# HG changeset patch
# User iuc
# Date 1477674199 14400
# Node ID 392255fa7ab985789df3f9e5951b097ae97c7dfd
# Parent  f5e44aad649808332473035a8253afaa7b0a830d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144

diff -r f5e44aad6498 -r 392255fa7ab9 COPYING
--- a/COPYING	Thu Oct 01 14:14:06 2015 -0400
+++ b/COPYING	Fri Oct 28 13:03:19 2016 -0400
@@ -1,9 +1,9 @@
-Copyright © 2015 The Genome Analysis Centre http://www.tgac.ac.uk/
+Copyright © 2013 Lionel Guy
 Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
-Copyright © 2013 Lionel Guy
+Copyright © 2015-2016 Earlham Institute http://earlham.ac.uk/
 Created by:
 Paolo Uva <paolo.uva@crs4.it>
-Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
+Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 Lionel Guy <lionel.guy@icm.uu.se>
 Philip Mabon <philipmabon@gmail.com>
 
diff -r f5e44aad6498 -r 392255fa7ab9 prokka.xml
--- a/prokka.xml	Thu Oct 01 14:14:06 2015 -0400
+++ b/prokka.xml	Fri Oct 28 13:03:19 2016 -0400
@@ -1,162 +1,204 @@
-<tool id="prokka" name="Prokka" version="1.11.0">
-  <description>prokaryotic genome annotation</description>
-  <requirements>
-    <requirement type="package" version="2.2.31">blast+</requirement>
-    <requirement type="package" version="3.1b2">hmmer</requirement>
-    <requirement type="package" version="1.2.36">aragorn</requirement>
-    <requirement type="package" version="2.60">prodigal</requirement>
-    <requirement type="package" version="24.3">tbl2asn</requirement>
-    <requirement type="package" version="20131122">gnu_parallel</requirement>
-    <requirement type="package" version="0.7">barrnap</requirement>
-    <requirement type="package" version="1.1">infernal</requirement>
-    <requirement type="package" version="0.1.6">minced</requirement>
-    <requirement type="package" version="1.11">prokka</requirement>
-  </requirements>
-  <version_command>prokka --version</version_command>
-  <command>
-    prokka
-    --cpus \${GALAXY_SLOTS:-8}
-    --quiet ## to avoid non-error messages written to stderr
-    --outdir outdir --prefix prokka ## used in outputs section
-    #if $locustag
-      --locustag "$locustag"
-    #end if
-    #if str($increment)
-      --increment $increment
-    #end if
-    --gffver $gffver
-    #if $compliant.compliant_select == "no"
-      #if $compliant.addgenes
+<tool id="prokka" name="Prokka" version="1.11.1">
+    <description>prokaryotic genome annotation</description>
+    <requirements>
+        <requirement type="package" version="1.11">prokka</requirement>
+    </requirements>
+    <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <version_command>prokka --version</version_command>
+    <command><![CDATA[
+prokka
+--cpus \${GALAXY_SLOTS:-8}
+--quiet ## to avoid non-error messages written to stderr
+--outdir outdir --prefix prokka ## used in outputs section
+#if $locustag
+    --locustag '$locustag'
+#end if
+#if str($increment)
+    --increment $increment
+#end if
+--gffver $gffver
+#if $compliant.compliant_select == "no"
+    #if $compliant.addgenes
         --addgenes
-      #end if
-      #if str($compliant.mincontig)
-        --mincontig $compliant.mincontig
-      #end if
-    #else
-      --compliant
-    #end if
-    #if $centre
-      --centre "$centre"
     #end if
-    #if $genus
-      --genus "$genus"
-    #end if
-    #if $species
-      --species "$species"
-    #end if
-    #if $strain
-      --strain "$strain"
-    #end if
-    #if $plasmid
-      --plasmid "$plasmid"
-    #end if
-    --kingdom $kingdom.kingdom_select
-    #if str($kingdom.gcode)
-      --gcode $kingdom.gcode
-    #end if
-    #if $usegenus
-      --usegenus
-    #end if
-    #if $proteins
-      --proteins $proteins
-    #end if
-    #if $metagenome
-      --metagenome
-    #end if
-    #if $fast
-      --fast
-    #end if
-    #if str($evalue)
-      --evalue $evalue
-    #end if
-    #if $rfam
-      --rfam
-    #end if
-    #if $norrna
-      --norrna
-    #end if
-    #if $notrna
-      --notrna
+    #if str($compliant.mincontig)
+        --mincontig $compliant.mincontig
     #end if
-    $input
-  </command>
-  <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-  <inputs>
-    <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
-    <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
-    <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
-      <validator type="in_range" min="1" />
-    </param>
-    <param name="gffver" type="select" label="GFF version (--gffver)">
-      <option value="3">3</option>
-      <option value="2">2</option>
-      <option value="1">1</option>
-    </param>
-    <conditional name="compliant">
-      <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
-        <option value="no">No</option>
-        <option value="yes">Yes</option>
-      </param>
-      <when value="no">
-        <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
-        <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
-      </when>
-      <when value="yes" />
-    </conditional>
