Galaxy |

Changeset 4:0834c823d4b9 (2018-02-12)

Previous changeset 3:6fcbee531de6 (2017-09-29) Next changeset 5:81df4950d65b (2018-12-04)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87

modified:
quast.xml

added:
static/images/Align_view.png
static/images/contig_view_noR.png
test-data/contigs1.fna
test-data/contigs2.fna
test-data/genes.gff
test-data/reference.fna
test-data/test1_output.tsv
test-data/test2_output.tsv

removed:
test-data/NC000913.3_1-6650.fasta
test-data/NC000913.3_1-6650.gff
test-data/Quast_report.tex
test-data/Quast_report.tsv
test-data/Quast_report.txt
test-data/Quast_report_withref.tsv
test-data/Quast_report_withref_withgenes.tsv
test-data/contigs_1.fasta

diff -r 6fcbee531de6 -r 0834c823d4b9 quast.xml
--- a/quast.xml Fri Sep 29 05:51:26 2017 -0400
+++ b/quast.xml Mon Feb 12 09:05:20 2018 -0500

[

b'@@ -1,7 +1,7 @@\n-<tool id="quast" name="Quast" version="4.5" >\n+<tool id="quast" name="Quast" version="4.6.3" >\n <description>Genome assembly Quality</description>\n <requirements>\n- <requirement type="package" version="4.5">quast</requirement>\n+ <requirement type="package" version="4.6.3">quast</requirement>\n </requirements>\n <stdio>\n <regex match="ERROR! exception caught!"\n@@ -34,104 +34,194 @@\n #end if\n --min-contig $min_contig\n -l\n- #set names = \',\'.join( [\'"\'+ re.sub(\'[^\\w\\-_]\', \'_\', str( $x.input.element_identifier))+\'"\' for $x in $files ])\n+ #set names = \',\'.join( [\'"\'+ re.sub(\'[^\\w\\-_]\', \'_\', str( $x.element_identifier))+\'"\' for $x in $input ])\n \n $names\n --contig-thresholds $threshold_contig\n- #for $k in $files:\n- #if $k.type_file == "scaffold":\n- -s\n- #end if\n- $k.input\n+ #for $k in $input:\n+ $k \n #end for\n &&\n- mv outputdir/report.txt \'$quast_out\' &&\n mv outputdir/report.tsv \'$quast_tsv\' &&\n- mv outputdir/report.tex \'$quast_tex\' &&\n- mv outputdir/icarus_viewers/contig_size_viewer.html \'$icarus\' &&\n- mv outputdir/report.html \'$report_html\'\n+ ## The sed string below removes non-functional "Main menu" button from the viewer\n+ sed \'\\:<div class="btn btn-inverse" id="to_main_menu_button">:,\\:</div>:d\' outputdir/icarus_viewers/contig_size_viewer.html > \'$contig_size_viewer\' &&\n+ #if $input_ref:\n+ ## The sed string below removes non-functional "Main menu" button from the viewer\n+ sed \'\\:<div class="btn btn-inverse" id="to_main_menu_button">:,\\:</div>:d\' outputdir/icarus_viewers/alignment_viewer.html > \'$alignment_viewer\' &&\n+ #end if\n+ ## The sed string below removes non-functional link from the report page\n+ sed "\\:<div id=\'icarus-json\'>:,\\:</div>:d" outputdir/report.html > \'$report_html\' &&\n+ mv outputdir/report.pdf \'$report_pdf\' &&\n+ mv outputdir/contigs_reports/misassemblies_report.tsv \'$mis_ass_tsv\' &&\n+ mv outputdir/contigs_reports/unaligned_report.tsv \'$unalign_tsv\' &&\n+ mv outputdir/quast.log \'$log_txt\'\n ]]>\n </command>\n <inputs>\n- <repeat name="files" title="Input assembly files" min="1">\n- <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/>\n- <param name="type_file" type="select" label="Type of data">\n- <option value="contig">Contig</option>\n- <option value="scaffold">Scaffold</option>\n- </param>\n- </repeat>\n+ <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/>\n+ <param name="type_file" type="select" label="Type of data">\n+ <option value="contig">Contig</option>\n+ <option