCTCTATCCAACGGTGGATGTCAGTACCGTCGAGTCAGTCACCACACTGAGCGCGGGCAATGCCGCCAAAATGTATATCGGTGGCACCCCCAAGCAATTCCCCGACCGTTATCGCGCCGTCAACAGTTCCACCTGGATCACTCCTCAGGCACCACCAACAATGGTGATCCAGGGAAATCACGACACCTTTGTCCCGCCATCCAGCGTGCGGAAATTCATCAATCGTGCCCGCCAGGCTGGAGTCCGGGTCGATCACGTACAGTTACCAATGCTCAATCACGCTTTCGATTCCCAGGCGCGCAACTCACTGGGATTCCAGGTCGTCACGAGCCTTGGGCAACGTTTCCTTACTAACCACTGA\n+>1747__A0A1N5AYP4__B1B09_10705 UniRef90_A0A1N5AYP4;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_002572615\n+ATGGATTGGGAGGCCACTGAGCTGACCGATCTCGACGTCACCGGTATTGATCACGAGGGCGGTTTCTCGGCCCTTGGCGTGCCCGACGAGATCGTTGCTGCTTTGGCCAAGACTGGCATTACCGATCCCTTCCGCATCCAGATCGCCGCCATCCCCGACGCCATCGCTGGGCGTGACGTGTTGGGCCGCGCCTCAACGGGTTCGGGTAAGACGTTGGCCTTTGGTGTCCCGCTGCTGTCGCGCCTGTCGGCCACCCCGCGTGAGGATAACCGGCCTCGAGCTCTCATCCTTTCTCCCACTCGTGAGCTGGCCATGCAGATTGCCGACGTGCTGTCCTCGCTGGCGTCCTCAATGGGGCTATCGACCATCCTCATCGCGGGTGGTATGAGCTACGGCCCGCAGACCAAGGCTTTTAAGAGGGGAGTCGACCTTGTTGTCGCCACCCCGGGGCGTCTGGTCGACCTCTTGGAGACTGGTGACGCCGACCTTTCCGGTGTCGCCGTGACTGTCCTCGACGAAGCCGATCACATGGCTGAACTGGGATTCATGGAGGCCGTTGGCTCGATCCTCGATGCCATTCCCGCTGACGGGCAGCGCCTGCTGTTCTCTGCCACCCTCGACGGTGCCGTTAACAAGTTGGTTAGGCGGTACATGCACGAGCCGGTTATCCACGAGGTCGACCCCGACAAGGGATCGGTCGCGACGATGACCCATCACGCTTTCCAGATCAAGCCTCACGAGAAGGTCGGGCTGATGTGCGAGATCGCTAACCGTAGCGGCCACACCATCGTCTTTGCTCGAACCCAGCGAGGTGCCTCCCGGATGGCCGAGCAACTGCGTGAGGCCGGCGTCATGGCTGGTGCTCTGCACGGCGGCCTGACCCAGGGTGCCCGTGCCCGCGTGTTGGCGGCATTCAAGGACGGTTCCCTGCCGGTCTTGGTTGCCACTGACGTCGCGGCCCGAGGAATTGACGTCGATGACGTCACTCTGGTGTTGCAAGTCGATCCGCCGATGAACTTCAAGGACTACCTGCACCGCTCCGGCCGTACCGCTCGCGCCGGACACGACGGGGCCGTCGTCTCTCTTGTCCTGCCGCATCAGCGTCGCACAATGGCTCGTTTGTACCGTCAAGCCGGGGTGAAGCCGGTAGAGGCCCAGGTCACGCGTGGCGACGACCACGTTGCCGAGGTGGCCGGTTGCAGCCCGGCCCTGGGCGCTCCTATTGACGAGAAGGATTACGAGGCTCTCGTCGCTCCCAAGCAGCAGCGCGGCAAGAAGGCTCGTGACGGAAAGCCTCGTCGTGGCAAGGGCGGACGCAACCGCGGTGGACGTGGATTCGACGGGGGCCGTCATCGCGGTCACGACTCCCGTGATCACCATGATCGTGGGCATGACTCGCGCGGACACAATTTCCGTGGCCGCGATCGTCGCGACATTGAGGCTAAATACGGCCGTTCCGGAAACGACACCTGGTGA\n+>1747__A0A3D8ZS35__CP884_00215 UniRef90_A0A3D8ZS35;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_003384705\n+ATGAACACCCACGACGTTCCGATGATCCTGTTCACCGTCGTCACACAGATGTGCGTTGGTGCCTTTTTGGTCCTTGGGACCGCCCACGTGGGGGCAGCCATCAGGGGACGCGAAAACAGCGTCGTGGAGCGGACCAGTCGCCCAGTGCTCTATGCCATCGGCCCGGCCATGGTATTCGGCCTCTTCGTCTCCATGTTTCATATGGGTTACCCGGCTCATACCCTCAACGTCTTGCGTCACCCGCAGACTTCCTGGCTATCGCGTGAAATCATGTTTGGCTCCGGCTTCGCCCTACTTGGCTTTGTCTTTGCCATGCTGAGTTGGTTTAAGCGACCTGCTTTCGCTATTCAGCGGGTTCTCGCGGTTGTCACCGCTATCGTTGGCATCGGACTGTTGGTGTGCGAGTCGATGATCTATTACTCCTTGGTGACGGTCCCGGCTTGGCACAGCTGGTGGGTGCCTTTCTCCTTTGCAGCGACGACCATCATCTTGGGAACTCTCTCAGTGGCCTGTGCACTCATGATCACCGCGATGGTGCGTCATCGTCACGAAACAGCTGTCCCCTCAGCCAGGGAAAAGCATCCGAAAACCACGGGCTGGTGGTCCCGGCACGTCACCGAGGAGATCCGTGCCATCAACGCTCCAACCGATGATCAGGAATGGGACCTGTCGTTGACGGTAACCAAATGGTGCTCCATCGGCGCCGCCGTGGTCTCGGTTGCCCTCATGGTGG'..b'TTGATATAGACACACAAGGAGGCAATGATGTGATTTATGGCGGTGATGGTCATGATACCCTAAAAGGAGGTGATGGCAATGATGTGATTTATGGCTCTGCAGTCTTTTATGATTTTGAACCCAAAGACAGTCAAAGACTACCTAAGCCAAAACAAGACAAAGAGGGTAATTTAATTGGGGTGGATAAAGATATTATTATTGGTGGCATGGGAAGAGATTTGATTGCAGCAGGGATTGGGGATGATATTATTTGGGTGGACAATGAACAAGCAGAGTCTAATAACACCCATAACAACGACAAAGGAGACTGGGCATTAGGCGGACAAGGAAGTGATGTGATTTATGGGGGAGCAAATAAAGACTTTTTACAAGGTGGGGCGGATAATGATTATGTGTATGGCGGTGGTGGCGATGATGTGATATTGGGTGATGGACATATTAGGTTTGGCATAAAAAATCAAGTGCTACGCAGTGATAATCAGATTTTAAGCATAGAGCATACCTACGACCAAGTCAATCACAAAGAAAACACCCTAAAACAAAAAACCGCAAATTTACAAGACTACAAAACCTTTGAATGGAACATTCAAGTAGATACTGACAAAATGGATTATCTCTTAACCAAACAAAAAGACATTGCTTTGGCAAATAATTACCATCTTTTAGACGAATCATACAAACACAATGCCAATGACTTTTTGTACGGCGGCAAGGGAGACGACCTTATCATCGGTCAATATGGCAATGATTATCTAGATGGTGGTGAGGGTGATGACATCCTATGGGGTGATGATAACAGAGATGAGGATATTGAAGGGAATGACACGCTAAAAGGCGGTGCAGGAAGAGATAGGCTAATTGGTGGCAAAGGGAATGATGCGTATGTGTTTGACCTAGAAGACCTAGCCAAAAGCGGGGCGGATGACAAAACCATCATTGACAGTGATAATGGTGGCATCATCAAAATCAATCATTATGATCTAACAGGCACACAGTTTTTTAAATCCGCCAATGCCAGCAACCTCTACCAAAGCGATGATGGCAAATTTGACTTGATAAGATACGATAACGGCAACTACAGCCTATTAAGCAAAGATTTCAACGCCTCCATTGCCATCAAAGACACCCCCATCACAAAAAATGGCGACAATGACATCTTGCTAGGCATGATACTAAAAGAAACCAAAAACACCGCTCCTATCGTTCATAATCCCGTCTCTGACCAGATGGTGTTGGCAGAGCGAGACATCGCACTCGGTCTTGGCGAGGTATTCTTCGATGCTGATGGTGATGAGCTGACGTATAGCATCCAAGGGGCGGATGGACTGCATTTTGACCCTGCTACAAAGATGCTAACAGGCAGGGCACCTGATAAAGGGGTATTTAACATCACATTGACCGCCACCGACCCCAAGGGCGAGCATGCCAATACCAGCTTCACACTAAGAGTAAATGAACGACCAACGCTCGTCTCTGCCTTGACTCTACCGCTTGTGCTAAGCCAAGATGATGCCATGATGCAGATAGGTCTAGATAAGCTGTTTGTTGATAACGATGGTGATGCGTTAAGTTATTCGCTATCGGCAAATTCTTTGAGCGGTATCTACATTGACAACAATCATCTCATCATAGACCCTGCGACCACAGAGATTGGCATGCATGACATTACCATAACAGCGACAGACAGCTTCGGTCAGAGTGTCAGTACCAATGCCAGCTTTACCATCAAAGGCAGTGAGCCCATCGTGATGCCAGAGCCTGTTCTGCCCATCACGCCAACGCCTGACCCCATCACTGTTGGTAAGCGATATGTGGGCAAGCTCGGTGCTGATGACATCACAGGTGATGATAAAGCCAATACCATCAATGGCCTGACAGGAGATGATGTCCTAAGTGGTGGTCGTGGTAATGACACGCTCATCGGTGGATTTGGTCATGACACTTTAATTGGCGGACTTGATAACGACCTGCTTGTCGGTGGCTATGGCAATGATACTTATCTGTATCACAAAGGCGATGGTCTGGACACGATTCGTGATGTTGGTGGGTTGGATATCTTAAAGATTTCGGGGCTGACGTTGTCTGATTTGGGCTTTGCCAAACAGGGCAATCATCTGTTTATTGATGTCAAGCAAAATGATGATGGCATTATTATTGAAGATTATTTCAAATCAGGCAGTATCATACCAAGCCAAAAATCATCCCCCAACATAGAACGTATCTACATCAATGATAAGTTTGTCGGGCATGATGAGATTATCAAGATGGCGGATGTGATTATTTAA\n+>60442__A0A378QWP5__cya_3 UniRef90_A0A378QWP5;k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi;GCA_900453335\n+ATGGCAGAGTTTGATAAAATCAAATATAAAATTGGTGTTATCGATAGTTTCATGAGCACAAAAACAGATAACATGTTTTATGCTAACGTCAAAGACTTTGAAAAAACAACCAAAATTATCAATGATACTTATGATAGGCTGATTAAGTCTGTTTATAGTGGACTCTATCCGCAAACTGTTCAGAATCGTTATGGCGATTTGATAGATATTGTGGTAGATGTCAAAGATGGTAATCTTCTGTTTGGTTTGGACATTAATCGACTGGTAAGCGACTTTAAGGCAAGGTTAGATGTAGGTGGTCAAACCGCAATGTCTGCCTTTGGCGATATCATGGAGTATTTTGCTTATCTTCAAGTGCAAACACGACCTAACATTGTTGGCAGAGATAAGTTGGTTAATTTGATAGAGCATGTTGTATCTAGCGTGCCAAAACATGAATTGGATGGTTGGATAAATGGTATTGATTTTAAGATTGATAGAGAATTACCAATTAAGATGGGCGATGCACAAGATAATCATTTAAATGGCGGTGCTGTGTTTGCAGGTGCTGGTAATGATCGGTTGACTGGAACTAAAAATTCTGACCTCCTATTTGGTCAAGATGGTAACGACACCCTAAATGGCGGTAACGGCGATGACATCTTAAATGGTGGTGCTGGCGATGATTATTTAAGCAATTCGGGTCAGAATAACGGTAATGACACTTACATCTTTAGTGGTGATTATGGTAATGACATCATTCATGACTCTGATTCAAATGTCTCTAAAGAACGCCATTAA\n+>90240__A0A378QWM4__NCTC12877_00123 