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Changeset 0:a370301694bc (2024-04-13)

Next changeset 1:4d25ff3d07a9 (2024-05-11)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6

added:
JoinProfiles.xml
macros.xml
test-data/CDS_Str_agalactiae.fasta
test-data/GCA_000007265.1_ASM726v1_genomic.fna
test-data/GCA_000007265.1_ASM726v1_schema_seed.zip
test-data/JoinedProfile.tsv
test-data/Streptococcus_agalactiae.trn
test-data/allelecallevaluator_report.html
test-data/allelecallevaluator_report_annotate.html
test-data/cds_coordinates.tsv
test-data/loci_summary_stats.tsv
test-data/results_alleles.tsv
test-data/results_alleles2.tsv
test-data/results_statistics.tsv
test-data/schema_seed_annotations.tsv

diff -r 000000000000 -r a370301694bc JoinProfiles.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/JoinProfiles.xml Sat Apr 13 16:09:33 2024 +0000

[

@@ -0,0 +1,38 @@
+<tool id="chewbbaca_joinprofiles" name="chewBBACA JoinProfiles" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Join allele calling results from different runs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py JoinProfiles
+            -p ${str($input1).replace(',', ' ')}
+            -o 'JoinedProfile.tsv'
+            $common
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="tsv" multiple="true" label="AlleleCall results" />
+        <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
+            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="diff"/>
+        </test>
+    </tests>
+    <help>
+chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
+
+The process creates a TSV file with the allelic profiles of all samples in the input files.
+
+.. class:: infomark
+
+**Important**
+
+It is necessary to pass the --common argument if the input files do not have the same set of loci (this option creates a new file only with the set of loci shared between all input files).
+    </help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

diff -r 000000000000 -r a370301694bc macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,48 @@
+<macros>
+    <token name="@CHEW_VERSION@">3.3.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@CHEW_VERSION@">chewbbaca</requirement>
+            <requirement type="package" version="2.15.0">blast</requirement>
+            <requirement type="package" version="3.0">zip</requirement>
+            <requirement type="package" version="2.1.11">fasttree</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1099/mgen.0.000166</citation>
+        </citations>
+    </xml>
+    <xml name="species_id">
+        <option value="1">Streptococcus pyogenes</option>
+        <option value="2">Acinetobacter baumannii</option>
+        <option value="3">Arcobacter butzleri</option>
+        <option value="4">Campylobacter jejuni</option>
+        <option value="5">Escherichia coli</option>
+        <option value="6">Listeria monocytogenes</option>
+        <option value="7">Yersinia enterocolitica</option>
+        <option value="8">Salmonella enterica</option>
+        <option value="9">Streptococcus agalactiae</option>
+        <option value="10">Brucella melitensis</option>
+        <option value="11">Brucella</option>
+        <option value="12">Clostridium perfringens</option>
+        <option value="13">Clostridium chauvoei</option>
+        <option value="14">Bacillus anthracis</option>
+        <option value="15">Klebsiella oxytoca</option>
+        <option value="16">Clostridium neonatale</option>
+    </xml>
+    <token name="@COMMON_INPUT@">
+        --bsr $blast_score_ratio
+        --l $minimum_length
+        --t $translation_table
+        --st $size_threshold
+    </token>
+    <xml name="common_param">
+        <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" />
+        <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
+        <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
+    </xml>
+</macros>

diff -r 000000000000 -r a370301694bc test-data/CDS_Str_agalactiae.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CDS_Str_agalactiae.fasta Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,28 @@
+>FJ801036.1 Streptococcus agalactiae strain ABC020023529 BibA gene, complete cds
+ATGAATAATAACGAAAAAAAAGTAAAATACTTTTTAAGAAAAACAGCTTATGGTTTGGCTTCAATGTCAG
+CGGCGTTTATAGTATGTAGTGGTATTGTAAATACTCCTACAGTGTCTGCTGATAGTCCTGATACATTAAA
+AGTCGAAAAATTAGGCAAATTGAAAGATGTGAAATCAGTTCATGAACTCACACCCATATCAATACCGAAC
+GAATTAAAAGGTGCTAAAGAGCAAGCACTTTCTTCAATAATTTCACATCCTAATATAACTAATTCGGAAG
+TAGACAAACTAGCTAGTGACTATAGTTTTAGAATTAATACATCTAATGATGTGAACGACGTTAAACGTCT
+ATTAAATGAATTTTATAACGCAGTTGCAAGGAAACAGTTAGATACAAATTCTGCTGACTACCGTAGTAAA
+ATTGATAATATCAGTACTACAGGTCTTGCGATAGCTCTTGAGGCTAAAGAAATTTATGAAGCAAATAAAT
+CTATATTACCTCATCGTTACAAAGATTCTGTTGGAACTTATGTGAACAGTTTTGAGGAAAGACGAAGTCC
+AGGAAAATTTAATATTTGGAATGGTCAGGAAGGATTTAATGCAGCTCAAAAATTGTTAGAAGATGTTAAA
+AAATTATTACTTGAGCTACAAAATTTAACAAAAAATAACAAACCAAATATTCAAGTACCTAAACAAGCAC
+CTACAGAAGCTGCAAAACCAGCTTTGTCACCAGAAGCCTTGACAAGATTGACTACATGGTATAATCAAGC
+TAAAGATCTGCTTAAAGATGATCAAGTAAAGGACAAATACGTAGATATACTTTCAGTTCAAAAAGCTGTT
+GACCAAGCTTATGATCATGTGGAAGAGGGAAAATTTATTACCACTGATCAAGCAAATCAATTAGCTAACA
+AGCTACGTGATGCTTTACAAAGTTTAGAATTAAAAGATAAAAAAGTAGCCAAACCAGTAGCTAAAGGTAC
+ATACGATGTTAAGTATGTAGACACAGAAGGAAAAGAAGTAGCTAAGTCACGTCACTTCGAAGGAGAAGAA
+GGCGCAGCTTTTGTCACTTCAGCGAAAGAAGTAGCGGGTTACAAACTTGTTAGAACGGAAGGCGCTGTTT
+CAAATGTCTTCACAGCAGGAGCACAAGTACGTACATATGTTTACGAAAAAGTAGCCAAACCAGTAGCTAA
+AGGTACATACGATGTTAAGTATGTAGACACAGAAGGAAAAGAAGTAGCTAAGTCGCGTCACTTCGAAGGA
+GAAGAAGGCGCAGCTTTTGTCACTTCAGCGAAAGAAGTAGCGGGTTACAAACTTGTTAGAACGGAAGGTG
+CTGTTTCAAATGTCTTCACAGCAGGAGCACAAGTACGTACATATGTTTACGAAAAAGTTAAACCAGAAGT
+TAAACCAGACGTTAAGCCAGAGGCCAAACCAGAGGCTAAGCCAGAAGTTAAACCAGACGTTAAGCCAGAG
+GCCAAACCAGAGGCTAAGCCAGAAGTTAAATCAGACGTTAAGCCAGAGGCTAAGCCAGAAGCCAAACCAG
+AGGCTAAACCAGAAGTTAAACCAGACGTTAAGCCAGAGGCTAAACCAGAAGCCAAGCCAGCAACCAAAAA
+ATCGGTTAATACTAGCGGAAACTTGGTGGCTAAAAAAGCTATTGAAAACAAAAAGTATAGTAAAAAATTA
+CCATCAACGGGTGAAGCCGCAAGTCCACTCTTAGCAATTGTATCACTAATTGTTATGTTAAGTGCAGGTC
+TTATTACGATAGTTTTAAAGCATAAAAAAAATTAA
+

