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changeset 0:2c7ac12ad75a draft

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"planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
author iuc
date Tue, 18 Feb 2020 15:58:57 -0500
parents
children 3c6e0e8df873
files fastani.xml macros.xml test-data/E.coli_1.fasta test-data/E.coli_2.fasta test-data/S.flexneri_1.fasta test-data/S.flexneri_2.fasta test-data/multi.out test-data/single.out
diffstat 8 files changed, 445 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastani.xml	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,106 @@
+<tool id="fastani" name="FastANI" version="@VERSION@">
+    <description> fast alignment-free computation of whole-genome Average Nucleotide Identity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>fastANI --version</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    #import re
+
+    ### SET UP INPUTS ###
+    #for $input_q in $query:
+        #set $file_name = re.sub('[^\w_]', '_', $input_q.element_identifier)
+        ln -fs '$input_q' '${file_name}_query' &&
+        echo '${file_name}_query' >> query.lst &&
+    #end for
+
+    #for $input_r in $reference:
+        #set $file_name = re.sub('[^\w_]', '_', $input_r.element_identifier)
+        ln -fs '$input_r' '${file_name}_ref' &&
+        echo '${file_name}_ref' >> ref.lst &&
+    #end for
+    
+
+    ### COMMAND ###
+
+    fastANI --ql query.lst --rl ref.lst -o output -t "\${GALAXY_SLOTS:-1}"
+
+    ]]></command>
+    <inputs>
+        <param name="query" type="data" format="fasta" multiple="true" label="Query Sequence(s)"
+        help="Specify any number of query sequences in fasta format as input." />
+        <param name="reference" type="data" format="fasta" multiple="true" label="Reference Sequence(s)"
+        help="Specify any number of reference sequences in fasta format as input." />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="query" value="E.coli_1.fasta" />
+            <param name="reference" value="S.flexneri_1.fasta" />
+            <output name="output" file="single.out" compare="sim_size" />
+        </test>
+        <test>
+            <param name="query" value="E.coli_1.fasta,E.coli_2.fasta" />
+            <param name="reference" value="S.flexneri_1.fasta,S.flexneri_2.fasta" />
+            <output name="output" file="multi.out" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+FastANI
+=======
+
+FastANI is developed for fast alignment-free computation of whole-genome
+Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide
+identity of orthologous gene pairs shared between two microbial genomes.
+FastANI supports pairwise comparison of both complete and draft genome
+assemblies. Its underlying procedure follows a similar workflow as described
+by `Goris et al. 2007 <https://doi.org/10.1099/ijs.0.64483-0>`_. However, it avoids expensive sequence alignments and
+uses `Mashmap <https://github.com/marbl/MashMap>`_ as its MinHash based sequence mapping engine to compute the
+orthologous mappings and alignment identity estimates. Based on our
+experiments with complete and draft genomes, its accuracy is on par with
+`BLAST-based ANI solver <http://enve-omics.ce.gatech.edu/ani/>`_ and it achieves two to three orders of magnitude
+speedup. Therefore, it is useful for pairwise ANI computation of large
+number of genome pairs. More details about its speed, accuracy and potential
+applications are described here: `"High Throughput ANI Analysis of 90K
+Prokaryotic Genomes Reveals Clear Species Boundaries" <https://doi-org.uml.idm.oclc.org/10.1038/s41467-018-07641-9>`_.
+
+Please visit the authors at: https://github.com/ParBLiSS/FastANI
+
+
+Inputs
+------
+
+**Query Sequence(s):**
+Input one or more query genomes in fasta format
+
+**Reference Sequence(s):**
+Input one or more reference genomes to be compared to the query genomes
+
+
+Output
+------
+
+Tabular table output with columns: Query Genome, Reference Genome, ANI Value, Count of Bidirectional Fragment Mappings, and Total Query Fragments.