-    <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
-    <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
-    <param name="species" type="text" value="" label="Species name (--species)" />
-    <param name="strain" type="text" value="" label="Strain name (--strain)" />
-    <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
-    <conditional name="kingdom">
-      <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
-        <option value="Archaea">Archaea</option>
-        <option value="Bacteria" selected="true">Bacteria</option>
-        <option value="Viruses">Viruses</option>
-      </param>
-      <when value="Archaea">
-        <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
-      </when>
-      <when value="Bacteria">
-        <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
-        <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
-          <option selected="true" value="none">N/A</option>
-          <option value="pos">positive</option>
-          <option value="neg">negative</option>
-        </param> SignalP is not FOSS -->
-      </when>
-      <when value="Viruses">
-        <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
-      </when>
-    </conditional>
-    <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
-    <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
-    <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
-    <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
-    <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
-      <validator type="in_range" min="0" />
-    </param>
-    <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
-    <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
-    <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
-  </inputs>
-  <outputs>
-    <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff" />
-    <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk" />
-    <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna" />
-    <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa" />
-    <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn" />
-    <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn" />
-    <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa" />
-    <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl" />
-    <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err" />
-    <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt" />
-    <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
-  </outputs>
-  <help>
+#else
+    --compliant
+#end if
+#if $centre
+    --centre '$centre'
+#end if
+#if $genus
+    --genus '$genus'
+#end if
+#if $species
+    --species '$species'
+#end if
+#if $strain
+    --strain '$strain'
+#end if
+#if $plasmid
+    --plasmid '$plasmid'
+#end if
+--kingdom $kingdom.kingdom_select
+#if str($kingdom.gcode)
+    --gcode $kingdom.gcode
+#end if
+#if $usegenus
+    --usegenus
+#end if
+#if $proteins
+    --proteins '$proteins'
+#end if
+#if $metagenome
+    --metagenome
+#end if
+#if $fast
+    --fast
+#end if
+#if str($evalue)
+    --evalue $evalue
+#end if
+#if $rfam
+    --rfam
+#end if
+#if $norrna
+    --norrna
+#end if
+#if $notrna
+    --notrna
+#end if
+$input
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
+        <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
+        <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
+        <param name="gffver" type="select" label="GFF version (--gffver)">
+            <option value="3">3</option>
+            <option value="2">2</option>
+            <option value="1">1</option>
+        </param>
+        <conditional name="compliant">
+            <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+                <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
+                <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
+            </when>
+            <when value="yes" />
+        </conditional>
+        <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
+        <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
+        <param name="species" type="text" value="" label="Species name (--species)" />
+        <param name="strain" type="text" value="" label="Strain name (--strain)" />
+        <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
+        <conditional name="kingdom">
+            <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
+                <option value="Archaea">Archaea</option>
+                <option value="Bacteria" selected="true">Bacteria</option>
+                <option value="Viruses">Viruses</option>
+            </param>
+            <when value="Archaea">
+                <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+            <when value="Bacteria">
+                <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+                <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
+                    <option selected="true" value="none">N/A</option>
