Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference

changeset 0:c917ef6807d7 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:47:36 -0500
parents
children
files match_plasmid_to_reference.py match_plasmid_to_reference.xml test-data/CP008719.fa test-data/CP008719.gbk test-data/JQ739157.fa test-data/JQ739157.gbk test-data/SRR9113487_plasmid_2719.fasta test-data/concatenated_mob_typer_reports.tsv test-data/outdir/mob_typer_record.tsv test-data/outdir/plasmid.fasta test-data/outdir/reference_plasmid.fasta test-data/outdir/reference_plasmid.gbk
diffstat 12 files changed, 1012 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match_plasmid_to_reference.py	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,156 @@
+#!/usr/bin/env python
+
+from __future__ import division, print_function
+
+import argparse
+import csv
+import errno
+import os
+import re
+import shutil
+
+
+MOB_TYPER_FIELDNAMES = [
+        "file_id",
+        "num_contigs",
+        "total_length",
+        "gc",
+        "rep_type(s)",
+        "rep_type_accession(s)",
+        "relaxase_type(s)",
+        "relaxase_type_accession(s)",
+        "mpf_type",
+        "mpf_type_accession(s)",
+        "orit_type(s)",
+        "orit_accession(s)",
+        "PredictedMobility",
+        "mash_nearest_neighbor",
+        "mash_neighbor_distance",
+        "mash_neighbor_cluster",
+        "NCBI-HR-rank",
+        "NCBI-HR-Name",
+        "LitRepHRPlasmClass",
+        "LitPredDBHRRank",
+        "LitPredDBHRRankSciName",
+        "LitRepHRRankInPubs",
+        "LitRepHRNameInPubs",
+        "LitMeanTransferRate",
+        "LitClosestRefAcc",
+        "LitClosestRefDonorStrain",
+        "LitClosestRefRecipientStrain",
+        "LitClosestRefTransferRate",
+        "LitClosestConjugTemp",
+        "LitPMIDs",
+        "LitPMIDsNumber",
+]
+
+
+def parse_mob_typer_report(mob_typer_report_path):
+    mob_typer_report = []
+
+    with open(mob_typer_report_path) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"', fieldnames=MOB_TYPER_FIELDNAMES)
+        for row in reader:
+            mob_typer_report.append(row)
+    return mob_typer_report
+
+
+def parse_genbank_accession(genbank_path):
+    with open(genbank_path, 'r') as f:
+        while True:
+            line = f.readline()
+            if line.startswith('ACCESSION'):
+                return line.strip().split()[1]
+
+
+def parse_fasta_accession(fasta_path):
+    with open(fasta_path, 'r') as f:
+        while True:
+            line = f.readline()
+            if line.startswith('>'):
+                return line.strip().split()[0][1:]
+
+
+def count_fasta_contigs(fasta_path):
+    contigs = 0
+    with open(fasta_path, 'r') as f:
+        for line in f:
+            if line.startswith('>'):
+                contigs += 1
+    return contigs
+
+
+def count_fasta_bases(fasta_path):
+    bases = 0
+    with open(fasta_path, 'r') as f:
+        for line in f:
+            line = line.strip()
+            if not line.startswith('>'):
+                bases += len(line)
+    return bases
+
+
+def compute_fasta_gc_percent(fasta_path):
+    gc_count = 0
+    total_bases_count = 0
+    with open(fasta_path, 'r') as f:
+        for line in f:
+            if not line.startswith('>'):
+                line = line.strip()
+                line_c_count = line.count('c') + line.count('C')
+                line_g_count = line.count('g') + line.count('G')
+                line_total_bases_count = len(line)
+                gc_count += line_c_count + line_g_count
+                total_bases_count += line_total_bases_count
+    return 100 * (gc_count / total_bases_count)
+
+
+def main(args):
+
+    # create output directory
+    try:
+        os.mkdir(args.outdir)
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir(args.outdir):
+            pass
+        else:
+            raise
+
+    # parse mob_typer report
+    mob_typer_report = parse_mob_typer_report(args.mob_typer_report)
+    num_plasmid_contigs = count_fasta_contigs(args.plasmid)
+    num_plasmid_bases = count_fasta_bases(args.plasmid)
+    plasmid_gc_percent = compute_fasta_gc_percent(args.plasmid)
+
+    with open(os.path.join(args.outdir, 'mob_typer_record.tsv'), 'w') as f:
+        mob_typer_record_writer = csv.DictWriter(f, delimiter="\t", quotechar='"', fieldnames=MOB_TYPER_FIELDNAMES)
+        mob_typer_record_writer.writeheader()
+        for record in mob_typer_report:
+            # match the plasmid against three properties in the MOB-Typer report:
+            # 1. number of contigs
+            # 2. total length of all contigs
+            # 3. G/C percent (within +/-0.1%)
+            if num_plasmid_contigs == int(record['num_contigs']) and \
+               num_plasmid_bases == int(record['total_length']) and \
+               abs(plasmid_gc_percent - float(record['gc'])) < 0.1:
+                for reference_plasmid in args.reference_plasmids_genbank:
+                    if parse_genbank_accession(reference_plasmid) == record['mash_nearest_neighbor']:
+                        shutil.copy2(reference_plasmid, os.path.join(args.outdir, "reference_plasmid.gbk"))
+
+                for reference_plasmid in args.reference_plasmids_fasta:
+                    if re.match(record['mash_nearest_neighbor'], parse_fasta_accession(reference_plasmid)) is not None:
+                        shutil.copy2(reference_plasmid, os.path.join(args.outdir, "reference_plasmid.fasta"))
+                mob_typer_record_writer.writerow(record)
+
+    shutil.copy2(args.plasmid, os.path.join(args.outdir, "plasmid.fasta"))
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--plasmid", help="plasmid assembly (fasta)")
+    parser.add_argument("--reference_plasmids_genbank", nargs='+', help="reference plasmids (genbank)")
+    parser.add_argument("--reference_plasmids_fasta", nargs='+', help="reference plasmids (fasta)")
+    parser.add_argument("--mob_typer_report", help="mob_typer reports (tsv)")
+    parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
+    args = parser.parse_args()
+    main(args)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/match_plasmid_to_reference.xml	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,57 @@
+<tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
+    <description>Pick plasmids containing specific genes</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        '$__tool_directory__/match_plasmid_to_reference.py'
+        --plasmid '${plasmid}'
+        --reference_plasmids_genbank
+        #for $reference_plasmid in $reference_plasmids_genbank:
+          '${reference_plasmid}'
+        #end for
+        --reference_plasmids_fasta
+        #for $reference_plasmid in $reference_plasmids_fasta:
+          '${reference_plasmid}'
+        #end for
+        --mob_typer_report '${concatenated_mob_typer_reports}'
+        --outdir outdir
+    ]]></command>
+    <inputs>
+        <param name="plasmid" type="data" format="fasta" />
+        <param name="reference_plasmids_genbank" type="data_collection" collection_type="list" format="genbank" />
+	<param name="reference_plasmids_fasta" type="data_collection" collection_type="list" format="fasta" />
+        <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
+    </inputs>
+    <outputs>
+        <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" label="Plasmid" format="fasta"/>
+        <data name="matched_reference_plasmid_genbank" from_work_dir="outdir/reference_plasmid.gbk" label="Reference Plasmid (genbank)" format="genbank"/>
+	<data name="matched_reference_plasmid_fasta" from_work_dir="outdir/reference_plasmid.fasta" label="Reference Plasmid (fasta)" format="fasta"/>
+	<data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" label="Matched MOB-Typer Record" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
+            <param name="reference_plasmids_genbank">
+                <collection type="list">
+                    <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
+                    <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
+                </collection>
+            </param>
+            <param name="reference_plasmids_fasta">
+                <collection type="list">
+                    <element name="CP008719" value="CP008719.fa" ftype="fasta" />
+                    <element name="JQ739157" value="JQ739157.fa" ftype="fasta" />
+                </collection>
+            </param>
+            <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
+            <output name="output_plasmid" file="outdir/plasmid.fasta" />
+            <output name="matched_reference_plasmid_genbank" file="outdir/reference_plasmid.gbk" />
+            <output name="matched_reference_plasmid_fasta" file="outdir/reference_plasmid.fasta" />
+            <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CP008719.fa	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,33 @@
+>CP008719.1 Escherichia coli strain ST648 plasmid pEC648_5, complete sequence
+TAGATTTAAACGGTATCAAGTTTGGATTTTTAAGAACGCATTCTTAGTTCTGGAAAAGAGCCAGCGGCAG
+GCTGAGGTGATAGGTACGAGATTGCATGCAATCTCTAGTGCTCTGTCTATCCTGCATTATCCTCAGCATT
+ATCCTCAGCATTATCCTCAGCCTTGCCAACTCGACACCAATGCAGGATAGACAATCCGATGTCAAATGTT
+AACACTCTGCGAGTGGTACATTTTCCCCGGATTATCGTCCTGAGCCTGCCGCTGGCTCTCTTTCTACCGC
+CTCGCTTTGCTCGTTGCTCAACGCCTCACAGACACGGATTAAAATCCGCATCCGTTCACCGTTTTTTAAA
+GTCCGTTAAAAGCATGATGCCATCTCCGAGAGTTAATCTCGTCAAATGCTAAATCGTGGGGGTCCCCTTT
+GGGGTTCCGATTTAGTGATTGACGACACCACCGATTAAAAAACTTATGCGGGGTGGATGGTTTCACGAAG
+TGAGGCCATCCACCTGTAAGACAGGGTTTTGTTTTTATTCCCTGTTTTGGTGATCGGGTGTGTGGAAAAG
+GTTGGGGTAAGCCGTTCGGGGGTGCTTGTTTTGGGGGGTTAAAATTGTGGTTATTTTTTGCGCAATTCTC
+GCGCGTGATCCTTGTATTTATACTTAAGGGATAAATGGCGGATATGAAATAGTGGTTTAGCCCAGTAATG
+ACGAGGCTTTGAGTGGGTTTTGACAGGTCAAAGAAAATGGAGCAGAATTGAGGCGTTTTTAATCGGCGTT
+GGGGAGTGCGTCAACACTCCCCAACATTTCGAATGTGTCACCTCAGCGGCAAACTCTGGTGACATGTACT
+GGCTCGCAATGCACAGGTACGTGATGAATATACCACATCAAATCACAGCCTGCCCAGATCGGAGCAGGCT
+TAATGTCAGAAGATAAATTCCTTTCGGACTACAGCCCCCGTGATGCAGTTTGGGATACCCAGCGCACGCT
+TACCGATTCTGTCGGGGGTATCTACCAGACTGCTGCTGAATTCGAGCGCTATGCACTCCGTATGGCCTCC
+TGTAGCGGTTTGTTACGTTTTGGTTGGTCTACCATCATGGAAACCGGAGAAACGCGCCTACGGCTTCGTA
+GTGCGCAATTTTGCCGTGTCCGTCATTGCCCTGTCTGCCAGTGGAGAAGAACCCTCATGTGGCAAGCCCG
+TTTTTATCAGGCTCTACCGAAAATCGTTGTGGATTACCCGTCTTCCCGATGGTTGTTTCTGACGTTAACT
+GTCAGGAACTGCGAGATAGGTGAACTTGGAACAGTCCTTACAGCAATGAATGCGGCGTTTAAGCGAATGG
+AAAAGCGAAAGGAGCTATCACCTGTTCAGGGGTGGATCAGGGCTACGGAGGTGACGCGAGGTAAGGATGG
+CAGCGCACATCCGCATTTTCACTGTCTGCTGATGGTGCAACCTTCTTGGTTTAAAGGGAAGAACTACGTT
+AAGCACGAACGTTGGGTAGAACTCTGGCGCGATTGCTTGCGGGTGAACTATGAGCCGAATATCGATATTC
+GGGCAGTAAAAACTAAGACAGGTGAGGTTGTGGCCAACGTTGCCGAGCAACTGCAAAGCGCGGTTGCTGA
+AACGCTGAAATACTCCGTTAAACCGGAAGATATGGCAAACGATCCTGAGTGGTTTCTTGAGCTGACGCGG
+CAGCTTCACAAGCGCCGTTTTATCTCGACCGGTGGGGCGCTAAAAAACGTCCTCCAGTTGGATCGAGAAA
+CCAATGAGGATCTTGTCATTGCCGACGATGTAGGGGATGGCACTGATGACGGGAAGCGGACGGCGTTTGT
+CTGGGATTCAGGTAAACGGCGTTACAAACGCGCCCCTGAGAAGGATAAATCGGATTAACGTATGAATATT
+AATATTGAATACCTGAATGGAAATAAGACTATTGGTTTATTTTTTTTAAGAAGTGAAGCGGTGATTCCTG
+ACAGGTTTAAAAACCTTATTTTGCTTATTGATGGATTAAGTTTTGGCACATTTGGTTTTCATCCGCACGA
+AGGTTTTGAGGATGAATTAATTTTATATATTCAGAAAACAAACGAGAGGGTAAAAACTCTTTTTGTGAAA
+A
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CP008719.gbk	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,130 @@
+LOCUS       CP008719                2101 bp    DNA     circular BCT 05-JAN-2016
+DEFINITION  Escherichia coli strain ST648 plasmid pEC648_5, complete sequence.
+ACCESSION   CP008719
+VERSION     CP008719.1
+DBLINK      BioProject: PRJNA248607
+            BioSample: SAMN02800875
+KEYWORDS    .
+SOURCE      Escherichia coli
+  ORGANISM  Escherichia coli
+            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
+            Enterobacteriaceae; Escherichia.
+REFERENCE   1  (bases 1 to 2101)
+  AUTHORS   Gao,Z.
+  TITLE     Complete Genome Sequence of Multiple Antibiotic Resistant
+            Escherichia coli Isolated from Pleural Effusion of Patients with
+            Empyema Thoracis
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 2101)
+  AUTHORS   Gao,Z.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (09-JUN-2014) Department of Respiratory and Critical care
+            medicine, Peking University People's hospital, Xizhimen South
+            Street, Beijing, Beijing 100101, China
+COMMENT     Annotation was added by the NCBI Prokaryotic Genome Annotation
+            Pipeline (released 2013). Information about the Pipeline can be
+            found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
+            
+            ##Genome-Assembly-Data-START##
+            Assembly Method       :: Newbler v. 2.3; Consed
+            Genome Coverage       :: 40x; 350x
+            Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000
+            ##Genome-Assembly-Data-END##
+            
+            ##Genome-Annotation-Data-START##
+            Annotation Provider          :: NCBI
+            Annotation Date              :: 06/13/2014 09:01:46
+            Annotation Pipeline          :: NCBI Prokaryotic Genome Annotation
+                                            Pipeline
+            Annotation Method            :: Best-placed reference protein set;
+                                            GeneMarkS+
+            Annotation Software revision :: 2.6 (rev. 437579)
+            Features Annotated           :: Gene; CDS; rRNA; tRNA; ncRNA;
+                                            repeat_region
+            Genes                        :: 4,807
+            CDS                          :: 4,578
+            Pseudo Genes                 :: 132
+            CRISPR Arrays                :: 2
+            rRNAs                        :: 21 (5S, 16S, 23S)
+            tRNAs                        :: 72
+            ncRNA                        :: 4
+            Frameshifted Genes           :: 116
+            ##Genome-Annotation-Data-END##
+FEATURES             Location/Qualifiers
+     source          1..2101
+                     /organism="Escherichia coli"
+                     /mol_type="genomic DNA"
+                     /strain="ST648"
+                     /db_xref="taxon:562"
+                     /plasmid="pEC648_5"
+     gene            join(1882..2101,1..47)
+                     /locus_tag="FH07_00765"
+     CDS             join(1882..2101,1..47)
+                     /locus_tag="FH07_00765"
+                     /inference="EXISTENCE: similar to AA
+                     sequence:RefSeq:WP_001024536.1"
+                     /note="Derived by automated computational analysis using
+                     gene prediction method: Protein Homology."