+
+Output table looks as such:
+
++------------+------------+-----------+--------+--------+
+|  Genome A  |  Genome C  |  97.5883  |  1405  |  1594  |
++------------+------------+-----------+--------+--------+
+|  Genome A  |  Genome D  |  95.6663  |  1405  |  1594  |
++------------+------------+-----------+--------+--------+
+|  Genome B  |  Genome C  |  92.4281  |  1409  |  1553  |
++------------+------------+-----------+--------+--------+
+|  Genome B  |  Genome D  |  99.9242  |  1396  |  1553  |
++------------+------------+-----------+--------+--------+
+
+|
+| Thanks to Thanh Lê for building the initial Galaxy wrapper.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,14 @@
+<macros>
+    <token name="@VERSION@">1.3</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="@VERSION@">fastani</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41467-018-07641-9</citation>
+       </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/E.coli_1.fasta	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,80 @@
+>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG
+GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
+AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG
+TAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG
+ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAA
+AACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT
+GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTG
+ATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTG
+CGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACAT
+GGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCG
+CCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACG
+GCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCC
+GCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGG
+CGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCG
+GTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCAC
+TTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCA
+ACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGG
+AAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGT
+TGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAG
+TTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATA
+TGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCG
+ATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATT
+CCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTA
+TCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATC
+ATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCT
+GCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCA
+GGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTT
+TTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCAC
+AACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
+GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTA
+TTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTT
+GAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
+AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTC
+ATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTG
+TTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
+GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGA
+TTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAAC
+TTCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
+CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACG
+TGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCA
+GCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
+AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTA
+AAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTT
+TCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATT
+CTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCG
+ACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
+CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTG
+GCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCAC
+CTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
+TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
+GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAA
+ACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
+AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAGACCGCGTGCTTTCTTAGCGT
+AGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAGGAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGC
+TTCACCGATTTAAAATACTCATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
+GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGAT
+AAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
+TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
+CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTCGCTGATGCGCATCAGCGTGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/E.coli_2.fasta	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,80 @@
+>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG
+GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
+AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGG
+TAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCG
+ATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAA
+AACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCT
+GGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTG
+ATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTG
+CGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACAT
+GGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCG
+CCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACG
+GCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCC
+GCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGG
+CGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCG
+GTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCAC
+TTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCA
+ACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGG
+AAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGT
+TGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAG
+TTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATA
+TGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCG
+ATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATT
+CCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTA
+TCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATC
+ATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCT
+GCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCA
+GGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTT
+TTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCAC
+AACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
+GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTA
+TTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTT
+GAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
+AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTC
+ATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTG
+TTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
+GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGA
+TTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAAC
+TTCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
+CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACG
+TGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCA
+GCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
+AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTA
+AAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTT
+TCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATT
+CTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCG
+ACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
+CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTG
+GCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCAC
+CTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
+TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
+GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAA
+ACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
+AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAGACCGCGTGCTTTCTTAGCGT
+AGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAGGAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGC
+TTCACCGATTTAAAATACTCATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
+GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGAT
+AAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
+TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
+CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTCGCTGATGCGCATCAGCGTGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S.flexneri_1.fasta	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,80 @@
+>NC_004337.2 Shigella flexneri 2a str. 301 chromosome, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG
+GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
+AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGT
+AACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA
+TATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGG
+CGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTG
+ACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAA
+ACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAA
+TGTCGATCGCCATTATGGCCGGCGTGTTAGAAGCGCGTGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTG
+GCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGA
+TCACATGGTGTTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGTAACGGTTCCGACT
+ACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGC
+GACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGC
+TAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTC
+AAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATG
+GCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGC
+CCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGC
+GAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGG
+CTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCG
+CGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCGA
+CCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGGC
+GTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGG
+CGTTGCCAACTCGAAGGCTCTGCTCACTAGTGTGCATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTTGCACAAGCCA
+AAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACC
+TCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAA
+CACCTCGTCGATGGATTACTATCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACG
+TTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGGTGAAGTTCTCCGGCATT
+CTTTCAGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGA
+AATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGTG
+AAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGTT
+GCCGCTTTTATGGCGAATCTGTCACAGCTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGT
+TTTGCGCTATGTTGGCAATATTGATGAAGATGGTGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGGAATGATCCGCTGT
+TCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTTTATAGCCACTATTATCAGCCGCTGCCGTTGGTGCTGCGCGGATAT
+GGTGCGGGCAATGACGTTACCGCTGCCGGTGTCTTTGCCGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACA
+TGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGGCACCCGTT
+GATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGA
+TAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTC
+CAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTG
+ATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGTAT
+CTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCA
+TCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGAATTAAAGTCTCGACGGCAGAAGCC
+CGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCTGGCTTCATTCACGCCTG
+CTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCTG
+GCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTC
+GCTCTATGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTT
+TGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACA
+ACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCG
+GAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAATGCGAAGATCCTCTCGGCGTTTAT
+TGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTG
+AAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAA
+ATGCTGACCCATATTGCGGATGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCTGCAGTGGCTCA
+TGCTTTCTACGGTTTGCCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGT
+TCTGTACGTTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCG
+TTTGATGATGAAGAACTGAAAGTGGCGCTGGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGAT
+TTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGGCGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACT
+TCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCATTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAAC
+GATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGT
+GAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAG
+CCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTA
+GCGTATCGTGCGCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAA
+AGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTT
+CACATAATCTGCCCGCCGATTTTTCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATC
+AGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAACGACAGGGAAAAAGGAGAAATTA
+TCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGA
+CCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTC
+GCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGG
+CTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACC
+CACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACAT
+CACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACG
+TTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATTGACTACAAA
+CTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATTA
+AAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAGACCGCGTGCTTTCTTAGCGTA
+GAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAGGAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCT
+TCACCGATTTAAAATACTCATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTG
+TTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATA
+AGGCTGCATTAAATCGAGCGGGCGCAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAAT
+CGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGCC
+GGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTCGCTGATGCGCATCAGCGTGCT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S.flexneri_2.fasta	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,80 @@
+>NC_004337.2 Shigella flexneri 2a str. 301 chromosome, complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTG
+GTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGAC
+AGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGT
+AACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA
+TATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGG
+CGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTG
+ACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAA
+ACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAA
+TGTCGATCGCCATTATGGCCGGCGTGTTAGAAGCGCGTGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTG
+GCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGA
+TCACATGGTGTTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGTAACGGTTCCGACT
+ACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGC
+GACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGC
+TAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTC
+AAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATG
+GCAATGTTCAGCGTTTCCGGCCCGGGGATGAAAGGGATGGTTGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGC
+CCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGC
+GAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGG
+CTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCG
+CGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCGA
+CCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGGC
+GTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGG
+CGTTGCCAACTCGAAGGCTCTGCTCACTAGTGTGCATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTTGCACAAGCCA
+AAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACC
+TCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAA
+CACCTCGTCGATGGATTACTATCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACG
+TTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGGTGAAGTTCTCCGGCATT
+CTTTCAGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGA
+AATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGTG
+AAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGTT
+GCCGCTTTTATGGCGAATCTGTCACAGCTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGT
+TTTGCGCTATGTTGGCAATATTGATGAAGATGGTGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGGAATGATCCGCTGT
+TCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTTTATAGCCACTATTATCAGCCGCTGCCGTTGGTGCTGCGCGGATAT
+GGTGCGGGCAATGACGTTACCGCTGCCGGTGTCTTTGCCGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACA
+TGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGGCACCCGTT
+GATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGA
+TAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTC
+CAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTG
+ATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGTAT
+CTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCA
+TCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGAATTAAAGTCTCGACGGCAGAAGCC
+CGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCTGGCTTCATTCACGCCTG
+CTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCTG
+GCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTC
+GCTCTATGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTT
+TGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACA
+ACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCG
+GAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAATGCGAAGATCCTCTCGGCGTTTAT
+TGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTG
+AAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAA
+ATGCTGACCCATATTGCGGATGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCTGCAGTGGCTCA
+TGCTTTCTACGGTTTGCCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGT
+TCTGTACGTTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCG
+TTTGATGATGAAGAACTGAAAGTGGCGCTGGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGAT
+TTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGGCGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACT
+TCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCATTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAAC
+GATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGT
+GAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAG
+CCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTA
+GCGTATCGTGCGCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAA
+AGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTT
+CACATAATCTGCCCGCCGATTTTTCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATC
+AGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAACGACAGGGAAAAAGGAGAAATTA
+TCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGA
+CCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTC
+GCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGG
+CTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACC
+CACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACAT
+CACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACG
+TTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATTGACTACAAA
+CTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATTA
+AAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAGACCGCGTGCTTTCTTAGCGTA
+GAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAGGAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCT
+TCACCGATTTAAAATACTCATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTG
+TTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATA
+AGGCTGCATTAAATCGAGCGGGCGCAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAAT
+CGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGCC
+GGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTCGCTGATGCGCATCAGCGTGCT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multi.out	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,4 @@
+E.coli_1.fasta	S.flexneri_1.fasta	98.7134	2	2
+E.coli_1.fasta	S.flexneri_2.fasta	98.7134	2	2
+E.coli_2.fasta	S.flexneri_1.fasta	98.7134	2	2
+E.coli_2.fasta	S.flexneri_2.fasta	98.7134	2	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/single.out	Tue Feb 18 15:58:57 2020 -0500
@@ -0,0 +1,1 @@
+E.coli_1.fasta	S.flexneri_1.fasta	98.7134	2	2