value="scaffold">Scaffold</option>\n+ </param>\n <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size"\n help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>\n- <param name="input_ref" type="data" format="fasta" label="Reference File" optional="True" argument="-R"\n+ <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True" argument="-R"\n help="Many metrics can\'t be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>\n- <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G"\n- help="File with gene positions in the reference genome. "/>\n- <param name="input_operon" type="data" format="txt" label="Operon Annotations" optional="True" argument="'..b'pbau.ru/manual.html#sec3.4>`_ (an HTML file)\n+ * `Alignment viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)\n+ * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format\n+ * Summary of `misassemblies <http://quast.bioinf.spbau.ru/manual.html#sec3.1.2>`_\n+ * Summary of `unaligned contigs <http://quast.bioinf.spbau.ru/manual.html#sec3.1.3>`_\n+ * Quast log (a file technical information about Quast tool execution)\n \n-- Input:\n- + The tool accepts assemblies and references in FASTA format.\n- + The tool accepts annotation and operon files in:\n- + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")\n- + the format used by NCBI for genes ("Summary (text)");\n- + four tab-separated columns: sequence name, gene/operon id, start position, end position\n+With the reference Quast produces a much more comprehensive set of results::\n \n-- Output:\n- + An assessment summary in plain text format\n- + An assessment summary in tabulation separated values format\n- + An assessment summary in LateX format\n- + An assessment summary in HTML format\n- + An HTML view of contig sizes wit Icarus\n+ Assembly pit_fna cef_fna car_fna\n+ # contigs (>= 0 bp) 100 91 94\n+ # contigs (>= 1000 bp) 62 58 61\n+ Total length (>= 0 bp) 6480635 6481216 6480271\n+ Total length (>= 1000 bp) 6466917 6468946 6467103\n+ # contigs 71 66 70\n+ Largest contig 848753 848766 662053\n+ Total length 6473173 6474698 6473810\n+ Reference length 6537648 6537648 6537648\n+ GC (%) 66.33 66.33 66.33\n+ Reference GC (%) 66.29 66.29 66.29\n+ N50 270269 289027 254671\n+ NG50 270269 289027 254671\n+ N75 136321 136321 146521\n+ NG75 136321 136321 136321\n+ L50 7 7 8\n+ LG50 7 7 8\n+ L75 15 15 16\n+ LG75 15 15 17\n+ # misassemblies 0 0 0\n+ # misassembled contigs 0 0 0\n+ Misassembled contigs length 0 0 0\n+ # local misassemblies 1 1 2\n+ # unaligned mis. contigs 0 0 0\n+ # unaligned contigs 0 + 0 0 + 0 0 + 0\n+ part part part\n+ Unaligned length 0 0 0\n+ Genome fraction (%) 99.015 99.038 99.025\n+ Duplication ratio 1.000 1.000 1.000\n+ # N\'s per 100 kbp 0.00 0.00 0.00\n+ # mismatches per 100 kbp 3.82 3.63 3.49\n+ # indels per 100 kbp 1.19 1.13 1.13\n+ Largest alignment 848753 848766 662053\n+ Total aligned length 6473163 6474660 6473792\n+ NA50 270269 289027 254671\n+ NGA50 270269 289027 254671\n+ NA75 136321 136321 146521\n+ NGA75 136321 136321 136321\n+ LA50 7 7 8\n+ LGA50 7 7 8\n+ LA75 15 15 16\n+ LGA75 15 15 17 \n \n+where, again, values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly. \n+\n+ Using reference also produces an **Alignment viewer**:\n+\n+.. image:: $PATH_TO_IMAGES/Align_view.png\n+ :width: 515\n+ :height: 395\n+\n+Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_).\n \n ]]>\n </help>\n'