+                    <option value="pos">positive</option>
+                    <option value="neg">negative</option>
+                </param> SignalP is not FOSS -->
+            </when>
+            <when value="Viruses">
+                <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+        </conditional>
+        <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
+        <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
+        <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
+        <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
+        <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
+        <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
+        <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
+        <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
+
+        <param name="outputs" type="select" multiple="true" label="Additional outputs">
+            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
+            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence</option>
+            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
+            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
+            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
+            <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
+            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
+            <option value="tbl" selected="True">Feature Table file</option>
+            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
+            <option value="txt" selected="True">Statistics relating to the annotated features found</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
+            <filter>'gff' in outputs</filter>
+        </data>
+        <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
+            <filter>'gbk' in outputs</filter>
+        </data>
+        <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
+            <filter>'fna' in outputs</filter>
+        </data>
+        <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
+            <filter>'faa' in outputs</filter>
+        </data>
+        <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
+             <filter>'ffn' in outputs</filter>
+        </data>
+        <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
+             <filter>'sqn' in outputs</filter>
+        </data>
+        <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
+             <filter>'fsa' in outputs</filter>
+        </data>
+        <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
+             <filter>'tbl' in outputs</filter>
+        </data>
+        <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
+             <filter>'err' in outputs</filter>
+        </data>
+        <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
+             <filter>'txt' in outputs</filter>
+        </data>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="phiX174.fasta" />
+            <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
+            <output name="out_gff" file="out.gff" />
+            <output name="out_gbk" file="out.gbk" lines_diff="14" />
+            <output name="out_fna" file="out.fna" />
+            <output name="out_faa" file="out.faa" />
+            <output name="out_ffn" file="out.ffn" />
+            <output name="out_sqn" file="out.sqn" lines_diff="84" />
+            <output name="out_fsa" file="out.fsa" />
+            <output name="out_tbl" file="out.tbl" />
+            <output name="out.err" file="out.err" />
+            <output name="out_txt" file="out.txt" />
+            <output name="out_log">
+                <assert_contents>
+                    <has_text text="Type 'prokka --citation' for more details." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
@@ -192,17 +234,18 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
+.. _Earlham Institute: http://earlham.ac.uk/
+.. _MIT license: https://opensource.org/licenses/MIT
 
 You can use this tool only if you agree to the license terms of: `Prokka`_.
 
 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btu135</citation>
-    <citation type="doi">10.1093/bioinformatics/btu153</citation>
-  </citations>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+        <citation type="doi">10.1093/bioinformatics/btu153</citation>
+    </citations>
 </tool>
diff -r f5e44aad6498 -r 392255fa7ab9 readme.rst
--- a/readme.rst	Thu Oct 01 14:14:06 2015 -0400
+++ b/readme.rst	Fri Oct 28 13:03:19 2016 -0400
@@ -17,13 +17,6 @@
 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
 
-Configuration
--------------
-
-prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
-
-If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
-
 Version history
 ---------------
 
@@ -41,8 +34,3 @@
 - prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param.
 - prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management.
 - prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6.