UniRef90_A0A378QWM4;k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae;GCA_900453285\n+ATGCTCACAAACCCCATTGACTATTTATCACAGGTTCATGACCCAAGGCGTCAAAACAAAAACCTGCTACACCCACTTAAAAACATTCTAACCATTGCCTTAACCGCAGTTATCTGTGGTTATCATGACTGGGTAGATATAGAAGACTTTGGCAATGAAAACAAAACATGGTTTGCCACATTTCTTGACTTAACTCATGGCATACCCTCACATGACACCTTTGGCAATGTCTTTAAACGCCTTAACAAAGATGAACTTAGTCGATACTTGAGTGAGTGGATAAATCAAACCCAAGCCAATCATCCACACATCGCCATTGATGGTAAATTCATCCAAGGTGGCTACAAAAATGACAACGCATTACAGCTTGTTACCGCCTTTGCCAGTCAAACCAAACTCATTCTTGCTCAAGTTGACATTGCTGATAAAAACAACGAAATTAGCACATTACCCCAACTGTTAAAACTCATTGATATCAGCGGTAGTATAGTGACAGCCGATGCCATTTACACCCCACAAACCCCAAATATGCTACAATACCCTAACATCCATTAA\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db-without-one-marker.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db-without-one-marker.json Mon Apr 19 20:54:50 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"markers": {"504553__GeneID:10498608": {"ext": ["GCA_003384495", "GCA_003384705", "GCA_003384195", "GCA_000144875", "GCA_003426255", "GCA_000376705", "GCA_000221125", "GCA_001469595", "GCA_002572575", "GCA_000144185", "GCA_003384345", "GCA_001481615", "GCA_000240015", "GCA_003384315", "GCA_000144485", "GCA_003384365", "GCA_000144735", "GCA_000178055", "GCA_001660115", "GCA_000144545", "GCA_000144245", "GCA_000735055", "GCA_001750535", "GCA_003384145", "GCA_003426625", "GCA_000144005", "GCA_003384485", "GCA_001469635", "GCA_000144505", "GCA_000144815", "GCA_000240055", "GCA_000144345", "GCA_003384395", "GCA_003390995", "GCA_003384555", "GCA_003426665", "GCA_000144895", "GCA_000144465", "GCA_900102845", "GCA_002572615", "GCA_002572665", "GCA_000194825", "GCA_003384585", "GCA_003384255", "GCA_000145195", "GCA_000144325", "GCA_000145575", "GCA_000231215", "GCA_000144365", "GCA_000144795", "GCA_002556485", "GCA_002572745", "GCA_003384445", "GCA_001660935", "GCA_001469655", "GCA_000145335", "GCA_000008345", "GCA_000488875", "GCA_001660945", "GCA_000145095", "GCA_003425775", "GCA_001469555", "GCA_000144145", "GCA_002775655", "GCA_000145155", "GCA_000302515", "GCA_000342585", "GCA_002572695", "GCA_000144285", "GCA_001660855", "GCA_000144775", "GCA_000144125", "GCA_000145375", "GCA_003384285", "GCA_003426225", "GCA_000144045", "GCA_001750525", "GCA_000730485", "GCA_002572655", "GCA_002572705", "GCA_003384385", "GCA_000147145", "GCA_001750555", "GCA_002861085", "GCA_002572835", "GCA_003426685", "GCA_000145455", "GCA_001660965", "GCA_000144445", "GCA_002572775", "GCA_002831715"], "score": 37.0, "clade": "t__Propionibacterium_phage_PAS50", "len": 663, "taxon": "k__Viruses|p__Viruses_unclassified|c__Viruses_unclassified|o__Caudovirales|f__Siphoviridae|g__Pa6virus|s__Propionibacterium_virus_PAS50|t__Propionibacterium_phage_PAS50"}, "386414__D1VYE0__HMPREF9019_1663": {"clade": "s__Prevotella_timonensis", "ext": [], "len": 1065, "score": 0, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis"}, "29394__H3NGH1__B5772_02200": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 972, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NFY1__B8A41_07655": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 534, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NC06__B8A41_08715": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 1317, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NDE2__B8A45_00965": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 699, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NFL8__B8A45_06985": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 582, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NDD1__B8A45_02325": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 480, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NE37__B8A45_05170": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 756, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NCU9__B8A45_08665": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 765, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "2'..b'roteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076675": ["2|1224|1236|91347|543|547|354276", 4289814], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000958695": ["2|1224|1236|91347|543|547|354276", 4336076], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900077255": ["2|1224|1236|91347|543|547|354276", 4482974], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075885": ["2|1224|1236|91347|543|547|354276", 4396160], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001487035": ["2|1224|1236|91347|543|547|354276", 4279410], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900077025": ["2|1224|1236|91347|543|547|354276", 4303785], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000952555": ["2|1224|1236|91347|543|547|354276", 4340464], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076755": ["2|1224|1236|91347|543|547|354276", 4236759], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000783855": ["2|1224|1236|91347|543|547|354276", 4188638], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001022075": ["2|1224|1236|91347|543|547|354276", 4412384], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001022255": ["2|1224|1236|91347|543|547|354276", 4385357], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075375": ["2|1224|1236|91347|543|547|354276", 4164369], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075395": ["2|1224|1236|91347|543|547|354276", 4013880], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_003261215": ["2|1224|1236|91347|543|547|354276", 5016502], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075185": ["2|1224|1236|91347|543|547|354276", 4392401], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_002192395": ["2|1224|1236|91347|543|547|354276", 4556770], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000958745": ["2|1224|1236|91347|543|547|354276", 4382425], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001025055": ["2|1224|1236|91347|543|547|354276", 4360879], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076455": ["2|1224|1236|91347|543|547|354276", 4404432]}, "merged_taxon": {}}\n\\ No newline at end of file\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db.fasta Mon Apr 19 20:54:50 2021 +0000