diff -r 000000000000 -r a370301694bc test-data/GCA_000007265.1_ASM726v1_genomic.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GCA_000007265.1_ASM726v1_genomic.fna Sat Apr 13 16:09:33 2024 +0000

b'@@ -0,0 +1,1500 @@\n+>AE009948.1 Streptococcus agalactiae 2603V/R, complete genome\n+AATTAACATTGTTGATTTTATTCTTCAACATCTGTGGAAAACTTTATTTTTTTATGGTACAATATAACAATAATTATCCA\n+CAAGACAATAAGGAAGAAGCTATGACGGAAAACGAACAACTATTTTGGAATAGAGTACTAGAGCTATCTCGTTCTCAAAT\n+AGCACCAGCAGCTTATGAATTTTTTGTTCTAGAGGCTAGACTCCTCAAAATTGAACATCAAACTGCAGTTATTACTTTAG\n+ATAACATTGAAATGAAAAAGCTATTCTGGGAACAAAATTTGGGGCCTGTTATCCTAACAGCTGGTTTTGAAATTTTCAAT\n+GCTGAAATTACAGCTAACTATGTCTCAAACGATTTACATTTACAAGAAACTAGTTTTTCTAACTACCAGCAATCTAGCAA\n+TGAAGTAAATACTTTACCAATTAGAAAAATCGACTCTAACCTTAAAGAGAAATATACTTTTGCTAATTTTGTTCAAGGAG\n+ATGAAAATAGATGGGCTGTTTCAGCATCAATTGCTGTAGCTGATAGTCCTGGCACGACTTATAATCCTCTATTTATCTGG\n+GGGGGACCTGGTCTAGGAAAGACGCATCTACTAAATGCTATTGGAAATCAAGTCTTAAGAGATAATCCAAACGCGAGGGT\n+TTTATACATCACTGCTGAGAATTTTATTAATGAATTTGTCAGTCATATTCGTTTAGATTCGATGGAAGAATTAAAAGAAA\n+AGTTTCGCAACTTAGACTTACTCCTGATTGATGATATTCAGTCGCTTGCTAAGAAAACCTTAGGGGGGACCCAAGAGGAG\n+TTCTTCAATACTTTCAATGCTTTACATACAAACGATAAACAAATCGTATTGACCAGTGACCGAAATCCAAATCAATTAAA\n+TGATCTAGAAGAACGTCTAGTCACGCGCTTTAGTTGGGGACTCCCAGTAAATATCACACCACCTGATTTTGAAACACGAG\n+TTGCTATTTTAACCAATAAAATTCAAGAATATCCTTATGATTTTCCTCAAGATACCATTGAATACTTAGCAGGAGAATTT\n+GATTCCAACGTACGTGAATTAGAAGGAGCCTTGAAAAATATTAGTCTAGTTGCTGACTTTAAGCATGCTAAAACTATTAC\n+AGTAGATATAGCTGCAGAAGCTATCAGAGCACGTAAAAATGATGGTCCTATTGTTACTGTCATTCCTATAGAAGAAATTC\n+AAATACAAGTTGGTAAATTCTATGGCGTAACTGTAAAAGAGATAAAAGCAACTAAAAGAACACAAGATATTGTCCTTGCA\n+AGACAGGTAGCCATGTACTTAGCTCGTGAGATGACAGATAACAGTCTCCCAAAAATAGGTAAAGAATTTGGGGGACGAGA\n+TCACTCAACTGTTCTCCACGCTTATAATAAAATAAAAAATATGGTTGCTCAAGATGACAACTTACGAATTGAGATAGAAA\n+CTATCAAAAATAAAATCAGATAGGCTTTGTGGATAAGTATCAGAAAAATACGAGACTTTTCCACAGGTTGTGAACAAGTT\n+ATTTTCCTTATGAATATTAAAGTTATAATACTTATTCACAACTTTAACAGGACCTACTATTACTACTAAATTTATACTAA\n+TATATAAAGGATATACTATGATTCATTTTTCAATAAATAAAAATTTCTTCTTGCATGCTCTAACGGTAACCAAACGAGCT\n+ATTAGTCATAAAAATGCGATTCCAATCCTTTCAACTGTTAAAATAGAAGTGACTAGGGATGCTATCATTTTAACGGGGTC\n+AAATGGACAAATTTCAATTGAAAATACTATTCCTGCTTCAAATGAAAATGCAGGTTTACTAGTAACGAATCCAGGCTCTA\n+TTTTGTTAGAAGCTGGTTTCTTTATTAATATTATTTCAAGTTTACCAGATGTAACTTTAGAATTTACAGAGATTGAACAA\n+CATCAAATTGTTCTTACTAGTGGAAAATCAGAGATTACTTTGAAAGGTAAGGATGTCGATCAATACCCTCGTCTGCAGGA\n+AATGACAACAGATACTCCATTAACATTAGAAACTAAACTGTTAAAATCAATTATTAATGAAACTGCTTTTGCTGCTAGCC\n+AACAAGAAAGCCGTCCAATCTTAACAGGTGTTCATTTGGTTATCAGTCAAAATAAATACTTTAAGGCTGTTGCGACAGAT\n+TCACACCGTATGAGTCAACGCACTTTCCAATTAGAGAAATCGGCTAATAATTTTGATTTGGTTGTTCCAAGTAAATCCCT\n+TCGAGAATTTTCGGCTGTTTTTACAGATGATATTGAAACTGTAGAGGTTTTCTTCTCAGATAGTCAAATGTTATTTAGAA\n+GTGAAAATATCAGCTTCTATACACGTTTGCTTGAAGGAAACTACCCTGATACTGATCGCCTCCTAACTAATCAGTTTGAA\n+ACCGAAATTATCTTTAATACAAATGCTTTACGCCATGCTATGGAACGTGCTTATTTAATTTCGAATGCAACTCAGAACGG\n+TACTGTTCGTTTAGAAATTCAAAATGAGACAGTCTCAGCTCATGTAAACTCTCCAGAAGTTGGTAAAGTTAATGAGGAAT\n+TGGATACTGTTAGTCTTAAAGGTGATAGTTTAAATATTAGCTTTAATCCAACTTACCTAATTGAATCTTTAAAAGCAGTA\n+AAAAGCGAAACAGTTACGATTCGATTTATTTCTCCAGTACGTCCATTTACTTTGACACCTGGTGAAGATACTGAAGATTT\n+CATCCAATTAATAACTCCTGTTCGTACTAACTAAATAAGAAAACTACCCAAGTTATTCTTGGGTAGTTTTCTTATTCTAA\n+GATATGCTATAATGATGAGTAATATGACTCTATATATAATAGCTAACCCCCATGCTGGTAATAAAAATGCCTCCACTATT\n+GTTGGTAAAATTCAGGAGCTTTATCATACTGAAGATATTTCTGTGTTCTATACAGAACAGAAAGATGATGAAAAAAAACA\n+AGTCATTAATATACTAAGGTCTTTTAAAGAAAGTGATCATCTAATGATTATAGGAGGAGATGGTACCTTATCAAAAGTAA\n+TGACTTATCTCCCCCAACATATTCCGTGCACTTATTATCCTGTTGGTTCGGGAAATGATTTTGCCAGAGCTTTGAAAATT\n+CCTAACCTCAAAGAAACCCTTACCGCTATTCAGACAGAAAGATTAAAGGAAATTAATTGCTTTATTTATGATAAAGGGCT\n+GATTTTGAATAGTTTAGATTTAGGTTTTGCAGCCTATGTCGTTTGGAAAGCATCTAACTCTAAAATAAAAAATATTTTGA\n+ATAGATATCGTCTAGGAAAAATAACTTACATTGTTATAGCTATCAAATCATTATTACATTCTTCTAAAGTACAAGTATTA\n+GTGGAAGGAGAGACAGGACAGCAGATAAAACTAAATGACCTTTATTTTTTCGCATTAGCAAATAACACTTATTTTGGAGG\n+TGGCATTACTATTTGGCCTAAAGCAAGTGCTTTAACTGCAGAGTTAGATATGGTTTACGCTAAAGGGCATACTTTTCTAA\n+AACGATTAAGTATTTTATTATCTTTGGTTTTTAAAAGGCATACTACCTCTAAAAGTATAAAACACCAGACTTTCAAAGCT\n+ATGACCGTATATTTTCCTAAAAATAGTTTGATTGAAATAGATGGCGAAATAGTTGAGTTAGATCAGATTAGTTTAAAATG\n+TCAAAAAAGGTATTTATATATGTAAGGAGAAAAGATGTATCAAGTTGGATCACTTGTTGAAATGAAAAAACCTCATGCTT\n+GTGTAATTAAAGAAACTGGTAAAAAGGCTAATCAATGGAAGGTACTGAGAGTAGGAGCTGAT'..b'AAGGTGACAATTCAAAAATTTGATCCATATATTAATATTGATCCAGGGACAATGAGCCCTTA\n+TCAACATGGAGAAGTTTATGTTACAGATGATGGTGCAGAAACTGACCTTGACCTTGGACACTACGAGCGTTTTATTGATA\n+TTAACTTAAACAAATATTCAAATGTTACAACGGGTAAGATTTATAGTGAAGTTCTTAAAAAAGAACGCCGTGGAGAATAC\n+CTTGGTGCAACTGTTCAAGTTATCCCACACGTTACAGATGCTTTGAAAGAAAAAATCAAACGTGCTGCGACAACTACAGA\n+TTCAGATGTTATTATTACTGAAGTTGGCGGTACTGTTGGAGATATTGAGAGCCTTCCGTTTTTAGAAGCACTTCGTCAAA\n+TGAAGGCAGATGTTGGTTCTGATAATGTTATGTACATTCATACAACGTTATTACCATACCTAAAGGCTGCCGGCGAAATG\n+AAAACAAAACCGACTCAACATTCTGTTAAAGAGTTACGTGGCCTAGGTATCCAACCTAATATGCTTGTTATCCGTACAGA\n+GCAACCAGCAGGTCAAAGTATTAAGAATAAATTGGCACAATTTTGTGATGTTGCACCAGAGGCTGTTATAGAGTCCCTTG\n+ACGTTGACCATATTTATCAAATTCCACTTAACATGCAAGCTCAAAATATGGATCAAATTGTTTGTGATCACTTGAAGCTT\n+GAGACACCTGCTGCTGATATGACAGAATGGTCAGCAATGGTTGATAAAGTAATGAACCTTGAGAAAAAAGTTAAAATTGC\n+ATTGGTTGGTAAATATGTTGAATTACCTGATGCCTACCTTTCAGTTGTGGAAGCCCTTAAGCACTCAGGGTACGTCAACG\n+ATGTTGCTATTGATCTAAAATGGGTAAATGCTGCTGAAGTGACAGAAGATAATATTAAAGAACTTGTCGGAGATGCAGAT\n+GGTATCATCGTTCCTGGTGGATTTGGCCAAAGAGGTAGTGAGGGTAAAATTGAAGCAATTCGCTATGCACGTGAAAATGA\n+TGTTCCAATGCTTGGTGTTTGTCTCGGAATGCAGCTAACTTGTGTCGAATTTGCGCGTAATGTTTTAAACCTTCATGGAG\n+CTAATTCAGCAGAGCTTGACCCTAAAACACCGTTCCCAATCATTGATATCATGCGTGATCAAATCGATATTGAAGATATG\n+GGTGGTACACTTCGCCTTGGTCTATATCCATGTAAATTGAAATCAGGTTCAAGAGCTGCGGCAGCTTATAATAATCAAGA\n+AGTTGTCCAACGTCGTCACCGTCACCGTTATGAATTTAATACAAAATTCCGTGAGCAATTTGAGGCTGCTGGATTTGTCT\n+TCTCAGGGGTATCACCGGATAATCGTTTGATGGAAGTTGTTGAGTTACCAGAGAAAAAATTCTTTGTTGCAGCACAATAC\n+CATCCAGAATTACAATCACGTCCTAACCATGCTGAAGAGCTTTACACAGCTTTTGTAACCGCAGCAGTTGAAAATATGAA\n+ATAACTTTATCGCCTCCCAGTATTAGGAGGCGATTTTATTTTTTTAGATAGTTTCACTATCAAAGTATCATTAGCTCTTT\n+TCTTTTTCTAAAAATAAGGTATAATAGGTTGCATGAAAAAGATTCGATTATCAAAGTTTATTAAAATGATTGTTGTTATT\n+TTGTTTTTAATTAGTGTAGCAGCTAGTTTTTATTTTTTCCACGTTGCCCAAGTTCGAGATGATAAATCCTTTATTTCAAA\n+TGGTCAACGTAAGCCTGGAAACTCTTTATATGCTTATGATAAATCCTTTGATAAGCTATTAAAGCAAAAAATAGAAATGA\n+CAAACCAAAATATAAAGCAAGTTGCTTGGTATGTTCCTGCTGTTAAGAAAACTCATAAGACAGCTGTTGTCGTTCATGGT\n+TTTGCGAATAGCAAAGAGAATATGAAGGCATATGGTTGGCTGTTTCATAAGTTAGGATACAATGTTCTTATGCCTGACAA\n+TATTGCACATGGTGAAAGTCATGGGCAGTTGATAGGCTATGGCTGGAACGACCGCGAGAACATTATCAAATGGACAGAAA\n+TGATAGTTGATAAGAATCCATCAAGCCAAATTACTTTATTTGGTGTTTCAATGGGTGGAGCAACAGTCATGATGGCTAGT\n+GGTGAAAAATTACCTAGTCAGGTTGTTAATATCATTGAAGATTGCGGTTATTCTAGTGTTTGGGATGAATTAAAATTTCA\n+GGCTAAAGAGATGTATGGTTTACCAGCCTTCCCACTCTTATATGAAGTTTCAACAATTTCTAAAATCAGAGCAGGTTTTT\n+CGTATGGACAAGCAAGTAGTGTCGAACAATTGAAAAAGAATAATTTACCAGCCCTCTTTATTCATGGTGATAAGGATAAT\n+TTTGTTCCAACAAGTATGGTTTATGACAACTATAAAGCTACAGCAGGTAAGAAAGAGCTTTATATTGTAAAAGGGGCAAA\n+ACATGCGAAATCTTTTGAAACAGAGCCAGAAAAATATGAGAAACGTATCTCTAGTTTTTTGAAAAAATATGAAAAATAAT\n+ATTGACAACAATATGATAAGTTGATATAATTTATTATGTTGTTAAGCGGGGATGGCGGAATTGGCAGACGCGCAAGACTA\n+AGGATCTTGTGACCGCTTTTGGTCGTGAGGGTTCAAGTCCCTCTCTCCGCAGACTAGTCGAGTTCATTTGGAACTCGACT\n+TTTTGCATATTTAAGATAAAGATGGAGTATCACATGTCAAAAGTACGTGGCTTTGAATTAGTTAGCCAATTTAGCAATAA\n+AGAGTTATTACCAAAACGAGAAACAGCTCACGCAGCTGGCTATGATTTAAAAGTAGCTAAAAAAACGGTTATTGAACCTG\n+GTGAAATTACATTGGTCCCGACCGGTATTAAAGCATACATGCAACCAGGGGAGGTCCTGTACCTTTATGATCGTTCATCG\n+AATCCACGTAAAAAAGGGATTGTCCTAATAAATTCAGTTGGTGTTATTGATGGTGACTACTATAATAACCAAGTCAATGA\n+AGGACATATTTTTGCACAGATGCAAAATATTACTGATCAGGCTGTTATTTTAGAAGAAGGGGAACGGATTGTTCAGGCTG\n+TTTTTGCCCCATTCTTATTGGCAGATGACGATCAGGCTACAGGAATGCGTACAGGTGGTTTTGGTAGTACTGGAAAATAA\n+AATTATTTTACGAATAATGTTAGAAAAGGCTAGACTTACTTCTTAGCCTTTTTTGATGAGAGTAAACTTATATTTTCTCT\n+AACTTGGTGTGATATAATGAGTGTACTAGTTATTTGGTACCAAGCTATCATATTAATTTAGAAGTTATAAAGGAGGCCTG\n+AGTGGCTAAGAAAAAATCAGTCTTCACCTGTCAAGAGTGTGGTTACCAATCACCTAAGTATTTGGGACGTTGTCCAAATT\n+GCTCAGCCTGGTCTTCATTTGTAGAAGAGGTTGAAGTTCAAGAAGTTAAAAATGCACGAGTTAGTTTGAACGGTGAAAAG\n+TCCCGACCGACGAAGTTAAAAGATGTTTCCTCAATTAACTATTCTAGAACTAAGACTGATATGGATGAATTTAACCGTGT\n+TCTAGGAGGCGGTGTTGTACCAGGAAGTTTGGTTCTGATTGGAGGAGACCCTGGGATAGGTAAATCTACTTTATTACTAC\n+AAGTATCAACTCAGCTAGCTAATAAAGGTACAGTATTATATGTCTCAGGTGAGGAATCTGCAGAACAGATTAAGTTACGA\n+AGTGAGCGTCTAGGCGATATCGATAATGAATTTTACCTTTATGCCGAGACTAATATGCAAAGTATTCGGTCGGAGATTGA\n+GAAGATTAAACCAGATTTTCTTATTATTGATTCTATACAAACTATTATGAGTCCCGAAGTATCAAGTGTCCAAGGCTCTG\n'