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /protein_id="ALV71377.1"
+                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF
+                     GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
+     gene            913..1878
+                     /locus_tag="FH07_00775"
+     CDS             913..1878
+                     /locus_tag="FH07_00775"
+                     /inference="EXISTENCE: similar to AA
+                     sequence:RefSeq:WP_012421200.1"
+                     /note="Derived by automated computational analysis using
+                     gene prediction method: Protein Homology."
+                     /codon_start=1
+                     /transl_table=11
+                     /product="Replication protein"
+                     /protein_id="ALV71376.1"
+                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM
+                     ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV
+                     VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG
+                     KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE
+                     VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL
+                     DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
+ORIGIN      
+        1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag
+       61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat
+      121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa
+      181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg
+      241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca
+      301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa
+      361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt
+      421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg
+      481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg
+      541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt
+      601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg
+      661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt
+      721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg
+      781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact
+      841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc
+      901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt
+      961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa
+     1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct
+     1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc
+     1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag
+     1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact
+     1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt
+     1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag
+     1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa
+     1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc
+     1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca
+     1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa
+     1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg
+     1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg
+     1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac
+     1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag
+     1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact
+     1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt
+     1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag
+     2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa
+     2101 a
+//
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JQ739157.fa	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,96 @@
+>JQ739157.2 Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete sequence
+AAGCTTATAGCAGTGTCACAGATGCGAAAAAGCAATTAAGTGCATATTTTGAGTTTTATAATTTGAAACG
+ACCTCATTCGAGTCTAGACAAAATGACACCAAATGAGTTTTACTATGATCAGCTACCCCAACAAAACAAG
+GTGGCTTAACTAGAGCGGAATATCACTTATAAATACGCTTTTAGTTGTTCAAACAAGTGGGACCACCTCT
+CTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTTGATGGAATTGCCCAATATTATTCAACA
+ATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAAT
+CGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTC
+GCGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGA
+TGAGCAGTTTGAATTAATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGAC
+CAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAGTTGCTATTATTGATTGTCCAT
+TTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATAT
+AGATCAAGATGATTTTGACGCTGAATTATGGGGAGACCATAGAACTTACCTAAGTCTATGGAATGAGTTA
+ACTGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAG
+ATAAATTCAATGAAATTTACTTTTTAGATCTTGGCCGTGCTGGGTTAGCTGATGAATTTGTAGATATATC
+CTTTGTTGAACGTTGCCTAAGAGAGGATGCCTCGGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAA
+AATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGATTCTAAGCATTATCTA
+AAAATACTTAATTGTCTTTTAACGTCGCTAAATTTTAAATAAATAAGTGAAGAGTGTTAGTGGAGCCACT
+GATTTAAAGTTGGCAGAGTAAAACTTGAAGTGCGACATAAACCACCTAATTAATTTAAAGGGTTTATGGA
+GTATATAAAATTGTCATACCATCATCTTAACTTTGAAGATCGTACTGCATTAATGCTTGAGTCAAGAAAA
+GAAGGCTTTTCAGCCAGAAAATTTGCTGAACTCATTAAAAGACATCCTAGTACGATCTATCGTGAGCTTA
+AAAGAAATAGCATCAATGACGTTTATCAAGCTCGATATGCTTCTGATAACACCTTCGCTAGACGTAGACG
+TGGTCACAGAAAACTCAAAATCGATTCAATCCTCTGGAAATTTATTGTTGAAGCGATCCGTTGTTTATGG
+TCTCCTCAGCAAATAGCAAAGCGTTTAAAGACATTTCCTGATTTGGATCAAACAATGAATGTAAGCCATA
+CAACGATTTATTCAACGATACGAGCATTACCAAAGGGTGAGTTGAAAAAAGACTTATTATCCTGTCTACG
+TCATGAAAATAAAAAGCGAAAAGCTAACGGTGAACCTAAAAAAGATTCTATATTACAGGATATTAAAACT
+ATTCATGAGCGCCCAGCCGAAGTTCAAGAAAGAAAAATACCGGGTCATTGGGAAGCTGATTTAATTAAAG
+GTAAAGACAATAAAAGTTCGATAGCAACACTTATTGAACGAAATACACGGCTCTGTATCTTGGCAACATT
+ACCTGATGCAAAGGCAGAATCAGTGCGCAAGGCTTTAACTGAAGCTCTGAAATATTTACCTGCAGAACTG
+CGTAAAACGTTGACCTATGACCGTGGACGTGAGATGTCAGAACATAAAATACTCGAAGAAGATTTAGGCA
+TAGATGTATATTTCTGTGACCCACATTCACCCTGGCAAAAAGGCACATGCGAAAATATGAATGGTTTAAT
+TAGGCAATATTTACCTAAAGGGATTGATTTAAATCAGGCAGATCAGCATTATTTAAATCAAGTTGCCATG
+TCACTGAATACTCGTCCTAGAAAGGCGTTAGATTGGCTTACACCATTAGAGAAATTTGCTCAGCTTGTTG
+ATTATCATATGGCTTTTGAAACTGTCGCACCTCATGTTTGAATTCGCCCCATATTTTTGCTACAGTGAAC
+CAAATTAAGATCATCTATTTACTAGGCCTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTT
+GATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTG
+AGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTG
+GCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTT
+CGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGG
+ACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGG
+TGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTA
+TGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTC
+GCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCC
+CCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGAT
+CAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCG
+CGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCG
+CCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAGCCATGGCTGACCACGTCACCCCCAA
+TCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAG
+GATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACC
+CAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGC
+GGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTG
+AGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGACCGCATG
+CCCGCGAAAATCAAGATTTGCGGGATCAGCACACCCGAGGCGCTCGATGCGACCATCGCGGCGCGGGCGG
+ACTATGCCGGGTTGGTGTTCTATCCAGCGTCGCCCCGTGCGGTTACGTCGAATGTCGCGGGCGCTTTGAC
+ATCGCGCGCAGCTGGCCAGATCGCCATGGTCGGTTTGTTCGTCGATGCGGATGATGCTGTCATCGCCGAC
+GCACTGGTGGCAGCCAAGCTGAACGCGCTGCAGCTGCACGGTTCGGAATCGCCCGAACGCGTGGCCCAGT
+TGCGCGCGCGGTTTGGCAAGCCGGTGTGGAAGGCGCTGCCCGTCGCCAGCGCCAGCGATGTCGCACGCGC
+CGCAGCCTATGCCGGGGCGGCGGACTTGATCTTGTTCGACGCCAAGACCCCCAAAGGCGCGCTGCCCGGC
+GGCATGGGGTTGGCGTTCGACTGGTCGCTGCTGGCCGGATATCGCGGTGCCTTGCCGTGGGGGCTGGCAG
+GCGGGCTAAATCCGACGAATGTTGCCGAGGCGATTGCGCGCACCGGAGCGCCGCTGGTCGATACCTCCAG
+CGGCGTCGAAAGCGCGCCGGGCGTCAAGGATACCGACAAGATTACCAATTTCGCCTTTGCGGTGCGCTTG
+GCCTAAATCGCGTCGATCAATAGGCGTCGTTCAGCGCAAAGATCGGCTTGCGGGTGCGCCACTGCCCTCG
+GGTGAAGTCGGGAAAATCTAACGTGCGATTGCCCTCAGCAATCGATTGTTCCGACAGAGGCGTGATCGCG
+CTCCAGGCCAGCGCGTCGTAAATGTCGATTGGCATCGGGGCCTTGGCCTTCAGCGCCTCGACAAAAGCGT
+GGATCACGAACCAGTCCATCCCGCCATGCCCGGCCCCTGCCGCCAGATCGGCGTAGCGTTTCCATAGCGG
+GTGATCGTATTTCGCAAACCAGCCCTCGGCAGGCTCCCAGCGGTGCGGCTGTGGGCTCTTGCCCTCCAGA
+TAGATCGACTTGTTGACGTCCATCCACAGCCCCTCGGTGCCTTGCACCCGAAAGCCGAGAGAATAGGGGC
+GCGGCAGCGAGGTGTCGTGGCACAGCATGATCGTTTCACCATTAGTGCAGCCGATCATGGTGTTGACCAC
+ATCACCCAGTGCGAATTTCACCTCGGCGTTGGGATGATCGGCAGAGCCGTTCTTGACGACATAATCATGC
+AGCCCGCGCGCCTTACAGCCGAAGCCGCCAGCGCCCGCTTCGCCCGGCAACGCGACCTTCAGGGTGCGGG
+TCTGCGGCGGGTAGCACACGCCGGCATCGGCGCAGCCCTGGTACTTCACGGTCAGGGTGGTCGCGCTCGC
+GCCGGCCGCGGGCGTGCCGGTGAGGGTGCCGAGCAATTCCTTGCGGTAGGTTTCGACGTCGCCGAAGAAT
+TCGTCGCGGTAGGCCTTGCCCTTCGGCAGCGCCATGGTCGCGCCGGTGAAGGCGGCATCGGCCTTGACCG
+AGGTGCGGTGCCGGTACAGGTAATAGCCGTCGGCGATCCGCCAGCGCACCTCGATGCGGTCCGGCGCGGT
+GGCCTGCGCGGACAGGACGAAGACCTCGTCGACCGGCGGCAGTTCGAAGTCCTGGGCGACGGCCGAGGTC
+GCGGGCAGCGCAAGCAGCAGGGCGAGCCCGGCCAGCCAGCGGCGCAGGCGGATCGTGGATGCGGTCATTG
+GCTCAGTTTACCGGTCGGCTCTCGGCGGCCAGCCATTGCAGGTATTCGGGCAGGCCGGACGCGGCTTCGA
+CCGCGAGCAGCTCCGGGAGTTCGTAGGGATATAGTATTTTATTAAATTCTTATGGGAAATGACGAATGTT
+AAATTATCTTAAGAGCTTTAATAATATCAATACTTATTTGATTTTATCGATAATTCTGCTGTTAATCATA
+ATATCTCTAGATTATTTCTAAACTGAATGAATGTTTATAATGAGTGATTCATATTGCTATTGAAATCGCC
+TTCTCACTTTGAAAGAAGGCGAGGATGAGGGACTTTTATGTTGAATTATCATTTTAAAAATGCCTTATAA
+AAGAAGCTTAATGTGTTTTCTTATATAGGTTTAAACATAATTGTTGTATATCTTAAATCCAATTGATCTT
+AAAATTTTCCTTTATTTTTTGTTATGAGTGCGAGAAAATTGTCAAAAAGGTCAATCAGACTGGGCGTTAA
+TTTGTTTTGCATACTTTTTCCTATATCGAATTAAAGTCATATAACTAACACCATAATCTTTAGCTATTTG
+AGTGAAAGGGTATGAATCGTCCTTATTTTTAAGGGTATGAATTAACTCTTTTAGTTTTTCTTCTGTAATC
+GCAGGCGATCTTCCCTTGTATTTACCTTTCTTTTTTTTAGCTAATTTAATTCCCTCTGCTTGATTCTCAC
+TAATAATACCCCTTTCAAGTTCAGCTACAGCGCCTAATACATGGAGTTGAAACTTATCGAACTTGTCATC
+TGAATTGGGGGTAAAGTTCAGGTTATTTTTGACAATATGAACAGACACTCCTTTTTTATTTAGCTTTTGA
+ACAATGGTTACAAGGTCAATCAAGCTACGTGCCAATCTAAAAACATCATGAGCGTACACAATGTCCCCAC
+TACGGACATAATCGAACATTTCCTGAAGTGCAGGGCGTTTGGCAGTCTTTCCGCTAAAATGATCAATAAA
+AGTTTTATCTAGCTCAAAGGGTAGATCATGGAGCTGTCTTTCAGGGTTTTGGTCTTTAGTGGATACACGG
+ATATACCCCACTCTTTGAAAGGGTGTGTTTTTAATTTGATCTTCAATATCTAAATTTTCTTTTTCCATAA
+CCAGTATAACAAAATTAGATAACCTCAATGTTATATCACATTAGATTAACAAAACAACCCTATTGTTATA
+GGGTTTTTAGGGTGTATTATTATATAACAATAGGGTATACCCTATTGTTATATATCTTCAGGTATAAGGA
+AAAATAACGATGATTAATTTTAATGATCTAAGCGAATCTGAATTATTAAGGATTGCACAGACTGGCATAT
+CAAACCGTATAGGATTGCGTACTTCAGGACATTG
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JQ739157.gbk	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,214 @@
+LOCUS       JQ739157                6544 bp    DNA     circular BCT 26-JUL-2016
+DEFINITION  Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete
+            sequence.
+ACCESSION   JQ739157
+VERSION     JQ739157.2
+KEYWORDS    .
+SOURCE      Acinetobacter pittii
+  ORGANISM  Acinetobacter pittii
+            Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
+            Moraxellaceae; Acinetobacter; Acinetobacter calcoaceticus/baumannii
+            complex.
+REFERENCE   1  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Epidemiological characteristics and genetic structure of blaNDM-1
+            in non-baumannii Acinetobacter spp. in China
+  JOURNAL   J. Antimicrob. Chemother. 67 (9), 2114-2122 (2012)
+   PUBMED   22604448
+REFERENCE   2  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (05-MAR-2012) Department of Infectious Diseases, Sir Run
+            Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
+            University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
+REFERENCE   3  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (12-MAY-2014) Department of Infectious Diseases, Sir Run
+            Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
+            University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
+  REMARK    Sequence update by submitter
+COMMENT     On May 12, 2014 this sequence version replaced JQ739157.1.