b'@@ -0,0 +1,182 @@\n+>13076__A0A2I1PE66__CYJ72_10760 UniRef90_A0A2I1PE66;k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis;GCA_002847845\n+ATGCTTGAAATGTATATCCAAGGTGTCTCTACAAGGAAAGTTTCGAAAGTTATTGAAAATTTATGTGGGAAAACCTATTCTAAATCATTTGTCTCTTCTCTTACGAAACAACTGGATGAAGAGGTTCGACAATGGCGTCATCACGATTTAAGTCCTGTCCAATACGCTTACCTAGTGGTGGATGTTATTTATATAAAAGTAAGAGAAAATCATAAGGTTGTATCCAAAGCGTGCCATATCGCTATTGGGATTAGTGAAGAAGGAAAACGAAGACTCCTTGGTTTTGACATCAGTGATGGCGAAAGTGATTACTCTTGGTCTCGTTTCTTTAACCACTTAAAAGAAAGAGGCCTAAATGGCCTTAAAATGGTCATATCTGATGCACACACGGGTCTAGTAAAAGCAATTAAGGAAAACTTCCTGAATGTTTCTTGGCAAAGATGTCAGGTTCACTTCTTAATGTATTTGGCAATAGGGAATTGCGTTAAACGGCAATTAATTTTGTATGCCACTTGCCATCACTATCTACTCATGAATTAA\n+>1747__A0A1N4YDI5__CP875_06750 UniRef90_A0A1N4YDI5;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_003384555\n+ATGTCCCGTGAGTACGGTGGACGCGTGGCTGACACGAAAACCTCCCGTCATTCCTGGCTACGCATCACTTCCGGTCTCGTCGGGCTGATCCTGACCCTGCCGGTACTGACGTGGTCAGTGGCCGCGATCCTCCCCTCACACAATGCCCTCACCTTCATCTCCTCCGTTCTGGTGGGATCGTTGGCTGTACCGGCTCTGGTCATCGCCGTCATCGCCTTCGTCCTCGCTCTTCTGGGACGAGGTGGTCTGCGAGTGGTGGCCGTTCTCTTCTCGGTGATGGCCCTCATCGTGCCAGTGGCGGCAACGGCGACGACGGCGTGGATCACGGACCGCGCCGGTGGACGTATCAACGTCGTCTCGGCATCTGCGGTGTCGTCGATGTCCGACCACCCTGACGAAACGGTCCGGTATGGATCCGGCCCTGACGAGACGGCCCAGATCTACCGTCCCCATAACCACAATGCCCCGGTACTTGTCGACATTCATGGTGGAGGATGGAGCACCGACGCCACCATGCCCGCCACGTTGAGATGGTTTTCCGACCATGGCTGGTTAGTCATTCGTCCCTCGTACACCCTGGCCACCCAGGGCCACCCCACCTGGAATACTGCACCAAAACAGGTAGCATGTGCCTGGGCCTGGAGCCTGTCCCACGTGAAAGAACTCGGTGGCGACCCTTCACAGGTATCGATCATGGGTGATTCCGCTGGTGGTGGAATGGCCATTAATCTCGCCTACGGCGCCGTCAGCGGAAAGTTGAAGAGTTCCTGCGGCTCAATACGGGCCCCGAAGTCAGTCCTCGCCCTCTATCCAACGGTGGATGTCAGTACCGTCGAGTCAGTCACCACACTGAGCGCGGGCAATGCCGCCAAAATGTATATCGGTGGCACCCCCAAGCAATTCCCCGACCGTTATCGCGCCGTCAACAGTTCCACCTGGATCACTCCTCAGGCACCACCAACAATGGTGATCCAGGGAAATCACGACACCTTTGTCCCGCCATCCAGCGTGCGGAAATTCATCAATCGTGCCCGCCAGGCTGGAGTCCGGGTCGATCACGTACAGTTACCAATGCTCAATCACGCTTTCGATTCCCAGGCGCGCAACTCACTGGGATTCCAGGTCGTCACGAGCCTTGGGCAACGTTTCCTTACTAACCACTGA\n+>1747__A0A1N5AYP4__B1B09_10705 UniRef90_A0A1N5AYP4;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_002572615\n+ATGGATTGGGAGGCCACTGAGCTGACCGATCTCGACGTCACCGGTATTGATCACGAGGGCGGTTTCTCGGCCCTTGGCGTGCCCGACGAGATCGTTGCTGCTTTGGCCAAGACTGGCATTACCGATCCCTTCCGCATCCAGATCGCCGCCATCCCCGACGCCATCGCTGGGCGTGACGTGTTGGGCCGCGCCTCAACGGGTTCGGGTAAGACGTTGGCCTTTGGTGTCCCGCTGCTGTCGCGCCTGTCGGCCACCCCGCGTGAGGATAACCGGCCTCGAGCTCTCATCCTTTCTCCCACTCGTGAGCTGGCCATGCAGATTGCCGACGTGCTGTCCTCGCTGGCGTCCTCAATGGGGCTATCGACCATCCTCATCGCGGGTGGTATGAGCTACGGCCCGCAGACCAAGGCTTTTAAGAGGGGAGTCGACCTTGTTGTCGCCACCCCGGGGCGTCTGGTCGACCTCTTGGAGACTGGTGACGCCGACCTTTCCGGTGTCGCCGTGACTGTCCTCGACGAAGCCGATCACATGGCTGAACTGGGATTCATGGAGGCCGTTGGCTCGATCCTCGATGCCATTCCCGCTGACGGGCAGCGCCTGCTGTTCTCTGCCACCCTCGACGGTGCCGTTAACAAGTTGGTTAGGCGGTACATGCACGAGCCGGTTATCCACGAGGTCGACCCCGACAAGGGATCGGTCGCGACGATGACCCATCACGCTTTCCAGATCAAGCCTCACGAGAAGGTCGGGCTGATGTGCGAGATCGCTAACCGTAGCGGCCACACCATCGTCTTTGCTCGAACCCAGCGAGGTGCCTCCCGGATGGCCGAGCAACTGCGTGAGGCCGGCGTCATGGCTGGTGCTCTGCACGGCGGCCTGACCCAGGGTGCCCGTGCCCGCGTGTTGGCGGCATTCAAGGACGGTTCCCTGCCGGTCTTGGTTGCCACTGACGTCGCGGCCCGAGGAATTGACGTCGATGACGTCACTCTGGTGTTGCAAGTCGATCCGCCGATGAACTTCAAGGACTACCTGCACCGCTCCGGCCGTACCGCTCGCGCCGGACACGACGGGGCCGTCGTCTCTCTTGTCCTGCCGCATCAGCGTCGCACAATGGCTCGTTTGTACCGTCAAGCCGGGGTGAAGCCGGTAGAGGCCCAGGTCACGCGTGGCGACGACCACGTTGCCGAGGTGGCCGGTTGCAGCCCGGCCCTGGGCGCTCCTATTGACGAGAAGGATTACGAGGCTCTCGTCGCTCCCAAGCAGCAGCGCGGCAAGAAGGCTCGTGACGGAAAGCCTCGTCGTGGCAAGGGCGGACGCAACCGCGGTGGACGTGGATTCGACGGGGGCCGTCATCGCGGTCACGACTCCCGTGATCACCATGATCGTGGGCATGACTCGCGCGGACACAATTTCCGTGGCCGCGATCGTCGCGACATTGAGGCTAAATACGGCCGTTCCGGAAACGACACCTGGTGA\n+>1747__A0A3D8ZS35__CP884_00215 UniRef90_A0A3D8ZS35;k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes;GCA_003384705\n+ATGAACACC'..b'TTGATATAGACACACAAGGAGGCAATGATGTGATTTATGGCGGTGATGGTCATGATACCCTAAAAGGAGGTGATGGCAATGATGTGATTTATGGCTCTGCAGTCTTTTATGATTTTGAACCCAAAGACAGTCAAAGACTACCTAAGCCAAAACAAGACAAAGAGGGTAATTTAATTGGGGTGGATAAAGATATTATTATTGGTGGCATGGGAAGAGATTTGATTGCAGCAGGGATTGGGGATGATATTATTTGGGTGGACAATGAACAAGCAGAGTCTAATAACACCCATAACAACGACAAAGGAGACTGGGCATTAGGCGGACAAGGAAGTGATGTGATTTATGGGGGAGCAAATAAAGACTTTTTACAAGGTGGGGCGGATAATGATTATGTGTATGGCGGTGGTGGCGATGATGTGATATTGGGTGATGGACATATTAGGTTTGGCATAAAAAATCAAGTGCTACGCAGTGATAATCAGATTTTAAGCATAGAGCATACCTACGACCAAGTCAATCACAAAGAAAACACCCTAAAACAAAAAACCGCAAATTTACAAGACTACAAAACCTTTGAATGGAACATTCAAGTAGATACTGACAAAATGGATTATCTCTTAACCAAACAAAAAGACATTGCTTTGGCAAATAATTACCATCTTTTAGACGAATCATACAAACACAATGCCAATGACTTTTTGTACGGCGGCAAGGGAGACGACCTTATCATCGGTCAATATGGCAATGATTATCTAGATGGTGGTGAGGGTGATGACATCCTATGGGGTGATGATAACAGAGATGAGGATATTGAAGGGAATGACACGCTAAAAGGCGGTGCAGGAAGAGATAGGCTAATTGGTGGCAAAGGGAATGATGCGTATGTGTTTGACCTAGAAGACCTAGCCAAAAGCGGGGCGGATGACAAAACCATCATTGACAGTGATAATGGTGGCATCATCAAAATCAATCATTATGATCTAACAGGCACACAGTTTTTTAAATCCGCCAATGCCAGCAACCTCTACCAAAGCGATGATGGCAAATTTGACTTGATAAGATACGATAACGGCAACTACAGCCTATTAAGCAAAGATTTCAACGCCTCCATTGCCATCAAAGACACCCCCATCACAAAAAATGGCGACAATGACATCTTGCTAGGCATGATACTAAAAGAAACCAAAAACACCGCTCCTATCGTTCATAATCCCGTCTCTGACCAGATGGTGTTGGCAGAGCGAGACATCGCACTCGGTCTTGGCGAGGTATTCTTCGATGCTGATGGTGATGAGCTGACGTATAGCATCCAAGGGGCGGATGGACTGCATTTTGACCCTGCTACAAAGATGCTAACAGGCAGGGCACCTGATAAAGGGGTATTTAACATCACATTGACCGCCACCGACCCCAAGGGCGAGCATGCCAATACCAGCTTCACACTAAGAGTAAATGAACGACCAACGCTCGTCTCTGCCTTGACTCTACCGCTTGTGCTAAGCCAAGATGATGCCATGATGCAGATAGGTCTAGATAAGCTGTTTGTTGATAACGATGGTGATGCGTTAAGTTATTCGCTATCGGCAAATTCTTTGAGCGGTATCTACATTGACAACAATCATCTCATCATAGACCCTGCGACCACAGAGATTGGCATGCATGACATTACCATAACAGCGACAGACAGCTTCGGTCAGAGTGTCAGTACCAATGCCAGCTTTACCATCAAAGGCAGTGAGCCCATCGTGATGCCAGAGCCTGTTCTGCCCATCACGCCAACGCCTGACCCCATCACTGTTGGTAAGCGATATGTGGGCAAGCTCGGTGCTGATGACATCACAGGTGATGATAAAGCCAATACCATCAATGGCCTGACAGGAGATGATGTCCTAAGTGGTGGTCGTGGTAATGACACGCTCATCGGTGGATTTGGTCATGACACTTTAATTGGCGGACTTGATAACGACCTGCTTGTCGGTGGCTATGGCAATGATACTTATCTGTATCACAAAGGCGATGGTCTGGACACGATTCGTGATGTTGGTGGGTTGGATATCTTAAAGATTTCGGGGCTGACGTTGTCTGATTTGGGCTTTGCCAAACAGGGCAATCATCTGTTTATTGATGTCAAGCAAAATGATGATGGCATTATTATTGAAGATTATTTCAAATCAGGCAGTATCATACCAAGCCAAAAATCATCCCCCAACATAGAACGTATCTACATCAATGATAAGTTTGTCGGGCATGATGAGATTATCAAGATGGCGGATGTGATTATTTAA\n+>60442__A0A378QWP5__cya_3 UniRef90_A0A378QWP5;k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi;GCA_900453335\n+ATGGCAGAGTTTGATAAAATCAAATATAAAATTGGTGTTATCGATAGTTTCATGAGCACAAAAACAGATAACATGTTTTATGCTAACGTCAAAGACTTTGAAAAAACAACCAAAATTATCAATGATACTTATGATAGGCTGATTAAGTCTGTTTATAGTGGACTCTATCCGCAAACTGTTCAGAATCGTTATGGCGATTTGATAGATATTGTGGTAGATGTCAAAGATGGTAATCTTCTGTTTGGTTTGGACATTAATCGACTGGTAAGCGACTTTAAGGCAAGGTTAGATGTAGGTGGTCAAACCGCAATGTCTGCCTTTGGCGATATCATGGAGTATTTTGCTTATCTTCAAGTGCAAACACGACCTAACATTGTTGGCAGAGATAAGTTGGTTAATTTGATAGAGCATGTTGTATCTAGCGTGCCAAAACATGAATTGGATGGTTGGATAAATGGTATTGATTTTAAGATTGATAGAGAATTACCAATTAAGATGGGCGATGCACAAGATAATCATTTAAATGGCGGTGCTGTGTTTGCAGGTGCTGGTAATGATCGGTTGACTGGAACTAAAAATTCTGACCTCCTATTTGGTCAAGATGGTAACGACACCCTAAATGGCGGTAACGGCGATGACATCTTAAATGGTGGTGCTGGCGATGATTATTTAAGCAATTCGGGTCAGAATAACGGTAATGACACTTACATCTTTAGTGGTGATTATGGTAATGACATCATTCATGACTCTGATTCAAATGTCTCTAAAGAACGCCATTAA\n+>90240__A0A378QWM4__NCTC12877_00123 UniRef90_A0A378QWM4;k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae;GCA_900453285\n+ATGCTCACAAACCCCATTGACTATTTATCACAGGTTCATGACCCAAGGCGTCAAAACAAAAACCTGCTACACCCACTTAAAAACATTCTAACCATTGCCTTAACCGCAGTTATCTGTGGTTATCATGACTGGGTAGATATAGAAGACTTTGGCAATGAAAACAAAACATGGTTTGCCACATTTCTTGACTTAACTCATGGCATACCCTCACATGACACCTTTGGCAATGTCTTTAAACGCCTTAACAAAGATGAACTTAGTCGATACTTGAGTGAGTGGATAAATCAAACCCAAGCCAATCATCCACACATCGCCATTGATGGTAAATTCATCCAAGGTGGCTACAAAAATGACAACGCATTACAGCTTGTTACCGCCTTTGCCAGTCAAACCAAACTCATTCTTGCTCAAGTTGACATTGCTGATAAAAACAACGAAATTAGCACATTACCCCAACTGTTAAAACTCATTGATATCAGCGGTAGTATAGTGACAGCCGATGCCATTTACACCCCACAAACCCCAAATATGCTACAATACCCTAACATCCATTAA\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db.json Mon Apr 19 20:54:50 2021 +0000