diff -r 000000000000 -r a370301694bc test-data/GCA_000007265.1_ASM726v1_schema_seed.zip

Binary file test-data/GCA_000007265.1_ASM726v1_schema_seed.zip has changed

diff -r 000000000000 -r a370301694bc test-data/JoinedProfile.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JoinedProfile.tsv Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,3 @@
+FILE GCA-000007265-protein1 GCA-000007265-protein10 GCA-000007265-protein100 GCA-000007265-protein101 GCA-000007265-protein102 GCA-000007265-protein103 GCA-000007265-protein104 GCA-000007265-protein105 GCA-000007265-protein106 GCA-000007265-protein107 GCA-000007265-protein108 GCA-000007265-protein109 GCA-000007265-protein11 GCA-000007265-protein110 GCA-000007265-protein111 GCA-000007265-protein112 GCA-000007265-protein113 GCA-000007265-protein114 GCA-000007265-protein12 GCA-000007265-protein13 GCA-000007265-protein14 GCA-000007265-protein16 GCA-000007265-protein19 GCA-000007265-protein2 GCA-000007265-protein20 GCA-000007265-protein21 GCA-000007265-protein22 GCA-000007265-protein23 GCA-000007265-protein24 GCA-000007265-protein25 GCA-000007265-protein26 GCA-000007265-protein27 GCA-000007265-protein28 GCA-000007265-protein29 GCA-000007265-protein3 GCA-000007265-protein30 GCA-000007265-protein31 GCA-000007265-protein32 GCA-000007265-protein33 GCA-000007265-protein34 GCA-000007265-protein35 GCA-000007265-protein36 GCA-000007265-protein37 GCA-000007265-protein38 GCA-000007265-protein39 GCA-000007265-protein40 GCA-000007265-protein41 GCA-000007265-protein42 GCA-000007265-protein43 GCA-000007265-protein44 GCA-000007265-protein45 GCA-000007265-protein46 GCA-000007265-protein47 GCA-000007265-protein48 GCA-000007265-protein49 GCA-000007265-protein5 GCA-000007265-protein50 GCA-000007265-protein51 GCA-000007265-protein52 GCA-000007265-protein53 GCA-000007265-protein54 GCA-000007265-protein55 GCA-000007265-protein56 GCA-000007265-protein57 GCA-000007265-protein58 GCA-000007265-protein59 GCA-000007265-protein6 GCA-000007265-protein60 GCA-000007265-protein61 GCA-000007265-protein62 GCA-000007265-protein63 GCA-000007265-protein64 GCA-000007265-protein65 GCA-000007265-protein66 GCA-000007265-protein67 GCA-000007265-protein68 GCA-000007265-protein69 GCA-000007265-protein7 GCA-000007265-protein70 GCA-000007265-protein71 GCA-000007265-protein72 GCA-000007265-protein74 GCA-000007265-protein75 GCA-000007265-protein76 GCA-000007265-protein77 GCA-000007265-protein79 GCA-000007265-protein8 GCA-000007265-protein80 GCA-000007265-protein81 GCA-000007265-protein82 GCA-000007265-protein84 GCA-000007265-protein85 GCA-000007265-protein86 GCA-000007265-protein87 GCA-000007265-protein9 GCA-000007265-protein93 GCA-000007265-protein94 GCA-000007265-protein95 GCA-000007265-protein96 GCA-000007265-protein97 GCA-000007265-protein98 GCA-000007265-protein99
+GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

diff -r 000000000000 -r a370301694bc test-data/Streptococcus_agalactiae.trn

Binary file test-data/Streptococcus_agalactiae.trn has changed

diff -r 000000000000 -r a370301694bc test-data/allelecallevaluator_report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/allelecallevaluator_report.html Sat Apr 13 16:09:33 2024 +0000