diff -r 6fcbee531de6 -r 0834c823d4b9 static/images/Align_view.png

Binary file static/images/Align_view.png has changed

diff -r 6fcbee531de6 -r 0834c823d4b9 static/images/contig_view_noR.png

Binary file static/images/contig_view_noR.png has changed

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/NC000913.3_1-6650.fasta
--- a/test-data/NC000913.3_1-6650.fasta Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,112 +0,0 @@
->NC_000913.3:1-6650
-AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
-TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
-TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
-ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
-AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
-CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
-ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
-AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
-GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
-CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
-CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
-AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
-ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
-GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
-GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
-GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
-TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
-GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
-ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
-ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
-CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
-ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
-GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
-ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
-CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
-CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
-TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
-GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
-ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
-TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
-AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
-CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
-AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
-CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
-CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
-TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
-GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
-TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
-GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
-GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
-GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
-TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
-TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
-ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
-TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
-CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
-GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
-GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
-TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
-CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
-GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
-AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
-GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
-GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
-TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
-GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
-CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
-GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
-AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
-GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
-CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
-CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
-ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
-GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
-GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
-GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
-GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
-GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
-AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
-TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
-CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
-TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
-GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
-CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
-GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
-TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
-CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
-GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
-CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
-GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
-AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
-CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
-GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
-TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
-CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
-ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
-ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
-AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
-CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
-AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
-GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
-GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
-TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
-GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
-CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
-TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
-AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
-ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
-GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
-ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
-GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
-GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
-GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
-GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
-CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
-GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
-CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
-GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
-TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
-AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
-AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/NC000913.3_1-6650.gff
--- a/test-data/NC000913.3_1-6650.gff Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-##gff-version 3
-#!gff-spec-version 1.21
-#!processor NCBI annotwriter
-#!genome-build ASM584v2
-#!genome-build-accession NCBI_Assembly:GCF_000005845.2
-##sequence-region NC_000913.3 1 4641652
-##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
-NC_000913.3 RefSeq region 1 4641652 . + . ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
-NC_000913.3 RefSeq gene 190 255 . + . ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001
-NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
-NC_000913.3 RefSeq gene 337 2799 . + . ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002
-NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
-NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003
-NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
-NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004
-NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11
-NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005
-NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11
-NC_000913.3 RefSeq repeat_region 5565 5669 . + . ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region
-NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006
-NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11
-###

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/Quast_report.tex
--- a/test-data/Quast_report.tex Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,25 +0,0 @@
-\documentclass[12pt,a4paper]{article}
-\begin{document}
-\begin{table}[ht]
-\begin{center}
-\caption{All statistics are based on contigs of size $\geq$ 500 bp, unless otherwise noted (e.g., "\# contigs ($\geq$ 0 bp)" and "Total length ($\geq$ 0 bp)" include all contigs).}
-\begin{tabular}{|l*{1}{|r}|}
-\hline
-Assembly & contigs\_1\_fasta \\ \hline
-\# contigs ($\geq$ 0 bp) & 3 \\ \hline
-\# contigs ($\geq$ 1000 bp) & 3 \\ \hline
-Total length ($\geq$ 0 bp) & 6710 \\ \hline
-Total length ($\geq$ 1000 bp) & 6710 \\ \hline
-\# contigs & 3 \\ \hline
-Largest contig & 3980 \\ \hline
-Total length & 6710 \\ \hline
-GC (\%) & 51.28 \\ \hline
-N50 & 3980 \\ \hline
-N75 & 1610 \\ \hline
-L50 & 1 \\ \hline
-L75 & 2 \\ \hline
-\# N's per 100 kbp & 0.00 \\ \hline
-\end{tabular}
-\end{center}
-\end{table}
-\end{document}

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/Quast_report.tsv
--- a/test-data/Quast_report.tsv Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-Assembly contigs_1_fasta
-# contigs (>= 0 bp) 3
-# contigs (>= 1000 bp) 3
-Total length (>= 0 bp) 6710
-Total length (>= 1000 bp) 6710
-# contigs 3
-Largest contig 3980
-Total length 6710
-GC (%) 51.28
-N50 3980
-N75 1610
-L50 1
-L75 2
-# N's per 100 kbp 0.00

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/Quast_report.txt
--- a/test-data/Quast_report.txt Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,16 +0,0 @@
-All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
-
-Assembly                   contigs_1_fasta
-# contigs (>= 0 bp)        3
-# contigs (>= 1000 bp)     3
-Total length (>= 0 bp)     6710
-Total length (>= 1000 bp)  6710
-# contigs                  3
-Largest contig             3980
-Total length               6710
-GC (%)                     51.28
-N50                        3980
-N75                        1610
-L50                        1
-L75                        2
-# N's per 100 kbp          0.00