-
-Development
------------
-
-Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.err
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.err	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,46 @@
+>PROKKA_00001 hypothetical protein
+ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC
+ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC
+AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT
+GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC
+GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC
+GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG
+TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
+AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
+>PROKKA_00002 hypothetical protein
+ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT
+ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
+>PROKKA_00003 hypothetical protein
+ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT
+TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT
+GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT
+TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC
+TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG
+TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
+CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT
+CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG
+TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT
+CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG
+CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG
+TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+CGCGATTCAATCATGACTTCGTGA
+>PROKKA_00004 hypothetical protein
+TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT
+TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA
+ACAATACTGTAG
+>PROKKA_00005 hypothetical protein
+ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT
+TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG
+GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT
+GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT
+AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
+ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA
+AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA
+AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA
+GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT
+AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT
+ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT
+GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC
+GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.faa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.faa	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,20 @@
+>PROKKA_00001 hypothetical protein
+MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY
+GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL
+FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM
+>PROKKA_00002 hypothetical protein
+MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF
+>PROKKA_00003 hypothetical protein
+MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY
+ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ
+FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL
+YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL
+QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS
+>PROKKA_00004 hypothetical protein
+MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL
+>PROKKA_00005 hypothetical protein
+MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG
+ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ
+NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV
+SAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKD
+GKADGIGSNLSRK
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.ffn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.ffn	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,46 @@
+>PROKKA_00001 hypothetical protein
+ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC
+ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC
+AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT
+GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC
+GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC
+GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG
+TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA
+AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA
+>PROKKA_00002 hypothetical protein
+ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT
+ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA
+>PROKKA_00003 hypothetical protein
+ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT
+TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT
+GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT
+TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC
+TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG
+TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG
+CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT
+CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG
+TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT
+CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG
+CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG
+TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT
+CGCGATTCAATCATGACTTCGTGA
+>PROKKA_00004 hypothetical protein
+TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT
+TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA
+ACAATACTGTAG
+>PROKKA_00005 hypothetical protein
+ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT
+TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG
+GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT
+GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT
+AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG
+ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA
+AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA
+AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA
+GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT
+AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT
+ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT
+GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC
+GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.fna	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,99 @@
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.fsa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.fsa	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,99 @@
+>contig1 [gcode=11] [organism=Genus species] [strain=strain]
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2 [gcode=11] [organism=Genus species] [strain=strain]
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3 [gcode=11] [organism=Genus species] [strain=strain]
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4 [gcode=11] [organism=Genus species] [strain=strain]
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5 [gcode=11] [organism=Genus species] [strain=strain]
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6 [gcode=11] [organism=Genus species] [strain=strain]
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7 [gcode=11] [organism=Genus species] [strain=strain]
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.gbk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.gbk	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,250 @@
+LOCUS       contig1                  350 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..350
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa
+       61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac
+      121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt
+      181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag
+      241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
+      301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc
+//
+LOCUS       contig2                  840 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..840
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             40..498
+                     /locus_tag="PROKKA_00001"
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI
+                     ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE
+                     FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"
+     CDS             498..614
+                     /locus_tag="PROKKA_00002"
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"
+ORIGIN      
+        1 tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa
+       61 tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg
+      121 gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac
+      181 cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga
+      241 taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat
+      301 cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt
+      361 attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta
+      421 cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt
+      481 gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc
+      541 cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg
+      601 gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata
+      661 ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc
+      721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga
+      781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta
+//
+LOCUS       contig3                  210 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..210
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 ctgtagacat ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta
+       61 agttcatgaa ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata
+      121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt
+      181 tgtttcaggg ttatttgaat atctataaca
+//
+LOCUS       contig4                 1260 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..1260
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             21..884
+                     /locus_tag="PROKKA_00003"
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQM
+                     TTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSN
+                     LWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEI
+                     QYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSY
+                     VSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRN
+                     LPTTRDSIMTS"
+ORIGIN      
+        1 actattttaa agcgccgtgg atgcctgacc gtaccgaggc taaccctaat gagcttaatc
+       61 aagatgatgc tcgttatggt ttccgttgct gccatctcaa aaacatttgg actgctccgc
+      121 ttcctcctga gactgagctt tctcgccaaa tgacgacttc taccacatct attgacatta
+      181 tgggtctgca agctgcttat gctaatttgc atactgacca agaacgtgat tacttcatgc
+      241 agcgttacca tgatgttatt tcttcatttg gaggtaaaac ctcttatgac gctgacaacc
+      301 gtcctttact tgtcatgcgc tctaatctct gggcatctgg ctatgatgtt gatggaactg
+      361 accaaacgtc gttaggccag ttttctggtc gtgttcaaca gacctataaa cattctgtgc
+      421 cgcgtttctt tgttcctgag catggcacta tgtttactct tgcgcttgtt cgttttccgc
+      481 ctactgcgac taaagagatt cagtacctta acgctaaagg tgctttgact tataccgata
+      541 ttgctggcga ccctgttttg tatggcaact tgccgccgcg tgaaatttct atgaaggatg
+      601 ttttccgttc tggtgattcg tctaagaagt ttaagattgc tgagggtcag tggtatcgtt
+      661 atgcgccttc gtatgtttct cctgcttatc accttcttga aggcttccca ttcattcagg
+      721 aaccgccttc tggtgatttg caagaacgcg tacttattcg ccaccatgat tatgaccagt
+      781 gtttccagtc cgttcagttg ttgcagtgga atagtcaggt taaatttaat gtgaccgttt
+      841 atcgcaatct gccgaccact cgcgattcaa tcatgacttc gtgataaaag attgagtgtg
+      901 aggttataac gccgaagcgg taaaaatttt aatttttgcc gctgaggggt tgaccaagcg
+      961 aagcgcggta ggttttctgc ttaggagttt aatcatgttt cagactttta tttctcgcca
+     1021 taattcaaac tttttttctg ataagctggt tctcacttct gttactccag cttcttcggc
+     1081 acctgtttta cagacaccta aagctacatc gtcaacgtta tattttgata gtttgacggt
+     1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc
+     1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc
+//
+LOCUS       contig5                  490 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..490
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             275..406
+                     /locus_tag="PROKKA_00004"
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL"
+ORIGIN      
+        1 ctgtttggtt cgctttgagt cttcttcggt tccgactacc ctcccgactg cctatgatgt
+       61 ttatcctttg aatggtcgcc atgatggtgg ttattatacc gtcaaggact gtgtgactat
+      121 tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt ggtttcatgg tttggtctaa
+      181 ctttaccgct actaaatgcc gcggattggt ttcgctgaat caggttatta aagagattat
+      241 ttgtctccag ccacttaagt gaggtgattt atgtttggtg ctattgctgg cggtattgct
+      301 tctgctcttg ctggtggcgc catgtctaaa ttgtttggag gcggtcaaaa agccgcctcc
+      361 ggtggcattc aaggtgatgt gcttgctacc gataacaata ctgtaggcat gggtgatgct
+      421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt
+      481 tttgtttctg
+//
+LOCUS       contig6                 1960 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..1960
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+     CDS             6..767
+                     /locus_tag="PROKKA_00005"
+                     /inference="ab initio prediction:Prodigal:2.60"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="hypothetical protein"
+                     /translation="MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRD
+                     YLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIA
+                     GIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQ
+                     AQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASG
+                     VVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"
+ORIGIN      
+        1 gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg
+       61 ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag
+      121 gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg
+      181 ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc
+      241 ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa
+      301 aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg
+      361 cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta
+      421 tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta
+      481 ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca
+      541 aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt
+      601 ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg
+      661 tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga
+      721 aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga
+      781 caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt
+      841 cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta
+      901 aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc
+      961 ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg
+     1021 gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc
+     1081 gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg
+     1141 tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat
+     1201 ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc
+     1261 ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt
+     1321 gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt
+     1381 tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca
+     1441 cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt
+     1501 ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg
+     1561 ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt
+     1621 tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc
+     1681 gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca
+     1741 gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc
+     1801 ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg
+     1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta
+     1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact
+//
+LOCUS       contig7                  276 bp    DNA     linear       11-OCT-2016
+DEFINITION  Genus species strain strain.
+ACCESSION   
+VERSION
+KEYWORDS    .
+SOURCE      Genus species
+  ORGANISM  Genus species
+            Unclassified.