+FEATURES             Location/Qualifiers
+     source          1..6544
+                     /organism="Acinetobacter pittii"
+                     /mol_type="genomic DNA"
+                     /strain="ABCA95"
+                     /db_xref="taxon:48296"
+                     /plasmid="pABCA95"
+     gene            375..1031
+                     /gene="aphA6"
+     misc_feature    375..1031
+                     /gene="aphA6"
+                     /note="similar to aphA6; aminoglycoside
+                     3'-phosphotransferase; 5' end of gene is missing"
+     mobile_element  1129..2215
+                     /mobile_element_type="insertion sequence:ISAba125"
+     repeat_region   1138..1154
+                     /note="IRL"
+                     /rpt_type=inverted
+     CDS             1186..2211
+                     /codon_start=1
+                     /transl_table=11
+                     /product="Transposase"
+                     /protein_id="AFK73837.1"
+                     /translation="MEYIKLSYHHLNFEDRTALMLESRKEGFSARKFAELIKRHPSTI
+                     YRELKRNSINDVYQARYASDNTFARRRRGHRKLKIDSILWKFIVEAIRCLWSPQQIAK
+                     RLKTFPDLDQTMNVSHTTIYSTIRALPKGELKKDLLSCLRHENKKRKANGEPKKDSIL
+                     QDIKTIHERPAEVQERKIPGHWEADLIKGKDNKSSIATLIERNTRLCILATLPDAKAE
+                     SVRKALTEALKYLPAELRKTLTYDRGREMSEHKILEEDLGIDVYFCDPHSPWQKGTCE
+                     NMNGLIRQYLPKGIDLNQADQHYLNQVAMSLNTRPRKALDWLTPLEKFAQLVDYHMAF
+                     ETVAPHV"
+     repeat_region   2190..2206
+                     /note="IRL"
+                     /rpt_type=inverted
+     gene            2312..3124
+                     /gene="blaNDM-1"
+     CDS             2312..3124
+                     /gene="blaNDM-1"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="metallo-beta-lactamase"
+                     /protein_id="AFK73838.1"
+                     /translation="MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQ
+                     RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQIL
+                     NWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHS
+                     LTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSL
+                     GNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"
+     gene            3128..3493
+                     /gene="bleo"
+     CDS             3128..3493
+                     /gene="bleo"
+                     /note="involved in resistance to bleomycin"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="bleomycin resistance protein"
+                     /protein_id="AFK73839.1"
+                     /translation="MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQ
+                     LEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLR
+                     IGYLIDPDCTLVRLIQNPD"
+     gene            3498..4133
+                     /gene="trpF"
+     misc_feature    3498..4133
+                     /gene="trpF"
+                     /note="similar to TrpF; phosphoribosyl anthranilate
+                     isomerase; 3' end not present"
+     gene            complement(4150..4830)
+                     /gene="tat"
+     misc_feature    complement(4150..4830)
+                     /gene="tat"
+                     /note="similar to TAT; twin-arginine translocation pathway
+                     signal sequence protein; 5' end of gene is missing."
+ORIGIN      
+        1 aagcttatag cagtgtcaca gatgcgaaaa agcaattaag tgcatatttt gagttttata
+       61 atttgaaacg acctcattcg agtctagaca aaatgacacc aaatgagttt tactatgatc
+      121 agctacccca acaaaacaag gtggcttaac tagagcggaa tatcacttat aaatacgctt
+      181 ttagttgttc aaacaagtgg gaccacctct ctcgcatttg cggggttttt aatgctgaat
+      241 aaaaggaaaa cttgatggaa ttgcccaata ttattcaaca atttattgga aacagcgttt
+      301 tagagccaaa taaaattggt cagtcgccat cggatgttta ttcttttaat cgaaataatg
+      361 aaactttttt tcttaagcga tctagcactt tatatacaga gaccacatac agtgtctctc
+      421 gcgaagcgaa aatgttgagt tggctctctg agaaattaaa ggtgcctgaa ctcatcatga
+      481 cttttcagga tgagcagttt gaattaatga tcactaaagc gatcaatgca aaaccaattt
+      541 cagcgctttt tttaacagac caagaattgc ttgctatcta taaggaggca ctcaatctgt
+      601 taaattcagt tgctattatt gattgtccat ttatttcaaa cattgatcat cggttaaaag
+      661 agtcaaaatt ttttattgat aaccaactcc ttgacgatat agatcaagat gattttgacg
+      721 ctgaattatg gggagaccat agaacttacc taagtctatg gaatgagtta actgagactc
+      781 gtgttgaaga aagattggtt ttttctcatg gcgatatcac ggatagtaat atttttatag
+      841 ataaattcaa tgaaatttac tttttagatc ttggccgtgc tgggttagct gatgaatttg
+      901 tagatatatc ctttgttgaa cgttgcctaa gagaggatgc ctcggaggaa actgctaaaa
+      961 tatttttaaa gcatttaaaa aatgatagac ctgacaaaag gaattatttt ttaaaacttg
+     1021 atgaattgaa ttgattctaa gcattatcta aaaatactta attgtctttt aacgtcgcta
+     1081 aattttaaat aaataagtga agagtgttag tggagccact gatttaaagt tggcagagta
+     1141 aaacttgaag tgcgacataa accacctaat taatttaaag ggtttatgga gtatataaaa
+     1201 ttgtcatacc atcatcttaa ctttgaagat cgtactgcat taatgcttga gtcaagaaaa
+     1261 gaaggctttt cagccagaaa atttgctgaa ctcattaaaa gacatcctag tacgatctat
+     1321 cgtgagctta aaagaaatag catcaatgac gtttatcaag ctcgatatgc ttctgataac
+     1381 accttcgcta gacgtagacg tggtcacaga aaactcaaaa tcgattcaat cctctggaaa
+     1441 tttattgttg aagcgatccg ttgtttatgg tctcctcagc aaatagcaaa gcgtttaaag
+     1501 acatttcctg atttggatca aacaatgaat gtaagccata caacgattta ttcaacgata
+     1561 cgagcattac caaagggtga gttgaaaaaa gacttattat cctgtctacg tcatgaaaat
+     1621 aaaaagcgaa aagctaacgg tgaacctaaa aaagattcta tattacagga tattaaaact
+     1681 attcatgagc gcccagccga agttcaagaa agaaaaatac cgggtcattg ggaagctgat
+     1741 ttaattaaag gtaaagacaa taaaagttcg atagcaacac ttattgaacg aaatacacgg
+     1801 ctctgtatct tggcaacatt acctgatgca aaggcagaat cagtgcgcaa ggctttaact
+     1861 gaagctctga aatatttacc tgcagaactg cgtaaaacgt tgacctatga ccgtggacgt
+     1921 gagatgtcag aacataaaat actcgaagaa gatttaggca tagatgtata tttctgtgac
+     1981 ccacattcac cctggcaaaa aggcacatgc gaaaatatga atggtttaat taggcaatat
+     2041 ttacctaaag ggattgattt aaatcaggca gatcagcatt atttaaatca agttgccatg
+     2101 tcactgaata ctcgtcctag aaaggcgtta gattggctta caccattaga gaaatttgct
+     2161 cagcttgttg attatcatat ggcttttgaa actgtcgcac ctcatgtttg aattcgcccc
+     2221 atatttttgc tacagtgaac caaattaaga tcatctattt actaggcctc gcatttgcgg
+     2281 ggtttttaat gctgaataaa aggaaaactt gatggaattg cccaatatta tgcacccggt
+     2341 cgcgaagctg agcaccgcat tagccgctgc attgatgctg agcgggtgca tgcccggtga
+     2401 aatccgcccg acgattggcc agcaaatgga aactggcgac caacggtttg gcgatctggt
+     2461 tttccgccag ctcgcaccga atgtctggca gcacacttcc tatctcgaca tgccgggttt
+     2521 cggggcagtc gcttccaacg gtttgatcgt cagggatggc ggccgcgtgc tggtggtcga
+     2581 taccgcctgg accgatgacc agaccgccca gatcctcaac tggatcaagc aggagatcaa
+     2641 cctgccggtc gcgctggcgg tggtgactca cgcgcatcag gacaagatgg gcggtatgga
+     2701 cgcgctgcat gcggcgggga ttgcgactta tgccaatgcg ttgtcgaacc agcttgcccc
+     2761 gcaagagggg atggttgcgg cgcaacacag cctgactttc gccgccaatg gctgggtcga
+     2821 accagcaacc gcgcccaact ttggcccgct caaggtattt taccccggcc ccggccacac
+     2881 cagtgacaat atcaccgttg ggatcgacgg caccgacatc gcttttggtg gctgcctgat
+     2941 caaggacagc aaggccaagt cgctcggcaa tctcggtgat gccgacactg agcactacgc
+     3001 cgcgtcagcg cgcgcgtttg gtgcggcgtt ccccaaggcc agcatgatcg tgatgagcca
+     3061 ttccgccccc gatagccgcg ccgcaatcac tcatacggcc cgcatggccg acaagctgcg
+     3121 ctgagccatg gctgaccacg tcacccccaa tctgccatcg cgcgatttcg atgtgacaga
+     3181 ggcgttttat gcgaagctgg gctttgcgac gagttggaag gatcgcggct ggatgatcct
+     3241 gcagcgcggc ggtttgcagc tcgaattctt cccctatcct gacctcgacc cagctacgag
+     3301 ctcgttcggc tgttgcctgc ggttggatga tctcgatgcc atggtggcat tggtgaacgc
+     3361 ggcgggagcc gaggaaaaaa gcaccggctg gccgcgcttc aaagctccgc aactggaggc
+     3421 gagcggcctg aggatcggct acctgatcga tcccgactgc acgctggtgc ggctgatcca
+     3481 gaaccccgac tgaccgcatg cccgcgaaaa tcaagatttg cgggatcagc acacccgagg
+     3541 cgctcgatgc gaccatcgcg gcgcgggcgg actatgccgg gttggtgttc tatccagcgt
+     3601 cgccccgtgc ggttacgtcg aatgtcgcgg gcgctttgac atcgcgcgca gctggccaga
+     3661 tcgccatggt cggtttgttc gtcgatgcgg atgatgctgt catcgccgac gcactggtgg
+     3721 cagccaagct gaacgcgctg cagctgcacg gttcggaatc gcccgaacgc gtggcccagt
+     3781 tgcgcgcgcg gtttggcaag ccggtgtgga aggcgctgcc cgtcgccagc gccagcgatg
+     3841 tcgcacgcgc cgcagcctat gccggggcgg cggacttgat cttgttcgac gccaagaccc
+     3901 ccaaaggcgc gctgcccggc ggcatggggt tggcgttcga ctggtcgctg ctggccggat
+     3961 atcgcggtgc cttgccgtgg gggctggcag gcgggctaaa tccgacgaat gttgccgagg
+     4021 cgattgcgcg caccggagcg ccgctggtcg atacctccag cggcgtcgaa agcgcgccgg