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/Quast_report_withref.tsv
--- a/test-data/Quast_report_withref.tsv Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,37 +0,0 @@
-Assembly contigs_1_fasta
-# contigs (>= 0 bp) 3
-# contigs (>= 1000 bp) 3
-Total length (>= 0 bp) 6710
-Total length (>= 1000 bp) 6710
-# contigs 3
-Largest contig 3980
-Total length 6710
-Reference length 6650
-GC (%) 51.28
-Reference GC (%) 52.00
-N50 3980
-NG50 3980
-N75 1610
-NG75 1610
-L50 1
-LG50 1
-L75 2
-LG75 2
-# misassemblies 0
-# misassembled contigs 0
-Misassembled contigs length 0
-# local misassemblies 0
-# unaligned mis. contigs 0
-# unaligned contigs 0 + 1 part
-Unaligned length 1950
-Genome fraction (%) 71.579
-Duplication ratio 1.000
-# N's per 100 kbp 0.00
-# mismatches per 100 kbp 0.00
-# indels per 100 kbp 0.00
-Largest alignment 2030
-Total aligned length 4760
-NA50 1610
-NGA50 1610
-LA50 2
-LGA50 2

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/Quast_report_withref_withgenes.tsv
--- a/test-data/Quast_report_withref_withgenes.tsv Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,38 +0,0 @@
-Assembly contigs_1_fasta
-# contigs (>= 0 bp) 3
-# contigs (>= 1000 bp) 3
-Total length (>= 0 bp) 6710
-Total length (>= 1000 bp) 6710
-# contigs 3
-Largest contig 3980
-Total length 6710
-Reference length 6650
-GC (%) 51.28
-Reference GC (%) 52.00
-N50 3980
-NG50 3980
-N75 1610
-NG75 1610
-L50 1
-LG50 1
-L75 2
-LG75 2
-# misassemblies 0
-# misassembled contigs 0
-Misassembled contigs length 0
-# local misassemblies 0
-# unaligned mis. contigs 0
-# unaligned contigs 0 + 1 part
-Unaligned length 1950
-Genome fraction (%) 71.579
-Duplication ratio 1.000
-# N's per 100 kbp 0.00
-# mismatches per 100 kbp 0.00
-# indels per 100 kbp 0.00
-# genes 3 + 3 part
-Largest alignment 2030
-Total aligned length 4760
-NA50 1610
-NGA50 1610
-LA50 2
-LGA50 2

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/contigs1.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs1.fna Mon Feb 12 09:05:20 2018 -0500

@@ -0,0 +1,99 @@
+>contig1
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
+>contig2
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG
+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
+>contig3
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
+ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
+TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
+TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
+CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
+TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
+AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
+CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
+TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
+CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
+ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
+ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
+GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA
+TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA
+AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC
+GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC
+AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC
+AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT
+TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
+TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC
+GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA
+TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG
+GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA
+GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA
+TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
+CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA
+AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC
+AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT
+TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT
+GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG
+CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC
+AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT
+TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA
+GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA
+AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC
+GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT
+ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA
+TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT
+CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT
+ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA
+TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA
+ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC
+TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA
+TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC
+CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG
+ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC
+CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG
+ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC
+AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC
+GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC
+ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG
+CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA
+CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAG

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/contigs2.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs2.fna Mon Feb 12 09:05:20 2018 -0500