+COMMENT     Annotated using prokka 1.11 from http://www.vicbioinformatics.com.
+FEATURES             Location/Qualifiers
+     source          1..276
+                     /organism="Genus species"
+                     /mol_type="genomic DNA"
+                     /strain="strain"
+ORIGIN      
+        1 tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat
+       61 gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc
+      121 gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt
+      181 tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg
+      241 cgcttcgata aaaatgattg gcgtatccaa cctgca
+//
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.gff	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,113 @@
+##gff-version 3
+##sequence-region contig1 1 350
+##sequence-region contig2 1 840
+##sequence-region contig3 1 210
+##sequence-region contig4 1 1260
+##sequence-region contig5 1 490
+##sequence-region contig6 1 1960
+##sequence-region contig7 1 276
+contig2	Prodigal:2.60	CDS	40	498	.	+	0	ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00001;product=hypothetical protein
+contig2	Prodigal:2.60	CDS	498	614	.	+	0	ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00002;product=hypothetical protein
+contig4	Prodigal:2.60	CDS	21	884	.	+	0	ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00003;product=hypothetical protein
+contig5	Prodigal:2.60	CDS	275	406	.	+	0	ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00004;product=hypothetical protein
+contig6	Prodigal:2.60	CDS	6	767	.	+	0	ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00005;product=hypothetical protein
+##FASTA
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA
+AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC
+TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT
+GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG
+TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT
+CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG
+GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC
+CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA
+TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT
+CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT
+ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT
+GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC
+CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG
+GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA
+TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC
+AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA
+TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA
+AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA
+TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT
+TGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC
+AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC
+TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA
+TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC
+AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC
+GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG
+ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC
+CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA
+TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG
+TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT
+ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG
+AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT
+GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG
+AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG
+AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA
+TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC
+ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT
+TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC
+TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT
+TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT
+TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA
+CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT
+TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT
+TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC
+GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT
+TTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG
+CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG
+GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG
+CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC
+TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA
+AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG
+CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA
+CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA
+AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT
+CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG
+TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA
+AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA
+CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA
+AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC
+ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG
+GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC
+GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG
+TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT
+GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT
+GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT
+TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA
+CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT
+TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG
+CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT
+TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA
+GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC
+CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG
+TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA
+AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT
+GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC
+GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT
+TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG
+CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.sqn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.sqn	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,836 @@
+Seq-entry ::= set {
+  class genbank ,
+  seq-set {
+    seq {
+      id {
+        local
+          str "contig1" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 350 ,
+        seq-data
+          iupacna "GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGA
+AAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAG
+AAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAA
+AACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACA
+TTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC" } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig2" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 840 ,
+            seq-data
+              iupacna "TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTG
+AACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAG
+ATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT
+GCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTT
+ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATG
+GCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTA
+CTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGG
+CGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGG
+TCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCG
+TATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGT
+TATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGA
+CTCTA" } } ,
+        seq {
+          id {
+            local
+              str "contig2_1" } ,