+     4081 gcgtcaagga taccgacaag attaccaatt tcgcctttgc ggtgcgcttg gcctaaatcg
+     4141 cgtcgatcaa taggcgtcgt tcagcgcaaa gatcggcttg cgggtgcgcc actgccctcg
+     4201 ggtgaagtcg ggaaaatcta acgtgcgatt gccctcagca atcgattgtt ccgacagagg
+     4261 cgtgatcgcg ctccaggcca gcgcgtcgta aatgtcgatt ggcatcgggg ccttggcctt
+     4321 cagcgcctcg acaaaagcgt ggatcacgaa ccagtccatc ccgccatgcc cggcccctgc
+     4381 cgccagatcg gcgtagcgtt tccatagcgg gtgatcgtat ttcgcaaacc agccctcggc
+     4441 aggctcccag cggtgcggct gtgggctctt gccctccaga tagatcgact tgttgacgtc
+     4501 catccacagc ccctcggtgc cttgcacccg aaagccgaga gaataggggc gcggcagcga
+     4561 ggtgtcgtgg cacagcatga tcgtttcacc attagtgcag ccgatcatgg tgttgaccac
+     4621 atcacccagt gcgaatttca cctcggcgtt gggatgatcg gcagagccgt tcttgacgac
+     4681 ataatcatgc agcccgcgcg ccttacagcc gaagccgcca gcgcccgctt cgcccggcaa
+     4741 cgcgaccttc agggtgcggg tctgcggcgg gtagcacacg ccggcatcgg cgcagccctg
+     4801 gtacttcacg gtcagggtgg tcgcgctcgc gccggccgcg ggcgtgccgg tgagggtgcc
+     4861 gagcaattcc ttgcggtagg tttcgacgtc gccgaagaat tcgtcgcggt aggccttgcc
+     4921 cttcggcagc gccatggtcg cgccggtgaa ggcggcatcg gccttgaccg aggtgcggtg
+     4981 ccggtacagg taatagccgt cggcgatccg ccagcgcacc tcgatgcggt ccggcgcggt
+     5041 ggcctgcgcg gacaggacga agacctcgtc gaccggcggc agttcgaagt cctgggcgac
+     5101 ggccgaggtc gcgggcagcg caagcagcag ggcgagcccg gccagccagc ggcgcaggcg
+     5161 gatcgtggat gcggtcattg gctcagttta ccggtcggct ctcggcggcc agccattgca
+     5221 ggtattcggg caggccggac gcggcttcga ccgcgagcag ctccgggagt tcgtagggat
+     5281 atagtatttt attaaattct tatgggaaat gacgaatgtt aaattatctt aagagcttta
+     5341 ataatatcaa tacttatttg attttatcga taattctgct gttaatcata atatctctag
+     5401 attatttcta aactgaatga atgtttataa tgagtgattc atattgctat tgaaatcgcc
+     5461 ttctcacttt gaaagaaggc gaggatgagg gacttttatg ttgaattatc attttaaaaa
+     5521 tgccttataa aagaagctta atgtgttttc ttatataggt ttaaacataa ttgttgtata
+     5581 tcttaaatcc aattgatctt aaaattttcc tttatttttt gttatgagtg cgagaaaatt
+     5641 gtcaaaaagg tcaatcagac tgggcgttaa tttgttttgc atactttttc ctatatcgaa
+     5701 ttaaagtcat ataactaaca ccataatctt tagctatttg agtgaaaggg tatgaatcgt
+     5761 ccttattttt aagggtatga attaactctt ttagtttttc ttctgtaatc gcaggcgatc
+     5821 ttcccttgta tttacctttc ttttttttag ctaatttaat tccctctgct tgattctcac
+     5881 taataatacc cctttcaagt tcagctacag cgcctaatac atggagttga aacttatcga
+     5941 acttgtcatc tgaattgggg gtaaagttca ggttattttt gacaatatga acagacactc
+     6001 cttttttatt tagcttttga acaatggtta caaggtcaat caagctacgt gccaatctaa
+     6061 aaacatcatg agcgtacaca atgtccccac tacggacata atcgaacatt tcctgaagtg
+     6121 cagggcgttt ggcagtcttt ccgctaaaat gatcaataaa agttttatct agctcaaagg
+     6181 gtagatcatg gagctgtctt tcagggtttt ggtctttagt ggatacacgg atatacccca
+     6241 ctctttgaaa gggtgtgttt ttaatttgat cttcaatatc taaattttct ttttccataa
+     6301 ccagtataac aaaattagat aacctcaatg ttatatcaca ttagattaac aaaacaaccc
+     6361 tattgttata gggtttttag ggtgtattat tatataacaa tagggtatac cctattgtta
+     6421 tatatcttca ggtataagga aaaataacga tgattaattt taatgatcta agcgaatctg
+     6481 aattattaag gattgcacag actggcatat caaaccgtat aggattgcgt acttcaggac
+     6541 attg
+//
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR9113487_plasmid_2719.fasta	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,4 @@
+>53_length=9674_depth=5.42x
+GTTTACTCATACCTAGATTCTACGTCAGTACTTCAAAAAGCATAATCAAAGCCTTGATAAATATGCATTCCTTCGAAATTCAGCTTTCACCCATTGGGTGAAAGAAAAGTGCTCAACATAAAATACTCGAAGAAGATTTAGGCATAGATGTATATTTCTGTGACCCACATTCACCCTGGCAAAAAGGCACATGCGAAAATATGAATGGTTTAATTAGGCAATATTTACCTAAAGGGATTGATTTAAATCAGGCAGATCAGCATTATTTAAATCAAGTTGCCATGTCACTGAATACTCGTCCTAGAAAGGCGTTAGATTGGCTTACACCATTAGAGAAATTTGCTCAGCTTGTTGATTATCATATGGCTTTTGAAACTGTCGCACCTCATGTTTGAATTCGCCCCATATTTTTGCTACAGTGAACCAAATTAAGATCATCTATTTACTAGGCCTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTTGATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAGCCATGGCTGACCACGTCACCCCCAATCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAGGATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACCCAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGCGGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTGAGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGACCGCATGCCCGCGAAAATCAAGATTTGCGGGATCAGCACACCCGAGGCGCTCGATGCGACCATCGCGGCGCGGGCGGACTATGCCGGGTTGGTGTTCTATCCAGCGTCGCCCCGTGCGGTTACGTCGAATGTCGCGGGCGCTTTGACATCGCGCGCAGCTGGCCAGATCGCCATGGTCGGTTTGTTCGTCGATGCGGATGATGCTGTCATCGCCGACGCACTGGTGGCAGCCAAGCTGAACGCGCTGCAGCTGCACGGTTCGGAATCGCCCGAACGCGTGGCCCAGTTGCGCGCGCGGTTTGGCAAGCCGGTGTGGAAGGCGCTGCCCGTCGCCAGCGCCAGCGATGTCGCACGCGCCGCAGCCTATGCCGGGGCGGCGGACTTGATCTTGTTCGACGCCAAGACCCCCAAAGGCGCGCTGCCCGGCGGCATGGGGTTGGCGTTCGACTGGTCGCTGCTGGCCGGATATCGCGGTGCCTTGCCGTGGGGGCTGGCAGGCGGGCTAAATCCGACGAATGTTGCCGAGGCGATTGCGCGCACCGGAGCGCCGCTGGTCGATACCTCCAGCGGCGTCGAAAGCGCGCCGGGCGTCAAGGATACCGACAAGATTACCAATTTCGCCTTTGCGGTGCGCTTGGCCTAAATCGCGTCGATCAATAGGCGTCGTTCAGCGCAAAGATCGGCTTGCGGGTGCGCCACTGCCCTCGGGTGAAGTCGGGAAAATCTAACGTGCGATTGCCCTCAGCAATCGATTGTTCCGACAGAGGCGTGATCGCGCTCCAGGCCAGCGCGTCGTAAATGTCGATTGGCATCGGGGCCTTGGCCTTCAGCGCCTCGACAAAAGCGTGGATCACGAACCAGTCCATCCCGCCATGCCCGGCCCCTGCCGCCAGATCGGCGTAGCGTTTCCATAGCGGGTGATCGTATTTCGCAAACCAGCCCTCGGCAGGCTCCCAGCGGTGCGGCTGTGGGCTCTTGCCCTCCAGATAGATCGACTTGTTGACGTCCATCCACAGCCCCTCGGTGCCTTGCACCCGAAAGCCGAGAGAATAGGGGCGCGGCAGCGAGGTGTCGTGGCACAGCATGATCGTTTCACCATTAGTGCAGCCGATCATGGTGTTGACCACATCACCCAGTGCGAATTTCACCTCGGCGTTGGGATGATCGGCAGAGCCGTTCTTGACGACATAATCATGCAGCCCGCGCGCCTTACAGCCGAAGCCGCCAGCGCCCGCTTCGCCCGGCAACGCGACCTTCAGGGTGCGGGTCTGCGGCGGGTAGCACACGCCGGCATCGGCGCAGCCCTGGTACTTCACGGTCAGGGTGGTCGCGCTCGCGCCGGCCGCGGGCGTGCCGGTGAGGGTGCCGAGCAATTCCTTGCGGTAGGTTTCGACGTCGCCGAAGAATTCGTCGCGGTAGGCCTTGCCCTTCGGCAGCGCCATGGTCGCGCCGGTGAAGGCGGCATCGGCCTTGACCGAGGTGCGGTGCCGGTACAGGTAATAGCCGTCGGCGATCCGCCAGCGCACCTCGATGCGGTCCGGCGCGGTGGCCTGCGCGGACAGGACGAAGACCTCGTCGACCGGCGGCAGTTCGAAGTCCTGGGCGACGGCCGAGGTCGCGGGCAGCGCAAGCAGCAGGGCGAGCCCGGCCAGCCAGCGGCGCAGGCGGATCGTGGATGCGGTCATTGGCTCAGTTTACCGGTCGGCTCTCGGCGGCCAGCCATTGCAGGTATTCGGGCAGGCCGGACGCGGCTTCGACCGCGAGCGGGTATAGGAAGTATAAACCACCTTTTTGCTCCTCATCCGAAGTATCTTACCTGAAATTCCCTCACTCGTTTACCGCTCAAGCCCCAATTTTAACTGCCGGTCCAGCCTAAACCGCTCTAATAAGGTTCGATTTGGCGGTAAAATCTCTAGCCTGATAGCTCGAGAGATACAAACTGCCCCACCGCCCCGTTTAAAAGTTGGCAGTGTTGAGCAGTGTTGGATTTGGGGTCGTCAGTCAAAGAGACGACTCTGTGATGGATCGAACAGGCTGGGAGTCAGTGGCGGCGCTCGTTCTGGTGGCAGCTCACGCTGCTTGGCGGCATTCGCCTTGGCTGTTTTCTGTTTCAGATGCTTGAGAATCTGCTCAATGACCTTCGGATCTTCGATGCTGGCAATCACTTTGACGTGACCGCCGCAGTGTTCGCAGACTTCAATATCAATATTGAAGACTCGCTTGAGGCGTTGCATCCAGGTCATGGCGCGGTGGCGCTCTGCAGGACTCTTGTCACGCCAGTTAGTATCGAGACCTTCCGATTTGTCGGGCTTCTTGCCCCGCTTGGCGGGTGTTACTTGAACTCGGTGTTTGCTGTTCGGTGCAAAGACGCCGTGGAAGCGTGTGAGGTTGACTCGCGGCTTAGGTACCAACGCAGCGAGTTTGGCGATGAAGTCCAGCGGCTCGAAGATCACATGGGTGGTGCCATTGCGGTACGGAGTTTTGAGCTCGTAACGCACCTGCCCATTGGCGGTTAATGCCAGACGTTTTTCTGAAACCGCTGGCCGACTAATGTAGCGACACAAGCGCTCAAGCTTATCCCGCTGATGCGCTTCGGCCATCACACCGGCGTGTAGCGAGAAACCAGCATGGTTGGCTACTCGACTGCTTGAGTCGGCTTTATCCTCACGCCCTGGCAAGGTTTGCAGGGTGAAGACTTTGCGCCCTTGCTGGGGGCCGACGGCAATGCGATACGTAACCGAAGCACCATGTAATTGAGTCAGCGTATCGTCTTCGCCCTCTTCCAGTGTCAACCACGTATTCTCGGCATCACGCTCCAAAATCCCACGCTTTTCCATGCAGCGAGCGATGCGATGGCTGAGGGTGTGAGCGAGCGTATTCAGCTCATCGTAAGTGGGTGCCTTGACACGATGGAAGCGTTGCTTGCCATAGTCATCTTCGGCATAGACACCATCGAGAAACAGCATGTGGTAGTGGACATTGAGATTTAGCGCGGAGCCAAAGCGTTGGATAAGAGTCACTGAGCCAGTTTGTGCAGAGGCTTTGGTGTAACCGGCTTTTTTGATCAGATGAGTTGAGAGTGTACGATAGACGATACTCAAGACCTGGCCCATCAGCTGGGGATGGCGAGCCAGCAAAAAGCGTAGCTGGAAAGGAAAGCTGAGCACCCACTGGCGAATGGGCTCCTTGGGGAAGACTTCGTCTATCAGCAGCGCCGCACTCTCGGCCATCCGGCGGGCACCGCAGCTAGGGCAAAAGCCGCGTCGTTTACAGCTGAAGGCGACCAGACGCTCGTGATGACAATCCTCGCAGCGAACCCGCATGAAACCATACTCCAGACGGCCACATTGGAGGAGGTCGTTGAATTCTTGTTGGATGTAGCGAGGCAGGTGTTGACCTTGGGCTTCGAGTGAGGCTTTGAAGGCTGGGTAGTGCTGCTCAACCAGCTGGTAGAGCAGCGTCTGGTCGGGTTGGTGGCGTTCGTAACCGTTTGTTTGAGTGGGCGATTGACTCGCCGTGGCGTTCCTTGCCAGCGACATGGGTATCCTCCGCTGATACTGTGGTTATGTACAGTATCAGCGGCTTGCGTTCAGACGTCCAGTCTGGCCCTAGACATCGCTAAATGCTTAACCCGCAATAGCCCTCACGAGTTGTTATCAGCCACTACCGGTTGAGCGAGAAGGTTTTGGGTTCAGGGTGCTATTGCTCCACCAATCACAATACTGAAGCCCCAACTGTTATCAGTTGGGGCTTTTTCTTGTCTGTTTGCGGCGGTTGCGTTTTATCGGTAGTCGTCGAGCTCTGCACCATCCCACATAAGAGCTTAACGGTGCGATCTTCAACGCCATCACACAAAACTTTCTTTTTCACGCACAGTCAACTTATTGGATGTTTTATTAACAACCCAAAAGGAGATATTTAGCGGGCGGCCGGAAGGTGAATGCTAGGCATGATCTAACCCTCGGTCTCTGGCGTCGCGACTGCGAAATTTCGCGAGGGTTTCCGAGAAGGTGATTGCGCTTCGCAGATCTCCAGGCGCGTGGGTGCGGACGTAGTCAGCGCCATTGCCGATCGCGTGAAGTTCCGCCGCAAGGCTCGCTGGACCCAGATCCTTTACAGGAAGGCCAACGGTGGCGCCCAAGAAGGATTTCCGCGACACCGAGACCAATAGCGGAAGCCCCAACGCCGACTTCAGCTTTTGAAGGTTCGACAGCACGTGCAGCGATGTTTCCGGTGCGGGGCTCAAGAAAAATCCCATCCCCGGATCGAGGATGAGCCGGTCGGCAGCGACCCCGCTCCGTCGCAAGGCGGAAACCCGCGCCTCGAAGAACCGCACAATCTCGTCGAGCGCGTCTTCGGGTCGAAGGTGACCGGTGCGGGTGGCGATGCCATCCCGCTGCGCTGAGTGCATAACCACCAGCCTGCAGTCCGCCTCAGCAATATCGGGATAGAGCGCAGGGTCAGGAAATCCTTGGATATCGTTCAGGTAGCCCACGCCGCGCTTGAGCGCATAGCGCTGGGTTTCCGGTTGGAAGCTGTCGATTGAAACACGGTGCATCTGATCGGACAGGGCGTCTAAGAGCGGCGCAATACGTCTGATCTCATCGGCCGGCGATACAGGCCTCGCGTCCGGATGGCTGGCGGCCGGTCCGACATCCACGACGTCTGATCCGACTCGCAGCATTTCGATCGCCGCGGTGACAGCGCCGGCGGGGTCTAGCCGCCGGCTCTCATCGAAGAAGGAGTCCTCGGTGAGATTCAGAATGCCGAACACCGTCACCATGGCGTCGGCCTCCGCAGCGACTTCCACGATGGGGATCGGGCGAGCAAAAAGGCAGCAATTATGAGCCCCATACCTACAAAGCCCCACGCATCAAGCTTTTGCCCATGAAGCAACCAGGCAATGGCTGTAATTATGACGACGCCGAGTCCCGACCAGACTGCATAAGCAACACCGACAGGGATGGATTTCAGAACCAGAGAAAGAAAATAAAATGCGATGCCATAACCGATTATGACAACGGCGGAAGGGGCAAGCTTAGTAAAGCCCTCGCTAGATTTTAATGCGGATGTTGCGATTACTTCGCCAACTATTGCGATAACAAGAAAAAGCCAGCCTTTCATGATATATCTCCCAATTTGTGTAGGGCTTATTATGCACGCTTAAAAATAATAAAAGCAGACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTAGTGCATCTAACGCCGGAGTTAAGCCGCCGCGCGTAGCGCGGTCGGCTTGAACGAATTGTTAGACATCATTTACCAACTGACTTGATGATCTCGCCTTTCACAAAGCGAATAAATTCTTCCAAGTGATCTGCGCGTGAGGCCAAGTGATCTTCTTTTTGTCCCAGATAAGCTTGCTTAGCTTCAAGTAAGACGGGCTGATACTGGGCAGGTAGGCGTTTTATTGCCCAGTCGGCAGCGACATCCTTCGGCGCGATTTTGCCGGTTATTGCGCTGTACCAAATGCGGGACAACGTAAGCACTACATTTCGCTCATCGCCGGCCCAGTCGGGCTGCGAGTTCCATAGCTTCAAGGTTTCCCTCAGCGCCTCGAATAGATCCTGTTCAGGAACCGGGTCAAAGAATTCCTCCGCTGCCGGACCTACCAAGGCAACGCTATGTTCTCTTGCTTTTGTAAGCAGGATAGCTAGATCAATGTCGATCATGGCTGGCTCGAAGATACCCGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGCTCGCGCTTAGCCGGATAACGCCACGGGATGATGTCGTCATGCACGACAAGGGTGACTTCTATAGCGCGGAGCGTCTCGCTCTCGCCAGGGAAAGCCGAAGCCTCCATAAGATCATTGAGCAATGCTCGCCGCGTCGTTTCATCAAGCTTTACGGCCACAGTAACCAACAAATCAATATCGCTGTATGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGCACGGCCAGCAACGTTGATTCCAGATGGCGCTCAATGACGCTTAGCACCTCTGATAGTTGGTTCGAAATTTCGATGGTCACCGCTTCCCTCATGATGTCTAACGGGCGAGGTAAGCCGACCGCAGAATGCGGGTCGGCTTGACCGAAATGTTAGAACCAGAAGCCAAAACGGATAACTTGAATTTGGCGACGGGCGCTAACCGTGAAAAAACGCTGCGCCACCGAGGCGGCACAGCACTGCAAAAACGATAGCTGCTTGCGCTTGCTACGCAAGGGCTAGAGGCCAAAAAGACTGAAAACCTGCGCAGCCCATGCAGGCGAAGCCCGGAAAAAAGGCAAAACAGGCACTGAATAACGCCTGAAAAGCTAAATGCCGTTTGAATAAACATGAGCTAAATAAAGCTGGGTTTAAGTGGTGCTAACGTTGGACGTAACGAGAGCCGGAGCGCAGCGGAGGGAACCAAAATGCGCAGCATTTTGGCGTCCCGTTGACGGAATGGTTAGCCGTTTCGACGCGCATAAACGGAGTGGGTGTACGGAATTACAGCTTGAATGGTTTCGGTTGAGACAAGCTCGAATTCTGTTTCGTTGAGCATTGGGAAGAAGGCGTCACCCTCGAAGGTTTGATGTACCTCAGATAGAAACACGCCGTGGGCGTGAGGTAGTGCCAGAGTGTATATCTCAGCTCCGCCCGCGACGTAGAGTTCATTGCCGAGTTCGGATGCCAAAGCGATAGCGTGCGACAGCGTTGAAACAACTACGCAGCCAGTGGCGCGGTAGTTAGCTTGGCGTGAGATTACCAATGTGTGACGGTTCGGTAGAGGCTTGCCGATAGACTCAAAGGTCTTTCGCCCCATGACAACGACTTTTCCCTCAGTGAGTCTGCGAAAAATCTTCTGCTCACCCGGAATTTTCCAGGGGATATTAGGACCATTGCCAATAACCCGATTGGCTCCCATCGCAGCAACGAGATAAATGCGTACTGATTCCGAGTTCATATGGCTAACTTTGTTTTAGGGCGACTGCCCTGCTGCGTAACATCGTTGCTGCTCCATAACATCAAACATCGACCCACGGCGTAACGCGCTTGCTGCTTGGATGCCCGAGGCATAGACTGTACAAAAAAACAGTCATAACAAGCCATGAAAACCGCCACTGCGCCGTTACCACCGCTGCGTTCGGTCAAGGTTCTGGACCAGTTGCGTGAGCGCATACGCTACTTGCATTACAGCTTACCAACCGAACAGGCTTATGTCCACTGGGTTCGTGCCTTCATCCGTTTCCACGGTGTGCGTCACCCGGCAACCTTGGGCAGCAGCGAAGTCGAGGCATTTCTGTCCTGGCTGGCGAACGAGCGCAAGGTTTCGGTCTCCACGCATCGTCAGGCATTGGCGGCCTTGCTGTTCTTCTACGGCAAGGTGCTGTGCACGGATCTGCCCTGGCTTCAGGAGATCGGAAGACCTCGGCCGTCGCGGCGCTTGCCGGTGGTGCTGACCCCGGATGAAGTGGTTCGCATCCTCGGTTTTCTGGAAGGCGAGCATCGTTTGTTCGCCCAGCTTCTGTATGGAACGGGCATGCGGATCAGTGAGGGTTTGCAACTGCGGGTCAAGGATCTGGATTTCGATCACGGCACGATCATCGTGCGGGAGGGCAAGGGCTCCAAGGATCGGGCCTTGATGTTACCCGAGAGCTTGGCACCCAGCCTGCGCGAGCAGCTGTCGCGTGCACGGGCATGGTGGCTGAAGGACCAGGCCGAGGGCCGCAGCGGCGTTGCGCTTCCCGACGCCCTTGAGCGGAAGTATCCGCGCGCCGGGCATTCCTGGCCGTGGTTCTGGGTTTTTGCGCAGCACACGCATTCGACCGATCCACGGAGCGGTGTCGTGCGTCGCCATCACATGTATGACCAGACCTTTCAGCGCGCCTTCAAACGTGCCGTAGAACAAGCAGGCATCACGAAGCCCGCCACACCGCACACCCTCCGCCACTCGTTCGCGACGGCCTTGCTCCGCAG
+>93_length=1443_depth=2.74x
+TGTACTGACCCCAAAAAGTTGGACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCTTATATTACTGAACTCATCAAGATAAAAACACTCCGACTTTAAGGTTCCAAAGAAACACTCCACCACAGCATTATCCAGACAATTGCCTTTTCTGGACATGCTTTGTTTAATACCATGTTCTTTAAGGATATTTTGATATCTTCTCATACGATACTGCCATCCCTGGTCAGAGTGCAGAACAGGATGCTCGTGAGGATTAAGCTTTTTGAATGCCTGATCGAGCATATTCTCAACCATGTTCATCACTGGTCTTTCCGAAAGGCTGTAAGAAATAACTTCGTTGTTGAAGAGATCTATTACTGGAGACAAATACAGCTTGCGCCCATTGACTGCAAATTCAGTAACATCGGTAACCCACTTCTCGTTTGGCCGCGTAGCCTTGAAATCTCTTTGGAGAACATTAGGGGCGGTTTGCCCTACCTCTCCTCTGTAAGAGCGGTATCGCTTGACCTTAATCGCTGCTTTAAGTGAGAGGGTTCCCATCAGGCGCTGAACAGCTTTATGGTTAATCTGTTTCCCTTCTCGATGAAGAGACAGCGTTACCCTACGGTATCCGTATCGGCCTCTATTCTCGTGATAAATCTCACTAATACGCTTTTTAACGTCCGCATACTTGTCAGGCTTGCTGAGAGCCTTTAGATGATAATAAAACGTACTGCGCGGTATCTCCGCAGCCCTGAGAAGCTCATCAAGAGGATAAAACTGCCTTAGCTCGTTGAGTACTTTCACTTTTTCGTGGGATGAGCTAAGGCTTTCAGCTTTTTTAGATACATAAGCCGCGTTTCAAGAAATCGAACTTGCCTTTCAAGATCCTCAATGCGTCGGTCTTTTGACAGCTCCAATGCTGATGCCGCTTTTTCTGGATCAACTGATATTGCAATGTTTCTTTTGGTGCCAATCTTGAGCGCGCGTAAACCAGCTTCTCCGCGCTCTTCATAGACCTTCAGCCACCTGGCTACAGAACCACTACCAGCAAGCATAAAGTGAGCAGCAGCCTGATTAAGGGACATGTGCTGCTCGATCACAGCTTTCACGACCTTAATACGCAACTCTGGATCAGCACTAACGCCTTTAGGTTTGGGAATTAAACCTTTTTCTCCATGTTTTTCATAGAGGGCAACCCATGTCCTGACCTGGGTTCGGGGGACACCAAAACGTGCCGAGATGATCCTGTAACCATCATCAGTTGTGAAGTAGTGATTCACGACTTCAAGGCGCTTTTCAAAAGGGTATTTTGGCTTTGACATATTAGGGGCTATTCCATTTCATCGTCCAACAAAATGGGTGCAGTACA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concatenated_mob_typer_reports.tsv	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,6 @@
+plasmid_1068	2	19016	50.54690786705932	-	-	-	-	-	-	-	-	Non-mobilizable	CP021680	0.00705245	1068	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
+plasmid_1550	5	106133	51.586217293396025	IncFIIA,IncFII,IncFIA	000136__AP014877_00014,000121__CP024805,000094__NZ_CP015070_00117	MOBF	NC_017627_00068	MPF_F	08-5333_00200,NC_008460_00107,NC_014615_00033,NC_010488_00021,NC_018966_00040,NC_017639_00100,NC_007675_00027,NC_013437_00116,NC_017639_00094,NC_019094_00090,NC_010409_00124,NC_022651_00077	-	-	Conjugative	CP011064	0.00476862	1550	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
+plasmid_2719	2	11117	55.03283259872268	-	-	-	-	-	-	-	-	Non-mobilizable	JQ739157	0.0496454	2719	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
+plasmid_739	1	8070	57.707558859975215	-	-	-	-	-	-	-	-	Non-mobilizable	KR259131	0.0401734	739	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
+plasmid_839	1	2100	47.142857142857146	Inc13	000058__CP000643_00001	-	-	-	-	-	-	Non-mobilizable	CP008719	0.00186568	839	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
+plasmid_novel_0	1	3684	46.19978284473398	ColRNAI_rep_cluster_1987,rep_cluster_2050	000019__CP000651_00005,001473__CP024541	-	-	-	-	-	-	Non-mobilizable	KU302807	0.0699663	197	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outdir/mob_typer_record.tsv	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,2 @@
+file_id	num_contigs	total_length	gc	rep_type(s)	rep_type_accession(s)	relaxase_type(s)	relaxase_type_accession(s)	mpf_type	mpf_type_accession(s)	orit_type(s)	orit_accession(s)	PredictedMobility	mash_nearest_neighbor	mash_neighbor_distance	mash_neighbor_cluster	NCBI-HR-rank	NCBI-HR-Name	LitRepHRPlasmClass	LitPredDBHRRank	LitPredDBHRRankSciName	LitRepHRRankInPubs	LitRepHRNameInPubs	LitMeanTransferRate	LitClosestRefAcc	LitClosestRefDonorStrain	LitClosestRefRecipientStrain	LitClosestRefTransferRate	LitClosestConjugTemp	LitPMIDs	LitPMIDsNumber
+plasmid_2719	2	11117	55.03283259872268	-	-	-	-	-	-	-	-	Non-mobilizable	JQ739157	0.0496454	2719	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outdir/plasmid.fasta	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,4 @@
+>53_length=9674_depth=5.42x
+GTTTACTCATACCTAGATTCTACGTCAGTACTTCAAAAAGCATAATCAAAGCCTTGATAAATATGCATTCCTTCGAAATTCAGCTTTCACCCATTGGGTGAAAGAAAAGTGCTCAACATAAAATACTCGAAGAAGATTTAGGCATAGATGTATATTTCTGTGACCCACATTCACCCTGGCAAAAAGGCACATGCGAAAATATGAATGGTTTAATTAGGCAATATTTACCTAAAGGGATTGATTTAAATCAGGCAGATCAGCATTATTTAAATCAAGTTGCCATGTCACTGAATACTCGTCCTAGAAAGGCGTTAGATTGGCTTACACCATTAGAGAAATTTGCTCAGCTTGTTGATTATCATATGGCTTTTGAAACTGTCGCACCTCATGTTTGAATTCGCCCCATATTTTTGCTACAGTGAACCAAATTAAGATCATCTATTTACTAGGCCTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTTGATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAGCCATGGCTGACCACGTCACCCCCAATCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAGGATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACCCAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGCGGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTGAGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGACCGCATGCCCGCGAAAATCAAGATTTGCGGGATCAGCACACCCGAGGCGCTCGATGCGACCATCGCGGCGCGGGCGGACTATGCCGGGTTGGTGTTCTATCCAGCGTCGCCCCGTGCGGTTACGTCGAATGTCGCGGGCGCTTTGACATCGCGCGCAGCTGGCCAGATCGCCATGGTCGGTTTGTTCGTCGATGCGGATGATGCTGTCATCGCCGACGCACTGGTGGCAGCCAAGCTGAACGCGCTGCAGCTGCACGGTTCGGAATCGCCCGAACGCGTGGCCCAGTTGCGCGCGCGGTTTGGCAAGCCGGTGTGGAAGGCGCTGCCCGTCGCCAGCGCCAGCGATGTCGCACGCGCCGCAGCCTATGCCGGGGCGGCGGACTTGATCTTGTTCGACGCCAAGACCCCCAAAGGCGCGCTGCCCGGCGGCATGGGGTTGGCGTTCGACTGGTCGCTGCTGGCCGGATATCGCGGTGCCTTGCCGTGGGGGCTGGCAGGCGGGCTAAATCCGACGAATGTTGCCGAGGCGATTGCGCGCACCGGAGCGCCGCTGGTCGATACCTCCAGCGGCGTCGAAAGCGCGCCGGGCGTCAAGGATACCGACAAGATTACCAATTTCGCCTTTGCGGTGCGCTTGGCCTAAATCGCGTCGATCAATAGGCGTCGTTCAGCGCAAAGATCGGCTTGCGGGTGCGCCACTGCCCTCGGGTGAAGTCGGGAAAATCTAACGTGCGATTGCCCTCAGCAATCGATTGTTCCGACAGAGGCGTGATCGCGCTCCAGGCCAGCGCGTCGTAAATGTCGATTGGCATCGGGGCCTTGGCCTTCAGCGCCTCGACAAAAGCGTGGATCACGAACCAGTCCATCCCGCCATGCCCGGCCCCTGCCGCCAGATCGGCGTAGCGTTTCCATAGCGGGTGATCGTATTTCGCAAACCAGCCCTCGGCAGGCTCCCAGCGGTGCGGCTGTGGGCTCTTGCCCTCCAGATAGATCGACTTGTTGACGTCCATCCACAGCCCCTCGGTGCCTTGCACCCGAAAGCCGAGAGAATAGGGGCGCGGCAGCGAGGTGTCGTGGCACAGCATGATCGTTTCACCATTAGTGCAGCCGATCATGGTGTTGACCACATCACCCAGTGCGAATTTCACCTCGGCGTTGGGATGATCGGCAGAGCCGTTCTTGACGACATAATCATGCAGCCCGCGCGCCTTACAGCCGAAGCCGCCAGCGCCCGCTTCGCCCGGCAACGCGACCTTCAGGGTGCGGGTCTGCGGCGGGTAGCACACGCCGGCATCGGCGCAGCCCTGGTACTTCACGGTCAGGGTGGTCGCGCTCGCGCCGGCCGCGGGCGTGCCGGTGAGGGTGCCGAGCAATTCCTTGCGGTAGGTTTCGACGTCGCCGAAGAATTCGTCGCGGTAGGCCTTGCCCTTCGGCAGCGCCATGGTCGCGCCGGTGAAGGCGGCATCGGCCTTGACCGAGGTGCGGTGCCGGTACAGGTAATAGCCGTCGGCGATCCGCCAGCGCACCTCGATGCGGTCCGGCGCGGTGGCCTGCGCGGACAGGACGAAGACCTCGTCGACCGGCGGCAGTTCGAAGTCCTGGGCGACGGCCGAGGTCGCGGGCAGCGCAAGCAGCAGGGCGAGCCCGGCCAGCCAGCGGCGCAGGCGGATCGTGGATGCGGTCATTGGCTCAGTTTACCGGTCGGCTCTCGGCGGCCAGCCATTGCAGGTATTCGGGCAGGCCGGACGCGGCTTCGACCGCGAGCGGGTATAGGAAGTATAAACCACCTTTTTGCTCCTCATCCGAAGTATCTTACCTGAAATTCCCTCACTCGTTTACCGCTCAAGCCCCAATTTTAACTGCCGGTCCAGCCTAAACCGCTCTAATAAGGTTCGATTTGGCGGTAAAATCTCTAGCCTGATAGCTCGAGAGATACAAACTGCCCCACCGCCCCGTTTAAAAGTTGGCAGTGTTGAGCAGTGTTGGATTTGGGGTCGTCAGTCAAAGAGACGACTCTGTGATGGATCGAACAGGCTGGGAGTCAGTGGCGGCGCTCGTTCTGGTGGCAGCTCACGCTGCTTGGCGGCATTCGCCTTGGCTGTTTTCTGTTTCAGATGCTTGAGAATCTGCTCAATGACCTTCGGATCTTCGATGCTGGCAATCACTTTGACGTGACCGCCGCAGTGTTCGCAGACTTCAATATCAATATTGAAGACTCGCTTGAGGCGTTGCATCCAGGTCATGGCGCGGTGGCGCTCTGCAGGACTCTTGTCACGCCAGTTAGTATCGAGACCTTCCGATTTGTCGGGCTTCTTGCCCCGCTTGGCGGGTGTTACTTGAACTCGGTGTTTGCTGTTCGGTGCAAAGACGCCGTGGAAGCGTGTGAGGTTGACTCGCGGCTTAGGTACCAACGCAGCGAGTTTGGCGATGAAGTCCAGCGGCTCGAAGATCACATGGGTGGTGCCATTGCGGTACGGAGTTTTGAGCTCGTAACGCACCTGCCCATTGGCGGTTAATGCCAGACGTTTTTCTGAAACCGCTGGCCGACTAATGTAGCGACACAAGCGCTCAAGCTTATCCCGCTGATGCGCTTCGGCCATCACACCGGCGTGTAGCGAGAAACCAGCATGGTTGGCTACTCGACTGCTTGAGTCGGCTTTATCCTCACGCCCTGGCAAGGTTTGCAGGGTGAAGACTTTGCGCCCTTGCTGGGGGCCGACGGCAATGCGATACGTAACCGAAGCACCATGTAATTGAGTCAGCGTATCGTCTTCGCCCTCTTCCAGTGTCAACCACGTATTCTCGGCATCACGCTCCAAAATCCCACGCTTTTCCATGCAGCGAGCGATGCGATGGCTGAGGGTGTGAGCGAGCGTATTCAGCTCATCGTAAGTGGGTGCCTTGACACGATGGAAGCGTTGCTTGCCATAGTCATCTTCGGCATAGACACCATCGAGAAACAGCATGTGGTAGTGGACATTGAGATTTAGCGCGGAGCCAAAGCGTTGGATAAGAGTCACTGAGCCAGTTTGTGCAGAGGCTTTGGTGTAACCGGCTTTTTTGATCAGATGAGTTGAGAGTGTACGATAGACGATACTCAAGACCTGGCCCATCAGCTGGGGATGGCGAGCCAGCAAAAAGCGTAGCTGGAAAGGAAAGCTGAGCACCCACTGGCGAATGGGCTCCTTGGGGAAGACTTCGTCTATCAGCAGCGCCGCACTCTCGGCCATCCGGCGGGCACCGCAGCTAGGGCAAAAGCCGCGTCGTTTACAGCTGAAGGCGACCAGACGCTCGTGATGACAATCCTCGCAGCGAACCCGCATGAAACCATACTCCAGACGGCCACATTGGAGGAGGTCGTTGAATTCTTGTTGGATGTAGCGAGGCAGGTGTTGACCTTGGGCTTCGAGTGAGGCTTTGAAGGCTGGGTAGTGCTGCTCAACCAGCTGGTAGAGCAGCGTCTGGTCGGGTTGGTGGCGTTCGTAACCGTTTGTTTGAGTGGGCGATTGACTCGCCGTGGCGTTCCTTGCCAGCGACATGGGTATCCTCCGCTGATACTGTGGTTATGTACAGTATCAGCGGCTTGCGTTCAGACGTCCAGTCTGGCCCTAGACATCGCTAAATGCTTAACCCGCAATAGCCCTCACGAGTTGTTATCAGCCACTACCGGTTGAGCGAGAAGGTTTTGGGTTCAGGGTGCTATTGCTCCACCAATCACAATACTGAAGCCCCAACTGTTATCAGTTGGGGCTTTTTCTTGTCTGTTTGCGGCGGTTGCGTTTTATCGGTAGTCGTCGAGCTCTGCACCATCCCACATAAGAGCTTAACGGTGCGATCTTCAACGCCATCACACAAAACTTTCTTTTTCACGCACAGTCAACTTATTGGATGTTTTATTAACAACCCAAAAGGAGATATTTAGCGGGCGGCCGGAAGGTGAATGCTAGGCATGATCTAACCCTCGGTCTCTGGCGTCGCGACTGCGAAATTTCGCGAGGGTTTCCGAGAAGGTGATTGCGCTTCGCAGATCTCCAGGCGCGTGGGTGCGGACGTAGTCAGCGCCATTGCCGATCGCGTGAAGTTCCGCCGCAAGGCTCGCTGGACCCAGATCCTTTACAGGAAGGCCAACGGTGGCGCCCAAGAAGGATTTCCGCGACACCGAGACCAATAGCGGAAGCCCCAACGCCGACTTCAGCTTTTGAAGGTTCGACAGCACGTGCAGCGATGTTTCCGGTGCGGGGCTCAAGAAAAATCCCATCCCCGGATCGAGGATGAGCCGGTCGGCAGCGACCCCGCTCCGTCGCAAGGCGGAAACCCGCGCCTCGAAGAACCGCACAATCTCGTCGAGCGCGTCTTCGGGTCGAAGGTGACCGGTGCGGGTGGCGATGCCATCCCGCTGCGCTGAGTGCATAACCACCAGCCTGCAGTCCGCCTCAGCAATATCGGGATAGAGCGCAGGGTCAGGAAATCCTTGGATATCGTTCAGGTAGCCCACGCCGCGCTTGAGCGCATAGCGCTGGGTTTCCGGTTGGAAGCTGTCGATTGAAACACGGTGCATCTGATCGGACAGGGCGTCTAAGAGCGGCGCAATACGTCTGATCTCATCGGCCGGCGATACAGGCCTCGCGTCCGGATGGCTGGCGGCCGGTCCGACATCCACGACGTCTGATCCGACTCGCAGCATTTCGATCGCCGCGGTGACAGCGCCGGCGGGGTCTAGCCGCCGGCTCTCATCGAAGAAGGAGTCCTCGGTGAGATTCAGAATGCCGAACACCGTCACCATGGCGTCGGCCTCCGCAGCGACTTCCACGATGGGGATCGGGCGAGCAAAAAGGCAGCAATTATGAGCCCCATACCTACAAAGCCCCACGCATCAAGCTTTTGCCCATGAAGCAACCAGGCAATGGCTGTAATTATGACGACGCCGAGTCCCGACCAGACTGCATAAGCAACACCGACAGGGATGGATTTCAGAACCAGAGAAAGAAAATAAAATGCGATGCCATAACCGATTATGACAACGGCGGAAGGGGCAAGCTTAGTAAAGCCCTCGCTAGATTTTAATGCGGATGTTGCGATTACTTCGCCAACTATTGCGATAACAAGAAAAAGCCAGCCTTTCATGATATATCTCCCAATTTGTGTAGGGCTTATTATGCACGCTTAAAAATAATAAAAGCAGACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTAGTGCATCTAACGCCGGAGTTAAGCCGCCGCGCGTAGCGCGGTCGGCTTGAACGAATTGTTAGACATCATTTACCAACTGACTTGATGATCTCGCCTTTCACAAAGCGAATAAATTCTTCCAAGTGATCTGCGCGTGAGGCCAAGTGATCTTCTTTTTGTCCCAGATAAGCTTGCTTAGCTTCAAGTAAGACGGGCTGATACTGGGCAGGTAGGCGTTTTATTGCCCAGTCGGCAGCGACATCCTTCGGCGCGATTTTGCCGGTTATTGCGCTGTACCAAATGCGGGACAACGTAAGCACTACATTTCGCTCATCGCCGGCCCAGTCGGGCTGCGAGTTCCATAGCTTCAAGGTTTCCCTCAGCGCCTCGAATAGATCCTGTTCAGGAACCGGGTCAAAGAATTCCTCCGCTGCCGGACCTACCAAGGCAACGCTATGTTCTCTTGCTTTTGTAAGCAGGATAGCTAGATCAATGTCGATCATGGCTGGCTCGAAGATACCCGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGCTCGCGCTTAGCCGGATAACGCCACGGGATGATGTCGTCATGCACGACAAGGGTGACTTCTATAGCGCGGAGCGTCTCGCTCTCGCCAGGGAAAGCCGAAGCCTCCATAAGATCATTGAGCAATGCTCGCCGCGTCGTTTCATCAAGCTTTACGGCCACAGTAACCAACAAATCAATATCGCTGTATGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGCACGGCCAGCAACGTTGATTCCAGATGGCGCTCAATGACGCTTAGCACCTCTGATAGTTGGTTCGAAATTTCGATGGTCACCGCTTCCCTCATGATGTCTAACGGGCGAGGTAAGCCGACCGCAGAATGCGGGTCGGCTTGACCGAAATGTTAGAACCAGAAGCCAAAACGGATAACTTGAATTTGGCGACGGGCGCTAACCGTGAAAAAACGCTGCGCCACCGAGGCGGCACAGCACTGCAAAAACGATAGCTGCTTGCGCTTGCTACGCAAGGGCTAGAGGCCAAAAAGACTGAAAACCTGCGCAGCCCATGCAGGCGAAGCCCGGAAAAAAGGCAAAACAGGCACTGAATAACGCCTGAAAAGCTAAATGCCGTTTGAATAAACATGAGCTAAATAAAGCTGGGTTTAAGTGGTGCTAACGTTGGACGTAACGAGAGCCGGAGCGCAGCGGAGGGAACCAAAATGCGCAGCATTTTGGCGTCCCGTTGACGGAATGGTTAGCCGTTTCGACGCGCATAAACGGAGTGGGTGTACGGAATTACAGCTTGAATGGTTTCGGTTGAGACAAGCTCGAATTCTGTTTCGTTGAGCATTGGGAAGAAGGCGTCACCCTCGAAGGTTTGATGTACCTCAGATAGAAACACGCCGTGGGCGTGAGGTAGTGCCAGAGTGTATATCTCAGCTCCGCCCGCGACGTAGAGTTCATTGCCGAGTTCGGATGCCAAAGCGATAGCGTGCGACAGCGTTGAAACAACTACGCAGCCAGTGGCGCGGTAGTTAGCTTGGCGTGAGATTACCAATGTGTGACGGTTCGGTAGAGGCTTGCCGATAGACTCAAAGGTCTTTCGCCCCATGACAACGACTTTTCCCTCAGTGAGTCTGCGAAAAATCTTCTGCTCACCCGGAATTTTCCAGGGGATATTAGGACCATTGCCAATAACCCGATTGGCTCCCATCGCAGCAACGAGATAAATGCGTACTGATTCCGAGTTCATATGGCTAACTTTGTTTTAGGGCGACTGCCCTGCTGCGTAACATCGTTGCTGCTCCATAACATCAAACATCGACCCACGGCGTAACGCGCTTGCTGCTTGGATGCCCGAGGCATAGACTGTACAAAAAAACAGTCATAACAAGCCATGAAAACCGCCACTGCGCCGTTACCACCGCTGCGTTCGGTCAAGGTTCTGGACCAGTTGCGTGAGCGCATACGCTACTTGCATTACAGCTTACCAACCGAACAGGCTTATGTCCACTGGGTTCGTGCCTTCATCCGTTTCCACGGTGTGCGTCACCCGGCAACCTTGGGCAGCAGCGAAGTCGAGGCATTTCTGTCCTGGCTGGCGAACGAGCGCAAGGTTTCGGTCTCCACGCATCGTCAGGCATTGGCGGCCTTGCTGTTCTTCTACGGCAAGGTGCTGTGCACGGATCTGCCCTGGCTTCAGGAGATCGGAAGACCTCGGCCGTCGCGGCGCTTGCCGGTGGTGCTGACCCCGGATGAAGTGGTTCGCATCCTCGGTTTTCTGGAAGGCGAGCATCGTTTGTTCGCCCAGCTTCTGTATGGAACGGGCATGCGGATCAGTGAGGGTTTGCAACTGCGGGTCAAGGATCTGGATTTCGATCACGGCACGATCATCGTGCGGGAGGGCAAGGGCTCCAAGGATCGGGCCTTGATGTTACCCGAGAGCTTGGCACCCAGCCTGCGCGAGCAGCTGTCGCGTGCACGGGCATGGTGGCTGAAGGACCAGGCCGAGGGCCGCAGCGGCGTTGCGCTTCCCGACGCCCTTGAGCGGAAGTATCCGCGCGCCGGGCATTCCTGGCCGTGGTTCTGGGTTTTTGCGCAGCACACGCATTCGACCGATCCACGGAGCGGTGTCGTGCGTCGCCATCACATGTATGACCAGACCTTTCAGCGCGCCTTCAAACGTGCCGTAGAACAAGCAGGCATCACGAAGCCCGCCACACCGCACACCCTCCGCCACTCGTTCGCGACGGCCTTGCTCCGCAG
+>93_length=1443_depth=2.74x
+TGTACTGACCCCAAAAAGTTGGACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCTTATATTACTGAACTCATCAAGATAAAAACACTCCGACTTTAAGGTTCCAAAGAAACACTCCACCACAGCATTATCCAGACAATTGCCTTTTCTGGACATGCTTTGTTTAATACCATGTTCTTTAAGGATATTTTGATATCTTCTCATACGATACTGCCATCCCTGGTCAGAGTGCAGAACAGGATGCTCGTGAGGATTAAGCTTTTTGAATGCCTGATCGAGCATATTCTCAACCATGTTCATCACTGGTCTTTCCGAAAGGCTGTAAGAAATAACTTCGTTGTTGAAGAGATCTATTACTGGAGACAAATACAGCTTGCGCCCATTGACTGCAAATTCAGTAACATCGGTAACCCACTTCTCGTTTGGCCGCGTAGCCTTGAAATCTCTTTGGAGAACATTAGGGGCGGTTTGCCCTACCTCTCCTCTGTAAGAGCGGTATCGCTTGACCTTAATCGCTGCTTTAAGTGAGAGGGTTCCCATCAGGCGCTGAACAGCTTTATGGTTAATCTGTTTCCCTTCTCGATGAAGAGACAGCGTTACCCTACGGTATCCGTATCGGCCTCTATTCTCGTGATAAATCTCACTAATACGCTTTTTAACGTCCGCATACTTGTCAGGCTTGCTGAGAGCCTTTAGATGATAATAAAACGTACTGCGCGGTATCTCCGCAGCCCTGAGAAGCTCATCAAGAGGATAAAACTGCCTTAGCTCGTTGAGTACTTTCACTTTTTCGTGGGATGAGCTAAGGCTTTCAGCTTTTTTAGATACATAAGCCGCGTTTCAAGAAATCGAACTTGCCTTTCAAGATCCTCAATGCGTCGGTCTTTTGACAGCTCCAATGCTGATGCCGCTTTTTCTGGATCAACTGATATTGCAATGTTTCTTTTGGTGCCAATCTTGAGCGCGCGTAAACCAGCTTCTCCGCGCTCTTCATAGACCTTCAGCCACCTGGCTACAGAACCACTACCAGCAAGCATAAAGTGAGCAGCAGCCTGATTAAGGGACATGTGCTGCTCGATCACAGCTTTCACGACCTTAATACGCAACTCTGGATCAGCACTAACGCCTTTAGGTTTGGGAATTAAACCTTTTTCTCCATGTTTTTCATAGAGGGCAACCCATGTCCTGACCTGGGTTCGGGGGACACCAAAACGTGCCGAGATGATCCTGTAACCATCATCAGTTGTGAAGTAGTGATTCACGACTTCAAGGCGCTTTTCAAAAGGGTATTTTGGCTTTGACATATTAGGGGCTATTCCATTTCATCGTCCAACAAAATGGGTGCAGTACA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outdir/reference_plasmid.fasta	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,96 @@