[

b'@@ -0,0 +1,16 @@\n+\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ <meta charset="UTF-8" />\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />\n+ <title>AlleleCall Report - React Edition</title>\n+</head>\n+<body style="background-color: #f6f6f6">\n+ <noscript> You need to enable JavaScript to run this app. </noscript>\n+ <div id="root"></div>\n+ <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0'..b', 0, 0], ["GCA-000007265-protein28", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein27", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein26", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein25", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein24", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein99", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein16", 3, 0, 1, 0.0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "annotations": [{"columns": []}, {"rows": []}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>\n+ <script src="./report_bundle.js"></script>\n+</body>\n+</html>\n+\n'

diff -r 000000000000 -r a370301694bc test-data/allelecallevaluator_report_annotate.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/allelecallevaluator_report_annotate.html Sat Apr 13 16:09:33 2024 +0000

[

b'@@ -0,0 +1,16 @@\n+\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+ <meta charset="UTF-8" />\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />\n+ <title>AlleleCall Report - React Edition</title>\n+</head>\n+<body style="background-color: #f6f6f6">\n+ <noscript> You need to enable JavaScript to run this app. </noscript>\n+ <div id="root"></div>\n+ <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0'..b'8E7R1", "", "", "", "", ""], ["GCA-000007265-protein64", "GCA_000007265", "AE009948.1", "79220", "79498", "64", "1", "Small ribosomal subunit protein uS19", "http://purl.uniprot.org/uniprot/Q1JE54", "", "", "", "", ""], ["GCA-000007265-protein52", "GCA_000007265", "AE009948.1", "66381", "66818", "52", "1", "protein-tyrosine-phosphatase", "http://purl.uniprot.org/uniprot/A0A0E1EJB3", "", "", "", "", ""], ["GCA-000007265-protein10", "GCA_000007265", "AE009948.1", "10295", "10666", "10", "1", "Cell division protein DivIC", "http://purl.uniprot.org/uniprot/Q8E7Y5", "", "", "", "", ""]]}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265:0.000000000);\\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>\n+ <script src="./report_bundle.js"></script>\n+</body>\n+</html>\n+\n'

diff -r 000000000000 -r a370301694bc test-data/cds_coordinates.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds_coordinates.tsv Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,115 @@
+Genome Contig Start Stop Protein_ID Coding_Strand
+GCA_000007265 AE009948.1 54 1463 1 1
+GCA_000007265 AE009948.1 1618 2754 2 1
+GCA_000007265 AE009948.1 2812 3705 3 1
+GCA_000007265 AE009948.1 3715 3912 4 1
+GCA_000007265 AE009948.1 4114 4317 5 1
+GCA_000007265 AE009948.1 4477 5592 6 1
+GCA_000007265 AE009948.1 5676 6251 7 1
+GCA_000007265 AE009948.1 6248 9745 8 1
+GCA_000007265 AE009948.1 10036 10308 9 1
+GCA_000007265 AE009948.1 10295 10666 10 1
+GCA_000007265 AE009948.1 10803 12089 11 1
+GCA_000007265 AE009948.1 12091 13365 12 1
+GCA_000007265 AE009948.1 13370 13912 13 1
+GCA_000007265 AE009948.1 13935 15911 14 1
+GCA_000007265 AE009948.1 17272 17466 15 -1
+GCA_000007265 AE009948.1 23103 23297 17 -1
+GCA_000007265 AE009948.1 92080 92274 88 -1
+GCA_000007265 AE009948.1 20579 20866 16 1
+GCA_000007265 AE009948.1 26410 26697 18 1
+GCA_000007265 AE009948.1 95387 95674 89 1
+GCA_000007265 AE009948.1 28902 30245 19 1
+GCA_000007265 AE009948.1 30369 31337 20 1
+GCA_000007265 AE009948.1 31334 32620 21 1
+GCA_000007265 AE009948.1 32610 33371 22 1
+GCA_000007265 AE009948.1 33434 34312 23 1
+GCA_000007265 AE009948.1 34390 35382 24 1
+GCA_000007265 AE009948.1 35393 35632 25 1
+GCA_000007265 AE009948.1 35756 36460 26 1
+GCA_000007265 AE009948.1 36583 40308 27 1
+GCA_000007265 AE009948.1 40720 42174 28 1
+GCA_000007265 AE009948.1 42202 43224 29 1
+GCA_000007265 AE009948.1 43392 43940 30 1
+GCA_000007265 AE009948.1 43963 44715 31 1
+GCA_000007265 AE009948.1 44735 46282 32 1
+GCA_000007265 AE009948.1 46475 47374 33 1
+GCA_000007265 AE009948.1 47521 48825 34 1
+GCA_000007265 AE009948.1 49072 49770 35 1
+GCA_000007265 AE009948.1 49817 51133 36 1
+GCA_000007265 AE009948.1 51221 52108 37 1
+GCA_000007265 AE009948.1 52118 52948 38 1
+GCA_000007265 AE009948.1 52961 53404 39 1
+GCA_000007265 AE009948.1 53424 54086 40 1
+GCA_000007265 AE009948.1 54083 55000 41 1
+GCA_000007265 AE009948.1 55017 55898 42 1
+GCA_000007265 AE009948.1 55906 56883 43 1
+GCA_000007265 AE009948.1 56906 57709 44 -1
+GCA_000007265 AE009948.1 57991 59256 45 1
+GCA_000007265 AE009948.1 59588 60025 46 1
+GCA_000007265 AE009948.1 60012 61103 47 1
+GCA_000007265 AE009948.1 61157 62548 48 1
+GCA_000007265 AE009948.1 62573 63871 49 1
+GCA_000007265 AE009948.1 64023 64934 50 1
+GCA_000007265 AE009948.1 65231 66229 51 1
+GCA_000007265 AE009948.1 66381 66818 52 1
+GCA_000007265 AE009948.1 66825 67205 53 1
+GCA_000007265 AE009948.1 67202 68980 54 1
+GCA_000007265 AE009948.1 69250 71892 55 1
+GCA_000007265 AE009948.1 72071 73087 56 1
+GCA_000007265 AE009948.1 73207 74697 57 1
+GCA_000007265 AE009948.1 74802 76082 58 1
+GCA_000007265 AE009948.1 76288 76596 59 1
+GCA_000007265 AE009948.1 76701 77327 60 1
+GCA_000007265 AE009948.1 77351 77974 61 1
+GCA_000007265 AE009948.1 77974 78270 62 1
+GCA_000007265 AE009948.1 78288 79121 63 1
+GCA_000007265 AE009948.1 79220 79498 64 1
+GCA_000007265 AE009948.1 79514 79858 65 1
+GCA_000007265 AE009948.1 79871 80524 66 1
+GCA_000007265 AE009948.1 80528 80941 67 1
+GCA_000007265 AE009948.1 80951 81157 68 1
+GCA_000007265 AE009948.1 81183 81443 69 1
+GCA_000007265 AE009948.1 81468 81836 70 1
+GCA_000007265 AE009948.1 81916 82221 71 1
+GCA_000007265 AE009948.1 82245 82787 72 1
+GCA_000007265 AE009948.1 82805 82990 73 1
+GCA_000007265 AE009948.1 83145 83543 74 1
+GCA_000007265 AE009948.1 83653 84189 75 1
+GCA_000007265 AE009948.1 84290 84646 76 1
+GCA_000007265 AE009948.1 84665 85159 77 1
+GCA_000007265 AE009948.1 85174 85353 78 1
+GCA_000007265 AE009948.1 85478 85918 79 1
+GCA_000007265 AE009948.1 85939 87243 80 1
+GCA_000007265 AE009948.1 87338 87976 81 1
+GCA_000007265 AE009948.1 88092 88310 82 1
+GCA_000007265 AE009948.1 88336 88452 83 1
+GCA_000007265 AE009948.1 88470 88835 84 1
+GCA_000007265 AE009948.1 88853 89236 85 1
+GCA_000007265 AE009948.1 89286 90224 86 1
+GCA_000007265 AE009948.1 90239 90625 87 1
+GCA_000007265 AE009948.1 97888 98076 90 1
+GCA_000007265 AE009948.1 98076 98246 91 1
+GCA_000007265 AE009948.1 98316 98486 92 1
+GCA_000007265 AE009948.1 98822 99082 93 -1
+GCA_000007265 AE009948.1 99401 99952 94 1
+GCA_000007265 AE009948.1 100172 100591 95 1
+GCA_000007265 AE009948.1 100791 101270 96 1
+GCA_000007265 AE009948.1 101392 102084 97 1
+GCA_000007265 AE009948.1 102081 102833 98 1
+GCA_000007265 AE009948.1 102830 103405 99 1
+GCA_000007265 AE009948.1 103548 104582 100 1
+GCA_000007265 AE009948.1 104624 105157 101 1
+GCA_000007265 AE009948.1 105338 107167 102 1
+GCA_000007265 AE009948.1 107456 108595 103 1
+GCA_000007265 AE009948.1 108709 109956 104 1
+GCA_000007265 AE009948.1 110027 110803 105 1
+GCA_000007265 AE009948.1 110766 111524 106 1
+GCA_000007265 AE009948.1 111534 111998 107 1
+GCA_000007265 AE009948.1 111995 112564 108 1
+GCA_000007265 AE009948.1 112601 113443 109 -1
+GCA_000007265 AE009948.1 113600 114883 110 1
+GCA_000007265 AE009948.1 115072 115647 111 1
+GCA_000007265 AE009948.1 115920 117524 112 1
+GCA_000007265 AE009948.1 117633 118559 113 1
+GCA_000007265 AE009948.1 118754 119200 114 1