[

b'@@ -0,0 +1,1 @@\n+{"markers": {"504553__GeneID:10498608": {"ext": ["GCA_000144505", "GCA_000144125", "GCA_000488875", "GCA_000178055", "GCA_001660965", "GCA_000144445", "GCA_003384145", "GCA_002572705", "GCA_001660935", "GCA_001750525", "GCA_000144775", "GCA_003390995", "GCA_001750535", "GCA_000008345", "GCA_003384705", "GCA_003384485", "GCA_002572745", "GCA_000144465", "GCA_000145375", "GCA_002775655", "GCA_001660855", "GCA_001660945", "GCA_000144875", "GCA_003426625", "GCA_000240055", "GCA_003426225", "GCA_003384285", "GCA_000144815", "GCA_000145095", "GCA_900102845", "GCA_001469595", "GCA_000145195", "GCA_003384365", "GCA_000145155", "GCA_003384255", "GCA_003384315", "GCA_000144345", "GCA_000240015", "GCA_000302515", "GCA_002831715", "GCA_000144285", "GCA_003426665", "GCA_001469635", "GCA_000144185", "GCA_002572835", "GCA_001660115", "GCA_000144325", "GCA_000144735", "GCA_000194825", "GCA_000376705", "GCA_000147145", "GCA_002572575", "GCA_000144795", "GCA_003384385", "GCA_000144895", "GCA_003425775", "GCA_003384345", "GCA_000231215", "GCA_003384555", "GCA_000735055", "GCA_000145575", "GCA_000144005", "GCA_003384195", "GCA_001469555", "GCA_003384585", "GCA_003384395", "GCA_000145455", "GCA_000144485", "GCA_003384495", "GCA_000342585", "GCA_003384445", "GCA_000144365", "GCA_000730485", "GCA_002861085", "GCA_002572615", "GCA_000144145", "GCA_002556485", "GCA_001481615", "GCA_000144245", "GCA_000144545", "GCA_000221125", "GCA_001469655", "GCA_003426685", "GCA_000144045", "GCA_002572665", "GCA_002572695", "GCA_002572655", "GCA_001750555", "GCA_003426255", "GCA_000145335", "GCA_002572775"], "score": 37.0, "clade": "t__Propionibacterium_phage_PAS50", "len": 663, "taxon": "k__Viruses|p__Viruses_unclassified|c__Viruses_unclassified|o__Caudovirales|f__Siphoviridae|g__Pa6virus|s__Propionibacterium_virus_PAS50|t__Propionibacterium_phage_PAS50"}, "386414__D1VYE0__HMPREF9019_1663": {"clade": "s__Prevotella_timonensis", "ext": [], "len": 1065, "score": 0, "taxon": "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis"}, "29394__H3NGH1__B5772_02200": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 972, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NFY1__B8A41_07655": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 534, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NC06__B8A41_08715": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 1317, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NDE2__B8A45_00965": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 699, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NFL8__B8A45_06985": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 582, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NDD1__B8A45_02325": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 480, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NE37__B8A45_05170": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 756, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "29394__H3NCU9__B8A45_08665": {"clade": "s__Dolosigranulum_pigrum", "ext": [], "len": 765, "score": 0, "taxon": "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum"}, "2'..b'roteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076675": ["2|1224|1236|91347|543|547|354276", 4289814], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000958695": ["2|1224|1236|91347|543|547|354276", 4336076], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900077255": ["2|1224|1236|91347|543|547|354276", 4482974], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075885": ["2|1224|1236|91347|543|547|354276", 4396160], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001487035": ["2|1224|1236|91347|543|547|354276", 4279410], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900077025": ["2|1224|1236|91347|543|547|354276", 4303785], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000952555": ["2|1224|1236|91347|543|547|354276", 4340464], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076755": ["2|1224|1236|91347|543|547|354276", 4236759], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000783855": ["2|1224|1236|91347|543|547|354276", 4188638], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001022075": ["2|1224|1236|91347|543|547|354276", 4412384], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001022255": ["2|1224|1236|91347|543|547|354276", 4385357], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075375": ["2|1224|1236|91347|543|547|354276", 4164369], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075395": ["2|1224|1236|91347|543|547|354276", 4013880], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_003261215": ["2|1224|1236|91347|543|547|354276", 5016502], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900075185": ["2|1224|1236|91347|543|547|354276", 4392401], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_002192395": ["2|1224|1236|91347|543|547|354276", 4556770], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_000958745": ["2|1224|1236|91347|543|547|354276", 4382425], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_001025055": ["2|1224|1236|91347|543|547|354276", 4360879], "k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter_cloacae_complex|t__GCA_900076455": ["2|1224|1236|91347|543|547|354276", 4404432]}, "merged_taxon": {}}\n\\ No newline at end of file\n'

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.1.bt2

Binary file test-data/test-db/test-db.1.bt2 has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.2.bt2

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diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.3.bt2

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diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.4.bt2

Binary file test-data/test-db/test-db.4.bt2 has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.pkl

Binary file test-data/test-db/test-db.pkl has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.rev.1.bt2

Binary file test-data/test-db/test-db.rev.1.bt2 has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test-db/test-db.rev.2.bt2

Binary file test-data/test-db/test-db.rev.2.bt2 has changed

diff -r 2cff76cf35c6 -r 3f05bf162005 test-data/test_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,6 @@
+# Tab separated with 4 columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - value (Galaxy records this in the Galaxy DB)
+# - path (folder name containing the Kraken DB)
+test-db-20210409 "Test Database" test-db ${__HERE__}/test-db
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 tool-data/metaphlan2_database.loc.sample
--- a/tool-data/metaphlan2_database.loc.sample Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of metagenomics files.
-#file has this format (white space characters are TAB characters)
-#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 tool-data/metaphlan_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan_database.loc.sample Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.
+#file has this format (white space characters are TAB characters)
+#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Mar 19 21:40:18 2021 +0000
+++ b/tool_data_table_conf.xml.sample Mon Apr 19 20:54:50 2021 +0000

@@ -1,6 +1,6 @@
<tables>
-    <table name="metaphlan2_database" comment_char="#">
+    <table name="metaphlan_database" comment_char="#">
         <columns>value, name, dbkey, path</columns>
-        <file path="tool-data/metaphlan2_database.loc" />
+        <file path="tool-data/metaphlan_database.loc" />
     </table>
</tables>

diff -r 2cff76cf35c6 -r 3f05bf162005 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Mon Apr 19 20:54:50 2021 +0000

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="metaphlan_database" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="${__HERE__}/test-data/test_database.loc" />
+    </table>
+</tables>
\ No newline at end of file

diff -r 2cff76cf35c6 -r 3f05bf162005 transform_json_to_pkl.py
--- a/transform_json_to_pkl.py Fri Mar 19 21:40:18 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import argparse
-import bz2
-import cPickle as pickle
-import json
-
-
-def transform_json_to_pkl(args):
-    with open(args.json_input, 'r') as json_file:
-        json_str = json_file.read()
-        metadata = json.loads(json_str)
-
-        for marker in metadata["markers"]:
-            a_set = set(metadata["markers"][marker]["ext"])
-            metadata["markers"][marker]["ext"] = a_set
-
-    pkl_output = bz2.BZ2File(args.pkl_output, 'w')
-    pickle.dump(metadata, pkl_output, pickle.HIGHEST_PROTOCOL)
-    pkl_output.close()
-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--json_input', required=True)
-    parser.add_argument('--pkl_output', required=True)
-    args = parser.parse_args()
-
-    transform_json_to_pkl(args)