+>JQ739157.2 Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete sequence
+AAGCTTATAGCAGTGTCACAGATGCGAAAAAGCAATTAAGTGCATATTTTGAGTTTTATAATTTGAAACG
+ACCTCATTCGAGTCTAGACAAAATGACACCAAATGAGTTTTACTATGATCAGCTACCCCAACAAAACAAG
+GTGGCTTAACTAGAGCGGAATATCACTTATAAATACGCTTTTAGTTGTTCAAACAAGTGGGACCACCTCT
+CTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTTGATGGAATTGCCCAATATTATTCAACA
+ATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAAT
+CGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTC
+GCGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGA
+TGAGCAGTTTGAATTAATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGAC
+CAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAGTTGCTATTATTGATTGTCCAT
+TTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATAT
+AGATCAAGATGATTTTGACGCTGAATTATGGGGAGACCATAGAACTTACCTAAGTCTATGGAATGAGTTA
+ACTGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAG
+ATAAATTCAATGAAATTTACTTTTTAGATCTTGGCCGTGCTGGGTTAGCTGATGAATTTGTAGATATATC
+CTTTGTTGAACGTTGCCTAAGAGAGGATGCCTCGGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAA
+AATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGATTCTAAGCATTATCTA
+AAAATACTTAATTGTCTTTTAACGTCGCTAAATTTTAAATAAATAAGTGAAGAGTGTTAGTGGAGCCACT
+GATTTAAAGTTGGCAGAGTAAAACTTGAAGTGCGACATAAACCACCTAATTAATTTAAAGGGTTTATGGA
+GTATATAAAATTGTCATACCATCATCTTAACTTTGAAGATCGTACTGCATTAATGCTTGAGTCAAGAAAA
+GAAGGCTTTTCAGCCAGAAAATTTGCTGAACTCATTAAAAGACATCCTAGTACGATCTATCGTGAGCTTA
+AAAGAAATAGCATCAATGACGTTTATCAAGCTCGATATGCTTCTGATAACACCTTCGCTAGACGTAGACG
+TGGTCACAGAAAACTCAAAATCGATTCAATCCTCTGGAAATTTATTGTTGAAGCGATCCGTTGTTTATGG
+TCTCCTCAGCAAATAGCAAAGCGTTTAAAGACATTTCCTGATTTGGATCAAACAATGAATGTAAGCCATA
+CAACGATTTATTCAACGATACGAGCATTACCAAAGGGTGAGTTGAAAAAAGACTTATTATCCTGTCTACG
+TCATGAAAATAAAAAGCGAAAAGCTAACGGTGAACCTAAAAAAGATTCTATATTACAGGATATTAAAACT
+ATTCATGAGCGCCCAGCCGAAGTTCAAGAAAGAAAAATACCGGGTCATTGGGAAGCTGATTTAATTAAAG
+GTAAAGACAATAAAAGTTCGATAGCAACACTTATTGAACGAAATACACGGCTCTGTATCTTGGCAACATT
+ACCTGATGCAAAGGCAGAATCAGTGCGCAAGGCTTTAACTGAAGCTCTGAAATATTTACCTGCAGAACTG
+CGTAAAACGTTGACCTATGACCGTGGACGTGAGATGTCAGAACATAAAATACTCGAAGAAGATTTAGGCA
+TAGATGTATATTTCTGTGACCCACATTCACCCTGGCAAAAAGGCACATGCGAAAATATGAATGGTTTAAT
+TAGGCAATATTTACCTAAAGGGATTGATTTAAATCAGGCAGATCAGCATTATTTAAATCAAGTTGCCATG
+TCACTGAATACTCGTCCTAGAAAGGCGTTAGATTGGCTTACACCATTAGAGAAATTTGCTCAGCTTGTTG
+ATTATCATATGGCTTTTGAAACTGTCGCACCTCATGTTTGAATTCGCCCCATATTTTTGCTACAGTGAAC
+CAAATTAAGATCATCTATTTACTAGGCCTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTT
+GATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTG
+AGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTG
+GCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTT
+CGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGG
+ACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGG
+TGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTA
+TGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTC
+GCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCC
+CCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGAT
+CAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCG
+CGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCG
+CCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAGCCATGGCTGACCACGTCACCCCCAA
+TCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAG
+GATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACC
+CAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGC
+GGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTG
+AGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGACCGCATG
+CCCGCGAAAATCAAGATTTGCGGGATCAGCACACCCGAGGCGCTCGATGCGACCATCGCGGCGCGGGCGG
+ACTATGCCGGGTTGGTGTTCTATCCAGCGTCGCCCCGTGCGGTTACGTCGAATGTCGCGGGCGCTTTGAC
+ATCGCGCGCAGCTGGCCAGATCGCCATGGTCGGTTTGTTCGTCGATGCGGATGATGCTGTCATCGCCGAC
+GCACTGGTGGCAGCCAAGCTGAACGCGCTGCAGCTGCACGGTTCGGAATCGCCCGAACGCGTGGCCCAGT
+TGCGCGCGCGGTTTGGCAAGCCGGTGTGGAAGGCGCTGCCCGTCGCCAGCGCCAGCGATGTCGCACGCGC
+CGCAGCCTATGCCGGGGCGGCGGACTTGATCTTGTTCGACGCCAAGACCCCCAAAGGCGCGCTGCCCGGC
+GGCATGGGGTTGGCGTTCGACTGGTCGCTGCTGGCCGGATATCGCGGTGCCTTGCCGTGGGGGCTGGCAG
+GCGGGCTAAATCCGACGAATGTTGCCGAGGCGATTGCGCGCACCGGAGCGCCGCTGGTCGATACCTCCAG
+CGGCGTCGAAAGCGCGCCGGGCGTCAAGGATACCGACAAGATTACCAATTTCGCCTTTGCGGTGCGCTTG
+GCCTAAATCGCGTCGATCAATAGGCGTCGTTCAGCGCAAAGATCGGCTTGCGGGTGCGCCACTGCCCTCG
+GGTGAAGTCGGGAAAATCTAACGTGCGATTGCCCTCAGCAATCGATTGTTCCGACAGAGGCGTGATCGCG
+CTCCAGGCCAGCGCGTCGTAAATGTCGATTGGCATCGGGGCCTTGGCCTTCAGCGCCTCGACAAAAGCGT
+GGATCACGAACCAGTCCATCCCGCCATGCCCGGCCCCTGCCGCCAGATCGGCGTAGCGTTTCCATAGCGG
+GTGATCGTATTTCGCAAACCAGCCCTCGGCAGGCTCCCAGCGGTGCGGCTGTGGGCTCTTGCCCTCCAGA
+TAGATCGACTTGTTGACGTCCATCCACAGCCCCTCGGTGCCTTGCACCCGAAAGCCGAGAGAATAGGGGC
+GCGGCAGCGAGGTGTCGTGGCACAGCATGATCGTTTCACCATTAGTGCAGCCGATCATGGTGTTGACCAC
+ATCACCCAGTGCGAATTTCACCTCGGCGTTGGGATGATCGGCAGAGCCGTTCTTGACGACATAATCATGC
+AGCCCGCGCGCCTTACAGCCGAAGCCGCCAGCGCCCGCTTCGCCCGGCAACGCGACCTTCAGGGTGCGGG
+TCTGCGGCGGGTAGCACACGCCGGCATCGGCGCAGCCCTGGTACTTCACGGTCAGGGTGGTCGCGCTCGC
+GCCGGCCGCGGGCGTGCCGGTGAGGGTGCCGAGCAATTCCTTGCGGTAGGTTTCGACGTCGCCGAAGAAT
+TCGTCGCGGTAGGCCTTGCCCTTCGGCAGCGCCATGGTCGCGCCGGTGAAGGCGGCATCGGCCTTGACCG
+AGGTGCGGTGCCGGTACAGGTAATAGCCGTCGGCGATCCGCCAGCGCACCTCGATGCGGTCCGGCGCGGT
+GGCCTGCGCGGACAGGACGAAGACCTCGTCGACCGGCGGCAGTTCGAAGTCCTGGGCGACGGCCGAGGTC
+GCGGGCAGCGCAAGCAGCAGGGCGAGCCCGGCCAGCCAGCGGCGCAGGCGGATCGTGGATGCGGTCATTG
+GCTCAGTTTACCGGTCGGCTCTCGGCGGCCAGCCATTGCAGGTATTCGGGCAGGCCGGACGCGGCTTCGA
+CCGCGAGCAGCTCCGGGAGTTCGTAGGGATATAGTATTTTATTAAATTCTTATGGGAAATGACGAATGTT
+AAATTATCTTAAGAGCTTTAATAATATCAATACTTATTTGATTTTATCGATAATTCTGCTGTTAATCATA
+ATATCTCTAGATTATTTCTAAACTGAATGAATGTTTATAATGAGTGATTCATATTGCTATTGAAATCGCC
+TTCTCACTTTGAAAGAAGGCGAGGATGAGGGACTTTTATGTTGAATTATCATTTTAAAAATGCCTTATAA
+AAGAAGCTTAATGTGTTTTCTTATATAGGTTTAAACATAATTGTTGTATATCTTAAATCCAATTGATCTT
+AAAATTTTCCTTTATTTTTTGTTATGAGTGCGAGAAAATTGTCAAAAAGGTCAATCAGACTGGGCGTTAA
+TTTGTTTTGCATACTTTTTCCTATATCGAATTAAAGTCATATAACTAACACCATAATCTTTAGCTATTTG
+AGTGAAAGGGTATGAATCGTCCTTATTTTTAAGGGTATGAATTAACTCTTTTAGTTTTTCTTCTGTAATC
+GCAGGCGATCTTCCCTTGTATTTACCTTTCTTTTTTTTAGCTAATTTAATTCCCTCTGCTTGATTCTCAC
+TAATAATACCCCTTTCAAGTTCAGCTACAGCGCCTAATACATGGAGTTGAAACTTATCGAACTTGTCATC
+TGAATTGGGGGTAAAGTTCAGGTTATTTTTGACAATATGAACAGACACTCCTTTTTTATTTAGCTTTTGA
+ACAATGGTTACAAGGTCAATCAAGCTACGTGCCAATCTAAAAACATCATGAGCGTACACAATGTCCCCAC
+TACGGACATAATCGAACATTTCCTGAAGTGCAGGGCGTTTGGCAGTCTTTCCGCTAAAATGATCAATAAA
+AGTTTTATCTAGCTCAAAGGGTAGATCATGGAGCTGTCTTTCAGGGTTTTGGTCTTTAGTGGATACACGG
+ATATACCCCACTCTTTGAAAGGGTGTGTTTTTAATTTGATCTTCAATATCTAAATTTTCTTTTTCCATAA
+CCAGTATAACAAAATTAGATAACCTCAATGTTATATCACATTAGATTAACAAAACAACCCTATTGTTATA
+GGGTTTTTAGGGTGTATTATTATATAACAATAGGGTATACCCTATTGTTATATATCTTCAGGTATAAGGA
+AAAATAACGATGATTAATTTTAATGATCTAAGCGAATCTGAATTATTAAGGATTGCACAGACTGGCATAT
+CAAACCGTATAGGATTGCGTACTTCAGGACATTG
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outdir/reference_plasmid.gbk	Tue Nov 12 22:47:36 2019 -0500
@@ -0,0 +1,214 @@
+LOCUS       JQ739157                6544 bp    DNA     circular BCT 26-JUL-2016
+DEFINITION  Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete
+            sequence.
+ACCESSION   JQ739157
+VERSION     JQ739157.2
+KEYWORDS    .
+SOURCE      Acinetobacter pittii
+  ORGANISM  Acinetobacter pittii
+            Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
+            Moraxellaceae; Acinetobacter; Acinetobacter calcoaceticus/baumannii
+            complex.
+REFERENCE   1  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Epidemiological characteristics and genetic structure of blaNDM-1
+            in non-baumannii Acinetobacter spp. in China
+  JOURNAL   J. Antimicrob. Chemother. 67 (9), 2114-2122 (2012)
+   PUBMED   22604448
+REFERENCE   2  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (05-MAR-2012) Department of Infectious Diseases, Sir Run
+            Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
+            University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
+REFERENCE   3  (bases 1 to 6544)
+  AUTHORS   Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (12-MAY-2014) Department of Infectious Diseases, Sir Run
+            Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang
+            University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China
+  REMARK    Sequence update by submitter
+COMMENT     On May 12, 2014 this sequence version replaced JQ739157.1.