@@ -0,0 +1,112 @@
+>NC_000913.3:1-6650
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
+TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
+CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
+GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
+CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
+CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
+AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
+ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
+GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
+GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
+TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
+GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
+ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
+ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
+CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
+GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
+ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
+CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
+CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
+TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
+GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
+TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
+CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
+AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
+CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
+CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
+GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
+TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
+GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
+GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
+GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
+TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
+ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
+TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
+CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
+GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
+GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
+TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
+GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
+AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
+GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
+GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
+TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
+GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
+GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
+AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
+GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
+CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
+CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
+ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
+GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
+GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
+GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
+GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
+GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
+AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
+TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
+CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
+TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
+GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
+CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
+GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
+TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
+CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
+CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
+GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
+AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
+CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
+GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
+TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
+ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
+ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
+AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
+CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
+AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
+GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
+TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
+GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
+CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
+TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
+AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
+ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
+ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
+GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
+GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
+GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
+GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
+CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
+CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
+GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
+TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
+AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
+AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/contigs_1.fasta
--- a/test-data/contigs_1.fasta Fri Sep 29 05:51:26 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,99 +0,0 @@
->contig1
-AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
-TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
-TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
-ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
-CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
-GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
-AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
-AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
-GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
-GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
-TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
-TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
-GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
-CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
-TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
-CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
->contig2
-ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
-GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
-TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
-GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
-AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
-CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
-TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
-GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
-TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
-CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
-AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
-GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
-TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG
-ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
-AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
-AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
-ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
-TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
-CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
-CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
-CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
-GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
-GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
->contig3
-GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
-ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
-TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
-TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
-CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
-TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
-CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
-AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
-CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
-TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
-CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
-ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
-GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
-ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
-GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA
-TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA
-AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC
-GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
-GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC
-AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC
-AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT
-TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
-TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC
-GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
-GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA
-TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG
-GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA
-GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA
-TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
-CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA
-AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC
-AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT
-TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT
-GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG
-CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC
-AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT
-TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA
-GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA
-AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC
-GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT
-ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA
-TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT
-CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT
-ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA
-TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA
-ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC
-TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA
-TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC
-CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG
-ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC
-CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG
-ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC
-AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC
-GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC
-ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG
-CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA
-CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAG

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/genes.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.gff Mon Feb 12 09:05:20 2018 -0500

@@ -0,0 +1,22 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM584v2
+#!genome-build-accession NCBI_Assembly:GCF_000005845.2
+##sequence-region NC_000913.3 1 4641652
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
+NC_000913.3 RefSeq region 1 4641652 . + . ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
+NC_000913.3 RefSeq gene 190 255 . + . ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001
+NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
+NC_000913.3 RefSeq gene 337 2799 . + . ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002
+NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
+NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003
+NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
+NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004
+NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11
+NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005
+NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11
+NC_000913.3 RefSeq repeat_region 5565 5669 . + . ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region
+NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006
+NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11
+###

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/reference.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fna Mon Feb 12 09:05:20 2018 -0500

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/test1_output.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_output.tsv Mon Feb 12 09:05:20 2018 -0500

@@ -0,0 +1,42 @@
+Assembly contigs2_fna contigs1_fna
+# contigs (>= 0 bp) 1 3
+# contigs (>= 1000 bp) 1 3
+Total length (>= 0 bp) 6650 6710
+Total length (>= 1000 bp) 6650 6710
+# contigs 1 3
+Largest contig 6650 3980
+Total length 6650 6710
+Reference length 6650 6650
+GC (%) 52.00 51.28
+Reference GC (%) 52.00 52.00
+N50 6650 3980
+NG50 6650 3980
+N75 6650 1610
+NG75 6650 1610
+L50 1 1
+LG50 1 1
+L75 1 2
+LG75 1 2
+# misassemblies 0 0
+# misassembled contigs 0 0
+Misassembled contigs length 0 0
+# local misassemblies 0 0
+# unaligned mis. contigs 0 0
+# unaligned contigs 0 + 0 part 0 + 1 part
+Unaligned length 0 1950
+Genome fraction (%) 100.000 71.579
+Duplication ratio 1.000 1.000
+# N's per 100 kbp 0.00 0.00
+# mismatches per 100 kbp 0.00 0.00
+# indels per 100 kbp 0.00 0.00
+# genes 6 + 0 part 3 + 3 part
+Largest alignment 6650 2030
+Total aligned length 6650 4760
+NA50 6650 1610
+NGA50 6650 1610
+NA75 6650 -
+NGA75 6650 -
+LA50 1 2
+LGA50 1 2
+LA75 1 -
+LGA75 1 -

diff -r 6fcbee531de6 -r 0834c823d4b9 test-data/test2_output.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_output.tsv Mon Feb 12 09:05:20 2018 -0500

@@ -0,0 +1,14 @@
+Assembly contigs2_fna contigs1_fna
+# contigs (>= 0 bp) 1 3
+# contigs (>= 1000 bp) 1 3
+Total length (>= 0 bp) 6650 6710
+Total length (>= 1000 bp) 6650 6710
+# contigs 1 3
+Largest contig 6650 3980
+Total length 6650 6710
+GC (%) 52.00 51.28
+N50 6650 3980
+N75 6650 1610
+L50 1 1
+L75 1 2
+# N's per 100 kbp 0.00 0.00