diff -r 000000000000 -r a370301694bc test-data/loci_summary_stats.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loci_summary_stats.tsv Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,103 @@
+Locus EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA LNF Total_CDS
+GCA-000007265-protein1 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein10 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein100 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein101 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein102 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein103 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein104 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein105 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein106 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein107 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein108 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein109 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein11 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein110 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein111 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein112 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein113 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein114 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein12 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein13 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein14 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein16 0 0 0 0 0 0 1 0 0 0 0 3
+GCA-000007265-protein19 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein2 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein20 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein21 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein22 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein23 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein24 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein25 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein26 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein27 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein28 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein29 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein3 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein30 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein31 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein32 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein33 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein34 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein35 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein36 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein37 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein38 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein39 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein40 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein41 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein42 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein43 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein44 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein45 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein46 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein47 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein48 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein49 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein5 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein50 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein51 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein52 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein53 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein54 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein55 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein56 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein57 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein58 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein59 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein6 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein60 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein61 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein62 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein63 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein64 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein65 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein66 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein67 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein68 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein69 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein7 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein70 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein71 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein72 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein74 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein75 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein76 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein77 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein79 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein8 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein80 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein81 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein82 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein84 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein85 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein86 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein87 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein9 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein93 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein94 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein95 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein96 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein97 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein98 1 0 0 0 0 0 0 0 0 0 0 1
+GCA-000007265-protein99 1 0 0 0 0 0 0 0 0 0 0 1

diff -r 000000000000 -r a370301694bc test-data/results_alleles.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results_alleles.tsv Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,2 @@
+FILE GCA-000007265-protein1 GCA-000007265-protein10 GCA-000007265-protein100 GCA-000007265-protein101 GCA-000007265-protein102 GCA-000007265-protein103 GCA-000007265-protein104 GCA-000007265-protein105 GCA-000007265-protein106 GCA-000007265-protein107 GCA-000007265-protein108 GCA-000007265-protein109 GCA-000007265-protein11 GCA-000007265-protein110 GCA-000007265-protein111 GCA-000007265-protein112 GCA-000007265-protein113 GCA-000007265-protein114 GCA-000007265-protein12 GCA-000007265-protein13 GCA-000007265-protein14 GCA-000007265-protein16 GCA-000007265-protein19 GCA-000007265-protein2 GCA-000007265-protein20 GCA-000007265-protein21 GCA-000007265-protein22 GCA-000007265-protein23 GCA-000007265-protein24 GCA-000007265-protein25 GCA-000007265-protein26 GCA-000007265-protein27 GCA-000007265-protein28 GCA-000007265-protein29 GCA-000007265-protein3 GCA-000007265-protein30 GCA-000007265-protein31 GCA-000007265-protein32 GCA-000007265-protein33 GCA-000007265-protein34 GCA-000007265-protein35 GCA-000007265-protein36 GCA-000007265-protein37 GCA-000007265-protein38 GCA-000007265-protein39 GCA-000007265-protein40 GCA-000007265-protein41 GCA-000007265-protein42 GCA-000007265-protein43 GCA-000007265-protein44 GCA-000007265-protein45 GCA-000007265-protein46 GCA-000007265-protein47 GCA-000007265-protein48 GCA-000007265-protein49 GCA-000007265-protein5 GCA-000007265-protein50 GCA-000007265-protein51 GCA-000007265-protein52 GCA-000007265-protein53 GCA-000007265-protein54 GCA-000007265-protein55 GCA-000007265-protein56 GCA-000007265-protein57 GCA-000007265-protein58 GCA-000007265-protein59 GCA-000007265-protein6 GCA-000007265-protein60 GCA-000007265-protein61 GCA-000007265-protein62 GCA-000007265-protein63 GCA-000007265-protein64 GCA-000007265-protein65 GCA-000007265-protein66 GCA-000007265-protein67 GCA-000007265-protein68 GCA-000007265-protein69 GCA-000007265-protein7 GCA-000007265-protein70 GCA-000007265-protein71 GCA-000007265-protein72 GCA-000007265-protein74 GCA-000007265-protein75 GCA-000007265-protein76 GCA-000007265-protein77 GCA-000007265-protein79 GCA-000007265-protein8 GCA-000007265-protein80 GCA-000007265-protein81 GCA-000007265-protein82 GCA-000007265-protein84 GCA-000007265-protein85 GCA-000007265-protein86 GCA-000007265-protein87 GCA-000007265-protein9 GCA-000007265-protein93 GCA-000007265-protein94 GCA-000007265-protein95 GCA-000007265-protein96 GCA-000007265-protein97 GCA-000007265-protein98 GCA-000007265-protein99
+GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

diff -r 000000000000 -r a370301694bc test-data/results_alleles2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results_alleles2.tsv Sat Apr 13 16:09:33 2024 +0000

diff -r 000000000000 -r a370301694bc test-data/results_statistics.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/results_statistics.tsv Sat Apr 13 16:09:33 2024 +0000