+FEATURES             Location/Qualifiers
+     source          1..6544
+                     /organism="Acinetobacter pittii"
+                     /mol_type="genomic DNA"
+                     /strain="ABCA95"
+                     /db_xref="taxon:48296"
+                     /plasmid="pABCA95"
+     gene            375..1031
+                     /gene="aphA6"
+     misc_feature    375..1031
+                     /gene="aphA6"
+                     /note="similar to aphA6; aminoglycoside
+                     3'-phosphotransferase; 5' end of gene is missing"
+     mobile_element  1129..2215
+                     /mobile_element_type="insertion sequence:ISAba125"
+     repeat_region   1138..1154
+                     /note="IRL"
+                     /rpt_type=inverted
+     CDS             1186..2211
+                     /codon_start=1
+                     /transl_table=11
+                     /product="Transposase"
+                     /protein_id="AFK73837.1"
+                     /translation="MEYIKLSYHHLNFEDRTALMLESRKEGFSARKFAELIKRHPSTI
+                     YRELKRNSINDVYQARYASDNTFARRRRGHRKLKIDSILWKFIVEAIRCLWSPQQIAK
+                     RLKTFPDLDQTMNVSHTTIYSTIRALPKGELKKDLLSCLRHENKKRKANGEPKKDSIL
+                     QDIKTIHERPAEVQERKIPGHWEADLIKGKDNKSSIATLIERNTRLCILATLPDAKAE
+                     SVRKALTEALKYLPAELRKTLTYDRGREMSEHKILEEDLGIDVYFCDPHSPWQKGTCE
+                     NMNGLIRQYLPKGIDLNQADQHYLNQVAMSLNTRPRKALDWLTPLEKFAQLVDYHMAF
+                     ETVAPHV"
+     repeat_region   2190..2206
+                     /note="IRL"
+                     /rpt_type=inverted
+     gene            2312..3124
+                     /gene="blaNDM-1"
+     CDS             2312..3124
+                     /gene="blaNDM-1"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="metallo-beta-lactamase"
+                     /protein_id="AFK73838.1"
+                     /translation="MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQ
+                     RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQIL
+                     NWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHS
+                     LTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSL
+                     GNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"
+     gene            3128..3493
+                     /gene="bleo"
+     CDS             3128..3493
+                     /gene="bleo"
+                     /note="involved in resistance to bleomycin"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="bleomycin resistance protein"
+                     /protein_id="AFK73839.1"
+                     /translation="MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQ
+                     LEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLR
+                     IGYLIDPDCTLVRLIQNPD"
+     gene            3498..4133
+                     /gene="trpF"
+     misc_feature    3498..4133
+                     /gene="trpF"
+                     /note="similar to TrpF; phosphoribosyl anthranilate
+                     isomerase; 3' end not present"
+     gene            complement(4150..4830)
+                     /gene="tat"
+     misc_feature    complement(4150..4830)
+                     /gene="tat"
+                     /note="similar to TAT; twin-arginine translocation pathway
+                     signal sequence protein; 5' end of gene is missing."
+ORIGIN      
+        1 aagcttatag cagtgtcaca gatgcgaaaa agcaattaag tgcatatttt gagttttata
+       61 atttgaaacg acctcattcg agtctagaca aaatgacacc aaatgagttt tactatgatc
+      121 agctacccca acaaaacaag gtggcttaac tagagcggaa tatcacttat aaatacgctt
+      181 ttagttgttc aaacaagtgg gaccacctct ctcgcatttg cggggttttt aatgctgaat
+      241 aaaaggaaaa cttgatggaa ttgcccaata ttattcaaca atttattgga aacagcgttt
+      301 tagagccaaa taaaattggt cagtcgccat cggatgttta ttcttttaat cgaaataatg
+      361 aaactttttt tcttaagcga tctagcactt tatatacaga gaccacatac agtgtctctc
+      421 gcgaagcgaa aatgttgagt tggctctctg agaaattaaa ggtgcctgaa ctcatcatga
+      481 cttttcagga tgagcagttt gaattaatga tcactaaagc gatcaatgca aaaccaattt
+      541 cagcgctttt tttaacagac caagaattgc ttgctatcta taaggaggca ctcaatctgt
+      601 taaattcagt tgctattatt gattgtccat ttatttcaaa cattgatcat cggttaaaag
+      661 agtcaaaatt ttttattgat aaccaactcc ttgacgatat agatcaagat gattttgacg
+      721 ctgaattatg gggagaccat agaacttacc taagtctatg gaatgagtta actgagactc
+      781 gtgttgaaga aagattggtt ttttctcatg gcgatatcac ggatagtaat atttttatag
+      841 ataaattcaa tgaaatttac tttttagatc ttggccgtgc tgggttagct gatgaatttg
+      901 tagatatatc ctttgttgaa cgttgcctaa gagaggatgc ctcggaggaa actgctaaaa
+      961 tatttttaaa gcatttaaaa aatgatagac ctgacaaaag gaattatttt ttaaaacttg
+     1021 atgaattgaa ttgattctaa gcattatcta aaaatactta attgtctttt aacgtcgcta
+     1081 aattttaaat aaataagtga agagtgttag tggagccact gatttaaagt tggcagagta
+     1141 aaacttgaag tgcgacataa accacctaat taatttaaag ggtttatgga gtatataaaa
+     1201 ttgtcatacc atcatcttaa ctttgaagat cgtactgcat taatgcttga gtcaagaaaa
+     1261 gaaggctttt cagccagaaa atttgctgaa ctcattaaaa gacatcctag tacgatctat
+     1321 cgtgagctta aaagaaatag catcaatgac gtttatcaag ctcgatatgc ttctgataac
+     1381 accttcgcta gacgtagacg tggtcacaga aaactcaaaa tcgattcaat cctctggaaa
+     1441 tttattgttg aagcgatccg ttgtttatgg tctcctcagc aaatagcaaa gcgtttaaag
+     1501 acatttcctg atttggatca aacaatgaat gtaagccata caacgattta ttcaacgata
+     1561 cgagcattac caaagggtga gttgaaaaaa gacttattat cctgtctacg tcatgaaaat
+     1621 aaaaagcgaa aagctaacgg tgaacctaaa aaagattcta tattacagga tattaaaact
+     1681 attcatgagc gcccagccga agttcaagaa agaaaaatac cgggtcattg ggaagctgat
+     1741 ttaattaaag gtaaagacaa taaaagttcg atagcaacac ttattgaacg aaatacacgg
+     1801 ctctgtatct tggcaacatt acctgatgca aaggcagaat cagtgcgcaa ggctttaact
+     1861 gaagctctga aatatttacc tgcagaactg cgtaaaacgt tgacctatga ccgtggacgt
+     1921 gagatgtcag aacataaaat actcgaagaa gatttaggca tagatgtata tttctgtgac
+     1981 ccacattcac cctggcaaaa aggcacatgc gaaaatatga atggtttaat taggcaatat
+     2041 ttacctaaag ggattgattt aaatcaggca gatcagcatt atttaaatca agttgccatg
+     2101 tcactgaata ctcgtcctag aaaggcgtta gattggctta caccattaga gaaatttgct
+     2161 cagcttgttg attatcatat ggcttttgaa actgtcgcac ctcatgtttg aattcgcccc
+     2221 atatttttgc tacagtgaac caaattaaga tcatctattt actaggcctc gcatttgcgg
+     2281 ggtttttaat gctgaataaa aggaaaactt gatggaattg cccaatatta tgcacccggt
+     2341 cgcgaagctg agcaccgcat tagccgctgc attgatgctg agcgggtgca tgcccggtga
+     2401 aatccgcccg acgattggcc agcaaatgga aactggcgac caacggtttg gcgatctggt
+     2461 tttccgccag ctcgcaccga atgtctggca gcacacttcc tatctcgaca tgccgggttt
+     2521 cggggcagtc gcttccaacg gtttgatcgt cagggatggc ggccgcgtgc tggtggtcga
+     2581 taccgcctgg accgatgacc agaccgccca gatcctcaac tggatcaagc aggagatcaa
+     2641 cctgccggtc gcgctggcgg tggtgactca cgcgcatcag gacaagatgg gcggtatgga
+     2701 cgcgctgcat gcggcgggga ttgcgactta tgccaatgcg ttgtcgaacc agcttgcccc
+     2761 gcaagagggg atggttgcgg cgcaacacag cctgactttc gccgccaatg gctgggtcga
+     2821 accagcaacc gcgcccaact ttggcccgct caaggtattt taccccggcc ccggccacac
+     2881 cagtgacaat atcaccgttg ggatcgacgg caccgacatc gcttttggtg gctgcctgat
+     2941 caaggacagc aaggccaagt cgctcggcaa tctcggtgat gccgacactg agcactacgc
+     3001 cgcgtcagcg cgcgcgtttg gtgcggcgtt ccccaaggcc agcatgatcg tgatgagcca
+     3061 ttccgccccc gatagccgcg ccgcaatcac tcatacggcc cgcatggccg acaagctgcg
+     3121 ctgagccatg gctgaccacg tcacccccaa tctgccatcg cgcgatttcg atgtgacaga
+     3181 ggcgttttat gcgaagctgg gctttgcgac gagttggaag gatcgcggct ggatgatcct
+     3241 gcagcgcggc ggtttgcagc tcgaattctt cccctatcct gacctcgacc cagctacgag
+     3301 ctcgttcggc tgttgcctgc ggttggatga tctcgatgcc atggtggcat tggtgaacgc
+     3361 ggcgggagcc gaggaaaaaa gcaccggctg gccgcgcttc aaagctccgc aactggaggc
+     3421 gagcggcctg aggatcggct acctgatcga tcccgactgc acgctggtgc ggctgatcca
+     3481 gaaccccgac tgaccgcatg cccgcgaaaa tcaagatttg cgggatcagc acacccgagg
+     3541 cgctcgatgc gaccatcgcg gcgcgggcgg actatgccgg gttggtgttc tatccagcgt
+     3601 cgccccgtgc ggttacgtcg aatgtcgcgg gcgctttgac atcgcgcgca gctggccaga
+     3661 tcgccatggt cggtttgttc gtcgatgcgg atgatgctgt catcgccgac gcactggtgg
+     3721 cagccaagct gaacgcgctg cagctgcacg gttcggaatc gcccgaacgc gtggcccagt
+     3781 tgcgcgcgcg gtttggcaag ccggtgtgga aggcgctgcc cgtcgccagc gccagcgatg
+     3841 tcgcacgcgc cgcagcctat gccggggcgg cggacttgat cttgttcgac gccaagaccc
+     3901 ccaaaggcgc gctgcccggc ggcatggggt tggcgttcga ctggtcgctg ctggccggat
+     3961 atcgcggtgc cttgccgtgg gggctggcag gcgggctaaa tccgacgaat gttgccgagg
+     4021 cgattgcgcg caccggagcg ccgctggtcg atacctccag cggcgtcgaa agcgcgccgg
+     4081 gcgtcaagga taccgacaag attaccaatt tcgcctttgc ggtgcgcttg gcctaaatcg
+     4141 cgtcgatcaa taggcgtcgt tcagcgcaaa gatcggcttg cgggtgcgcc actgccctcg
+     4201 ggtgaagtcg ggaaaatcta acgtgcgatt gccctcagca atcgattgtt ccgacagagg
+     4261 cgtgatcgcg ctccaggcca gcgcgtcgta aatgtcgatt ggcatcgggg ccttggcctt
+     4321 cagcgcctcg acaaaagcgt ggatcacgaa ccagtccatc ccgccatgcc cggcccctgc
+     4381 cgccagatcg gcgtagcgtt tccatagcgg gtgatcgtat ttcgcaaacc agccctcggc
+     4441 aggctcccag cggtgcggct gtgggctctt gccctccaga tagatcgact tgttgacgtc
+     4501 catccacagc ccctcggtgc cttgcacccg aaagccgaga gaataggggc gcggcagcga
+     4561 ggtgtcgtgg cacagcatga tcgtttcacc attagtgcag ccgatcatgg tgttgaccac
+     4621 atcacccagt gcgaatttca cctcggcgtt gggatgatcg gcagagccgt tcttgacgac
+     4681 ataatcatgc agcccgcgcg ccttacagcc gaagccgcca gcgcccgctt cgcccggcaa
+     4741 cgcgaccttc agggtgcggg tctgcggcgg gtagcacacg ccggcatcgg cgcagccctg
+     4801 gtacttcacg gtcagggtgg tcgcgctcgc gccggccgcg ggcgtgccgg tgagggtgcc
+     4861 gagcaattcc ttgcggtagg tttcgacgtc gccgaagaat tcgtcgcggt aggccttgcc
+     4921 cttcggcagc gccatggtcg cgccggtgaa ggcggcatcg gccttgaccg aggtgcggtg
+     4981 ccggtacagg taatagccgt cggcgatccg ccagcgcacc tcgatgcggt ccggcgcggt
+     5041 ggcctgcgcg gacaggacga agacctcgtc gaccggcggc agttcgaagt cctgggcgac
+     5101 ggccgaggtc gcgggcagcg caagcagcag ggcgagcccg gccagccagc ggcgcaggcg
+     5161 gatcgtggat gcggtcattg gctcagttta ccggtcggct ctcggcggcc agccattgca
+     5221 ggtattcggg caggccggac gcggcttcga ccgcgagcag ctccgggagt tcgtagggat
+     5281 atagtatttt attaaattct tatgggaaat gacgaatgtt aaattatctt aagagcttta
+     5341 ataatatcaa tacttatttg attttatcga taattctgct gttaatcata atatctctag
+     5401 attatttcta aactgaatga atgtttataa tgagtgattc atattgctat tgaaatcgcc
+     5461 ttctcacttt gaaagaaggc gaggatgagg gacttttatg ttgaattatc attttaaaaa
+     5521 tgccttataa aagaagctta atgtgttttc ttatataggt ttaaacataa ttgttgtata
+     5581 tcttaaatcc aattgatctt aaaattttcc tttatttttt gttatgagtg cgagaaaatt
+     5641 gtcaaaaagg tcaatcagac tgggcgttaa tttgttttgc atactttttc ctatatcgaa
+     5701 ttaaagtcat ataactaaca ccataatctt tagctatttg agtgaaaggg tatgaatcgt
+     5761 ccttattttt aagggtatga attaactctt ttagtttttc ttctgtaatc gcaggcgatc
+     5821 ttcccttgta tttacctttc ttttttttag ctaatttaat tccctctgct tgattctcac
+     5881 taataatacc cctttcaagt tcagctacag cgcctaatac atggagttga aacttatcga
+     5941 acttgtcatc tgaattgggg gtaaagttca ggttattttt gacaatatga acagacactc
+     6001 cttttttatt tagcttttga acaatggtta caaggtcaat caagctacgt gccaatctaa
+     6061 aaacatcatg agcgtacaca atgtccccac tacggacata atcgaacatt tcctgaagtg
+     6121 cagggcgttt ggcagtcttt ccgctaaaat gatcaataaa agttttatct agctcaaagg
+     6181 gtagatcatg gagctgtctt tcagggtttt ggtctttagt ggatacacgg atatacccca
+     6241 ctctttgaaa gggtgtgttt ttaatttgat cttcaatatc taaattttct ttttccataa
+     6301 ccagtataac aaaattagat aacctcaatg ttatatcaca ttagattaac aaaacaaccc
+     6361 tattgttata gggtttttag ggtgtattat tatataacaa tagggtatac cctattgtta
+     6421 tatatcttca ggtataagga aaaataacga tgattaattt taatgatcta agcgaatctg
+     6481 aattattaag gattgcacag actggcatat caaaccgtat aggattgcgt acttcaggac
+     6541 attg
+//
+