# HG changeset patch
# User iuc
# Date 1582059537 18000
# Node ID 2c7ac12ad75aec94f613bd6544c107e5730dc893
"planemo upload commit 01a4c6cb401a89acddd991825fcaa304052d275f"
diff -r 000000000000 -r 2c7ac12ad75a fastani.xml
--- /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 @@
+
+ fast alignment-free computation of whole-genome Average Nucleotide Identity
+
+ macros.xml
+
+
+ fastANI --version
+
+ > 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}"
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `_. However, it avoids expensive sequence alignments and
+uses `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 `_ 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" `_.
+
+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.
+ ]]>
+
+
diff -r 000000000000 -r 2c7ac12ad75a macros.xml
--- /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 @@
+
+ 1.3
+
+
+ fastani
+
+
+
+
+
+ 10.1038/s41467-018-07641-9
+
+
+
diff -r 000000000000 -r 2c7ac12ad75a test-data/E.coli_1.fasta
--- /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
diff -r 000000000000 -r 2c7ac12ad75a test-data/E.coli_2.fasta
--- /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
diff -r 000000000000 -r 2c7ac12ad75a test-data/S.flexneri_1.fasta
--- /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
diff -r 000000000000 -r 2c7ac12ad75a test-data/S.flexneri_2.fasta
--- /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
diff -r 000000000000 -r 2c7ac12ad75a test-data/multi.out
--- /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
diff -r 000000000000 -r 2c7ac12ad75a test-data/single.out
--- /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