@@ -0,0 +1,2 @@
+FILE EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA LNF Invalid CDSs Classified_CDSs Total_CDSs
+GCA_000007265 101 0 0 0 0 0 1 0 0 0 0 0 104 114

diff -r 000000000000 -r a370301694bc test-data/schema_seed_annotations.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/schema_seed_annotations.tsv Sat Apr 13 16:09:33 2024 +0000

b'@@ -0,0 +1,103 @@\n+Locus\tGenome\tContig\tStart\tStop\tProtein_ID\tCoding_Strand\tUniprot_Name\tUniProt_URL\tProteome_ID\tProteome_Product\tProteome_Gene_Name\tProteome_Species\tProteome_BSR\n+GCA-000007265-protein111\tGCA_000007265\tAE009948.1\t115072\t115647\t111\t1\tProbable DNA-directed RNA polymerase subunit delta\thttp://purl.uniprot.org/uniprot/Q3K3S3\t\t\t\t\t\n+GCA-000007265-protein25\tGCA_000007265\tAE009948.1\t35393\t35632\t25\t1\tAcyl carrier protein\thttp://purl.uniprot.org/uniprot/Q8E7X3\t\t\t\t\t\n+GCA-000007265-protein101\tGCA_000007265\tAE009948.1\t104624\t105157\t101\t1\tProtein GrpE\thttp://purl.uniprot.org/uniprot/Q3K3T3\t\t\t\t\t\n+GCA-000007265-protein31\tGCA_000007265\tAE009948.1\t43963\t44715\t31\t1\tN-acetyltransferase domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E7W7\t\t\t\t\t\n+GCA-000007265-protein79\tGCA_000007265\tAE009948.1\t85478\t85918\t79\t1\tLarge ribosomal subunit protein uL15\thttp://purl.uniprot.org/uniprot/Q3K3V0\t\t\t\t\t\n+GCA-000007265-protein108\tGCA_000007265\tAE009948.1\t111995\t112564\t108\t1\tUPF0340 protein SAK_0153\thttp://purl.uniprot.org/uniprot/Q3K3S6\t\t\t\t\t\n+GCA-000007265-protein58\tGCA_000007265\tAE009948.1\t74802\t76082\t58\t1\tProbable multidrug resistance protein NorM\thttp://purl.uniprot.org/uniprot/A0A0E1EEL2\t\t\t\t\t\n+GCA-000007265-protein32\tGCA_000007265\tAE009948.1\t44735\t46282\t32\t1\tBifunctional purine biosynthesis protein PurH\thttp://purl.uniprot.org/uniprot/P67545\t\t\t\t\t\n+GCA-000007265-protein69\tGCA_000007265\tAE009948.1\t81183\t81443\t69\t1\tSmall ribosomal subunit protein uS17\thttp://purl.uniprot.org/uniprot/B5XJ45\t\t\t\t\t\n+GCA-000007265-protein80\tGCA_000007265\tAE009948.1\t85939\t87243\t80\t1\tProtein translocase subunit SecY\thttp://purl.uniprot.org/uniprot/Q8E7S1\t\t\t\t\t\n+GCA-000007265-protein62\tGCA_000007265\tAE009948.1\t77974\t78270\t62\t1\tLarge ribosomal subunit protein uL23\thttp://purl.uniprot.org/uniprot/Q8E7T6\t\t\t\t\t\n+GCA-000007265-protein8\tGCA_000007265\tAE009948.1\t6248\t9745\t8\t1\tTranscription-repair-coupling factor\thttp://purl.uniprot.org/uniprot/Q8E7Y7\t\t\t\t\t\n+GCA-000007265-protein28\tGCA_000007265\tAE009948.1\t40720\t42174\t28\t1\tAmidophosphoribosyltransferase\thttp://purl.uniprot.org/uniprot/A0A8I2JU49\t\t\t\t\t\n+GCA-000007265-protein113\tGCA_000007265\tAE009948.1\t117633\t118559\t113\t1\tAB hydrolase-1 domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E289\t\t\t\t\t\n+GCA-000007265-protein107\tGCA_000007265\tAE009948.1\t111534\t111998\t107\t1\tECF transporter S component\thttp://purl.uniprot.org/uniprot/A0A1F0CHU0\t\t\t\t\t\n+GCA-000007265-protein46\tGCA_000007265\tAE009948.1\t59588\t60025\t46\t1\tN5-carboxyaminoimidazole ribonucleotide mutase\thttp://purl.uniprot.org/uniprot/A0A380JAU3\t\t\t\t\t\n+GCA-000007265-protein35\tGCA_000007265\tAE009948.1\t49072\t49770\t35\t1\tPutative N-acetylmannosamine-6-phosphate 2-epimerase\thttp://purl.uniprot.org/uniprot/P65518\t\t\t\t\t\n+GCA-000007265-protein43\tGCA_000007265\tAE009948.1\t55906\t56883\t43\t1\tAlpha/beta fold hydrolase\thttp://purl.uniprot.org/uniprot/A0A0E1EEK2\t\t\t\t\t\n+GCA-000007265-protein67\tGCA_000007265\tAE009948.1\t80528\t80941\t67\t1\tLarge ribosomal subunit protein uL16\thttp://purl.uniprot.org/uniprot/Q3K3W2\t\t\t\t\t\n+GCA-000007265-protein94\tGCA_000007265\tAE009948.1\t99401\t99952\t94\t1\tProlyl-tRNA synthetase\thttp://purl.uniprot.org/uniprot/Q8E2A6\t\t\t\t\t\n+GCA-000007265-protein75\tGCA_000007265\tAE009948.1\t83653\t84189\t75\t1\tLarge ribosomal subunit protein uL6\thttp://purl.uniprot.org/uniprot/Q8E2B9\t\t\t\t\t\n+GCA-000007265-protein36\tGCA_000007265\tAE009948.1\t49817\t51133\t36\t1\tUncharacterized protein\thttp://purl.uniprot.org/uniprot/Q8E7W2\t\t\t\t\t\n+GCA-000007265-protein59\tGCA_000007265\tAE009948.1\t76288\t76596\t59\t1\tSmall ribosomal subunit protein uS10\thttp://purl.uniprot.org/uniprot/A2RC13\t\t\t\t\t\n+GCA-000007265-protein30\tGCA_000007265\tAE009948.1\t43392\t43940\t30\t1\tPhosphoribosylglycinamide formyltransferase\thttp://purl.uniprot.org/uniprot/A0A8I2FG92\t\t\t\t\t\n+GCA-000007265-protein34\tGCA_000007265\tAE009948.1\t47521\t48825\t34\t1\tLysM domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E7W4\t\t\t\t\t\n+GCA-000007265-protein6\tGCA_000007265\tAE009948.1\t4477\t5592\t6\t1\tRibosome-binding ATPase YchF\thttp://purl.uniprot.org/unipro'..b"p://purl.uniprot.org/uniprot/Q8E7Y3\t\t\t\t\t\n+GCA-000007265-protein40\tGCA_000007265\tAE009948.1\t53424\t54086\t40\t1\tBeta-carotene 15,15'-monooxygenase\thttp://purl.uniprot.org/uniprot/A0A1F0CI38\t\t\t\t\t\n+GCA-000007265-protein56\tGCA_000007265\tAE009948.1\t72071\t73087\t56\t1\tAlcohol dehydrogenase\thttp://purl.uniprot.org/uniprot/X5K0V4\t\t\t\t\t\n+GCA-000007265-protein3\tGCA_000007265\tAE009948.1\t2812\t3705\t3\t1\tdiacylglycerol kinase family protein\thttp://purl.uniprot.org/uniparc/UPI0002BB2C63\t\t\t\t\t\n+GCA-000007265-protein7\tGCA_000007265\tAE009948.1\t5676\t6251\t7\t1\tPeptidyl-tRNA hydrolase\thttp://purl.uniprot.org/uniprot/Q8E2I1\t\t\t\t\t\n+GCA-000007265-protein53\tGCA_000007265\tAE009948.1\t66825\t67205\t53\t1\tMORN motif family protein\thttp://purl.uniprot.org/uniprot/A0A1F0CHD6\t\t\t\t\t\n+GCA-000007265-protein16\tGCA_000007265\tAE009948.1\t20579\t20866\t16\t1\tRNAase\thttp://purl.uniprot.org/uniprot/U5P1X6\t\t\t\t\t\n+GCA-000007265-protein63\tGCA_000007265\tAE009948.1\t78288\t79121\t63\t1\tLarge ribosomal subunit protein uL2\thttp://purl.uniprot.org/uniprot/Q3K3W6\t\t\t\t\t\n+GCA-000007265-protein26\tGCA_000007265\tAE009948.1\t35756\t36460\t26\t1\tPhosphoribosylaminoimidazole-succinocarboxamide synthase\thttp://purl.uniprot.org/uniprot/Q8E2G4\t\t\t\t\t\n+GCA-000007265-protein106\tGCA_000007265\tAE009948.1\t110766\t111524\t106\t1\tpyridoxal kinase\thttp://purl.uniprot.org/uniprot/Q8E7Q4\t\t\t\t\t\n+GCA-000007265-protein37\tGCA_000007265\tAE009948.1\t51221\t52108\t37\t1\tABC transmembrane type-1 domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E7W1\t\t\t\t\t\n+GCA-000007265-protein5\tGCA_000007265\tAE009948.1\t4114\t4317\t5\t1\tGbs0005 protein\thttp://purl.uniprot.org/uniprot/Q8E7Z0\t\t\t\t\t\n+GCA-000007265-protein71\tGCA_000007265\tAE009948.1\t81916\t82221\t71\t1\tLarge ribosomal subunit protein uL24\thttp://purl.uniprot.org/uniprot/Q3K3V8\t\t\t\t\t\n+GCA-000007265-protein68\tGCA_000007265\tAE009948.1\t80951\t81157\t68\t1\tLarge ribosomal subunit protein uL29\thttp://purl.uniprot.org/uniprot/A2RC22\t\t\t\t\t\n+GCA-000007265-protein47\tGCA_000007265\tAE009948.1\t60012\t61103\t47\t1\tN5-carboxyaminoimidazole ribonucleotide synthase\thttp://purl.uniprot.org/uniprot/A0A0E1EJA7\t\t\t\t\t\n+GCA-000007265-protein99\tGCA_000007265\tAE009948.1\t102830\t103405\t99\t1\tMannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E7R0\t\t\t\t\t\n+GCA-000007265-protein102\tGCA_000007265\tAE009948.1\t105338\t107167\t102\t1\tChaperone protein DnaK\thttp://purl.uniprot.org/uniprot/P0A3J2\t\t\t\t\t\n+GCA-000007265-protein96\tGCA_000007265\tAE009948.1\t100791\t101270\t96\t1\tCompetence-specific sigma factor ComX\thttp://purl.uniprot.org/uniprot/Q8E7R3\t\t\t\t\t\n+GCA-000007265-protein66\tGCA_000007265\tAE009948.1\t79871\t80524\t66\t1\tSmall ribosomal subunit protein uS3\thttp://purl.uniprot.org/uniprot/A2RC20\t\t\t\t\t\n+GCA-000007265-protein20\tGCA_000007265\tAE009948.1\t30369\t31337\t20\t1\tRibose-phosphate pyrophosphokinase 1\thttp://purl.uniprot.org/uniprot/Q8E2H0\t\t\t\t\t\n+GCA-000007265-protein57\tGCA_000007265\tAE009948.1\t73207\t74697\t57\t1\tThreonine synthase\thttp://purl.uniprot.org/uniprot/A0A0E1EJC0\t\t\t\t\t\n+GCA-000007265-protein42\tGCA_000007265\tAE009948.1\t55017\t55898\t42\t1\tN-acetylmannosamine kinase\thttp://purl.uniprot.org/uniprot/A0A0E1EJA4\t\t\t\t\t\n+GCA-000007265-protein14\tGCA_000007265\tAE009948.1\t13935\t15911\t14\t1\tATP-dependent zinc metalloprotease FtsH\thttp://purl.uniprot.org/uniprot/Q8E7Y0\t\t\t\t\t\n+GCA-000007265-protein76\tGCA_000007265\tAE009948.1\t84290\t84646\t76\t1\tLarge ribosomal subunit protein uL18\thttp://purl.uniprot.org/uniprot/Q3K3V3\t\t\t\t\t\n+GCA-000007265-protein98\tGCA_000007265\tAE009948.1\t102081\t102833\t98\t1\tPeptidase M15B domain-containing protein\thttp://purl.uniprot.org/uniprot/Q8E7R1\t\t\t\t\t\n+GCA-000007265-protein64\tGCA_000007265\tAE009948.1\t79220\t79498\t64\t1\tSmall ribosomal subunit protein uS19\thttp://purl.uniprot.org/uniprot/Q1JE54\t\t\t\t\t\n+GCA-000007265-protein52\tGCA_000007265\tAE009948.1\t66381\t66818\t52\t1\tprotein-tyrosine-phosphatase\thttp://purl.uniprot.org/uniprot/A0A0E1EJB3\t\t\t\t\t\n+GCA-000007265-protein10\tGCA_000007265\tAE009948.1\t10295\t10666\t10\t1\tCell division protein DivIC\thttp://purl.uniprot.org/uniprot/Q8E7Y5\t\t\t\t\t\n"