+          descr {
+            title "hypothetical protein PROKKA_00001 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 152 ,
+            seq-data
+              ncbieaa "MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCV
+EACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTD
+VLTDAEENVRQKLRAEGVM" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 3 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 151 ,
+                        id
+                          local
+                            str "contig2_1" } } } } } } ,
+        seq {
+          id {
+            local
+              str "contig2_2" } ,
+          descr {
+            title "hypothetical protein PROKKA_00002 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 38 ,
+            seq-data
+              ncbieaa "MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 4 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 37 ,
+                        id
+                          local
+                            str "contig2_2" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 1 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig2_1" ,
+                location
+                  int {
+                    from 39 ,
+                    to 497 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig2" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.60" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "PROKKA_00001" } } } } ,
+              {
+                id
+                  local
+                    id 2 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig2_2" ,
+                location
+                  int {
+                    from 497 ,
+                    to 613 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig2" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.60" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "PROKKA_00002" } } } } } } } } ,
+    seq {
+      id {
+        local
+          str "contig3" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 210 ,
+        seq-data
+          iupacna "CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT
+AAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTT
+CTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA" } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig4" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 1260 ,
+            seq-data
+              iupacna "ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCT
+TAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGAC
+TGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA
+TACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGA
+CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAAC
+GTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGG
+CACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC
+TTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGT
+TTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTC
+TCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTAT
+TCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC
+CGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCC
+GAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTA
+ATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCA
+GCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCT
+GGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCT
+GATATTGCTTTTGATGCCGACCCTAAATTTTTTGC" } } ,
+        seq {
+          id {
+            local
+              str "contig4_1" } ,
+          descr {
+            title "hypothetical protein PROKKA_00003 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 287 ,
+            seq-data
+              ncbieaa "MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMG
+LQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSV
+PRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQW
+YRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 6 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 286 ,
+                        id
+                          local
+                            str "contig4_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 5 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig4_1" ,
+                location
+                  int {
+                    from 20 ,
+                    to 883 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig4" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.60" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "PROKKA_00003" } } } } } } } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig5" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 490 ,
+            seq-data
+              iupacna "CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTAT
+GATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCC
+CGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTT
+TCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTG
+GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCA
+TTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCT
+CTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG" } } ,
+        seq {
+          id {
+            local
+              str "contig5_1" } ,
+          descr {
+            title "hypothetical protein PROKKA_00004 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 43 ,
+            seq-data
+              ncbieaa "MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 8 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 42 ,
+                        id
+                          local
+                            str "contig5_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 7 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig5_1" ,
+                location
+                  int {
+                    from 274 ,
+                    to 405 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig5" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.60" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "PROKKA_00004" } } } } } } } } ,
+    set {
+      class nuc-prot ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      seq-set {
+        seq {
+          id {
+            local
+              str "contig6" } ,
+          descr {
+            molinfo {
+              biomol genomic } } ,
+          inst {
+            repr raw ,
+            mol dna ,
+            length 1960 ,
+            seq-data
+              iupacna "GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCAC
+TTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCG
+TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT
+TGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAA
+TGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAA
+TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCA
+ACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAAT
+CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTC
+TCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGG
+TATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTC
+TAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGT
+TCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGA
+GGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTT
+GGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGC
+TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCC
+CCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGT
+TACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAA
+AGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTT
+GATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATT
+AGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGG
+TCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT
+TCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAA
+TCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGA
+CGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGT
+TGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATG
+GAACAACTCACTAAAAACCAAGCTGTCGCTACT" } } ,
+        seq {
+          id {
+            local
+              str "contig6_1" } ,
+          descr {
+            title "hypothetical protein PROKKA_00005 [Genus species]" ,
+            molinfo {
+              biomol peptide ,
+              tech concept-trans } } ,
+          inst {
+            repr raw ,
+            mol aa ,
+            length 253 ,
+            seq-data
+              ncbieaa "MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNA
+WERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTA
+RVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNV
+VTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK" } ,
+          annot {
+            {
+              data
+                ftable {
+                  {
+                    id
+                      local
+                        id 10 ,
+                    data
+                      prot {
+                        name {
+                          "hypothetical protein" } } ,
+                    location
+                      int {
+                        from 0 ,
+                        to 252 ,
+                        id
+                          local
+                            str "contig6_1" } } } } } } } ,
+      annot {
+        {
+          data
+            ftable {
+              {
+                id
+                  local
+                    id 9 ,
+                data
+                  cdregion {
+                    frame one ,
+                    code {
+                      id 11 } } ,
+                product
+                  whole
+                    local
+                      str "contig6_1" ,
+                location
+                  int {
+                    from 5 ,
+                    to 766 ,
+                    strand plus ,
+                    id
+                      local
+                        str "contig6" } ,
+                qual {
+                  {
+                    qual "inference" ,
+                    val "ab initio prediction:Prodigal:2.60" } } ,
+                xref {
+                  {
+                    data
+                      gene {
+                        locus-tag "PROKKA_00005" } } } } } } } } ,
+    seq {
+      id {
+        local
+          str "contig7" } ,
+      descr {
+        source {
+          org {
+            taxname "Genus species" ,
+            orgname {
+              mod {
+                {
+                  subtype strain ,
+                  subname "strain" } } ,
+              gcode 11 } } } ,
+        molinfo {
+          biomol genomic } ,
+        comment "Annotated using prokka 1.11 from
+ http://www.vicbioinformatics.com" ,
+        user {
+          type
+            str "NcbiCleanup" ,
+          data {
+            {
+              label
+                str "method" ,
+              data
+                str "SeriousSeqEntryCleanup" } ,
+            {
+              label
+                str "version" ,
+              data
+                int 8 } ,
+            {
+              label
+                str "month" ,
+              data
+                int 10 } ,
+            {
+              label
+                str "day" ,
+              data
+                int 11 } ,
+            {
+              label
+                str "year" ,
+              data
+                int 2016 } } } ,
+        create-date
+          std {
+            year 2016 ,
+            month 10 ,
+            day 11 } } ,
+      inst {
+        repr raw ,
+        mol dna ,
+        length 276 ,
+        seq-data
+          iupacna "TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAA
+TGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGA
+AGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGA
+CGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA" } } } }
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.tbl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.tbl	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,27 @@
+>Feature contig1
+>Feature contig2
+40	498	CDS
+			inference	ab initio prediction:Prodigal:2.60
+			locus_tag	PROKKA_00001
+			product	hypothetical protein
+498	614	CDS
+			inference	ab initio prediction:Prodigal:2.60
+			locus_tag	PROKKA_00002
+			product	hypothetical protein
+>Feature contig3
+>Feature contig4
+21	884	CDS
+			inference	ab initio prediction:Prodigal:2.60
+			locus_tag	PROKKA_00003
+			product	hypothetical protein
+>Feature contig5
+275	406	CDS
+			inference	ab initio prediction:Prodigal:2.60
+			locus_tag	PROKKA_00004
+			product	hypothetical protein
+>Feature contig6
+6	767	CDS
+			inference	ab initio prediction:Prodigal:2.60
+			locus_tag	PROKKA_00005
+			product	hypothetical protein
+>Feature contig7
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.txt	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,4 @@
+organism: Genus species strain 
+contigs: 7
+bases: 5386
+CDS: 5
diff -r f5e44aad6498 -r 392255fa7ab9 test-data/phiX174.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta	Fri Oct 28 13:03:19 2016 -0400
@@ -0,0 +1,85 @@
+>contig1
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+>contig2
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+>contig3
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+>contig4
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+>contig5
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+>contig6
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+>contig7
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r f5e44aad6498 -r 392255fa7ab9 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Oct 01 14:14:06 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="blast+" version="2.2.31">
-    <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="hmmer" version="3.1b2">
-    <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="aragorn" version="1.2.36">
-    <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="prodigal" version="2.60">
-    <repository changeset_revision="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="tbl2asn" version="24.3">
-    <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="gnu_parallel" version="20131122">
-    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="barrnap" version="0.7">
-    <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="infernal" version="1.1">
-    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="minced" version="0.1.6">
-    <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="prokka" version="1.11">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.tar.gz</action>
-        <action type="shell_command">bin/prokka --setupdb</action>
-        <action type="move_directory_files">
-          <source_directory>.</source_directory>
-          <destination_directory>$INSTALL_DIR</destination_directory>
-        </action>
-        <action type="set_environment">
-          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-Warning: Prokka includes custom databases and is thus about a 360 MB download!
-
-Dependencies of Prokka which needs to be installed separately:
-- Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
-- Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ).
-    </readme>
-  </package>
-</tool_dependency>