| Next changeset 1:0b967e0ceb18 (2019-10-17) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5" |
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added:
est-abundance.xml macros.xml test-data/NC_003198.1_1kb.fasta test-data/NC_003198.1_simulated_R1.fastq test-data/NC_003198.1_simulated_R2.fastq test-data/NC_003198.1_simulated_bracken_report.txt test-data/NC_003198.1_simulated_kraken_report.txt test-data/NC_011750.1_1kb.fasta test-data/NC_011750.1_simulated_R1.fastq test-data/NC_011750.1_simulated_R2.fastq test-data/NC_011750.1_simulated_bracken_report.txt test-data/NC_011750.1_simulated_kraken_report.txt test-data/bracken_databases.loc test-data/reproduce_test_data.sh test-data/test_db/database.kraken test-data/test_db/database100mers.kmer_distrib test-data/test_db/database100mers.kraken test-data/test_db/hash.k2d test-data/test_db/library/added/9C7DdW7GAD.fna test-data/test_db/library/added/9C7DdW7GAD.fna.masked test-data/test_db/library/added/cWk1IBlK73.fna test-data/test_db/library/added/cWk1IBlK73.fna.masked test-data/test_db/library/added/prelim_map.txt test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt test-data/test_db/opts.k2d test-data/test_db/seqid2taxid.map test-data/test_db/taxo.k2d tool-data/bracken_databases.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r b7b1c8bf7ae0 est-abundance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/est-abundance.xml Wed Oct 16 16:57:55 2019 -0400 |
| [ |
| @@ -0,0 +1,65 @@ +<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@VERSION@+galaxy0"> + <description>Bayesian Reestimation of Abundance with KrakEN</description> + <macros> + <import>macros.xml</import> + </macros> + <edam_topics> + <edam_topic>topic_3174</edam_topic> + <edam_topic>topic_3697</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2238</edam_operation> + </edam_operations> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + est_abundance.py + -i '$input' + -k '$kmer_distr.fields.path' + -l $level + -t $threshold + -o '$report' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Kraken report file" /> + <param label="Select a Kmer distribution" name="kmer_distr" type="select"> + <options from_data_table="bracken_databases"> + <validator message="No database is available" type="no_options" /> + </options> + </param> + <param name="level" type="select" label="Level" help="Level to push all reads to" > + <option value="S" selected="true">Species</option> + <option value="G">Genus</option> + <option value="F">Family</option> + <option value="O">Order</option> + <option value="C">Class</option> + <option value="P">Phylum</option> + <option value="D">Domain</option> + </param> + <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag" + help="Threshold for the minimum number of reads kraken must assign to a classification for that + classification to be considered in the final abundance estimation." /> + </inputs> + <outputs> + <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" /> + </outputs> + <tests> + <test> + <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> + <param name="level" value="S" /> + <param name="bracken_database" value="test_entry"/> + <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/> + </test> + <test> + <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/> + <param name="level" value="S" /> + <param name="bracken_database" value="test_entry"/> + <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/> + </test> + </tests> + <help> + <![CDATA[ + Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r b7b1c8bf7ae0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Oct 16 16:57:55 2019 -0400 |
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| @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">2.5</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bracken</requirement> + </requirements> + </xml> + <xml name="version"> + <version_command>echo @WRAPPER_VERSION@</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.7717/peerj-cs.104</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_1kb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_1kb.fasta Wed Oct 16 16:57:55 2019 -0400 |
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| @@ -0,0 +1,14 @@ +>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome +AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATATCGCCAGCAGC +ACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGGCGGGCAGATACTTTAACCAA +TATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACAACATCCATGAACCGCATCAGCACCACC +ACCATTACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG +CCCGCACCTGAACAGTGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAA +GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC +AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTGGCGATGATTG +AAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAACGTATTTTTTCTGACCTGCT +CGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCGAACAAGAATTC +GCTCAGATCAAACATGTTTTGCATGGTATCAGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGC +TGATTTGCCGTGGCGAAAAAATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGT +CACGGTGATCGATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG +GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCGGGCTTTACTG |
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| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_R1.fastq Wed Oct 16 16:57:55 2019 -0400 |
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| b"@@ -0,0 +1,180 @@\n+@NC_003198.1-90/1\n+AATAAAAATGACAGAGTTCACAACATCCATGAACCGCATCAGCACTACCACCATGACCACCATCACGATTACTACAGGTAACTCTGCGGGCGGACGCGTA\n++\n+@CCF1FFF2HHHF@29I)IJIHIGIJGJE?CHJJBJGJHGHFJJH#J>2G0IJI#EHD=JFDDACF#GCE=J#;FC>DEA5F##D0B>CD9##CAA>B5D\n+@NC_003198.1-88/1\n+TCATAACAGGGGAAATTTATTGAAATTAAATATATCGCCAGCAGCACATGAACAGGTTTCGGACTGTGATGAATTTAAAAAGTTATTGACTTCGGCGCTC\n++\n+CCCFDFFBDHDHHJF#2#<GJGJJA#JJEE#JJII;?IEGIIBAGGBGGDJCIJ#JJJI;=I6#CI=DDD#31;ABDC#>H#CDECCDB>DC##DAD##?\n+@NC_003198.1-86/1\n+GGCGATACGGCGAGTTGATTCCGCGATATCGACGGTAGATTCAAGGTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCCTGAGGCGAAGT\n++\n+@CCFFF?DCHCH+IJ#GIJHICHGHHJHGGEIJCIGJJJ?GJIGHHGJ=GDJII?<A;GHFJDE6#J'IG>?F#E>C>=EDCDAADCC#9?C#D#9D#>C\n+@NC_003198.1-84/1\n+CACAGAAAAAAGCCCGCACCTGAACAGTTCGGGCTTTTTTTTCGATCTGAGATCACGAGTTAACAAGCATGCGAGTGTTGAAGTACTGCAGAACATCAGT\n++\n+@CCFFFD<HDFHHJIJIJJJJFFJJJIF+JIGGDDJJIJJJFHIE#F#JFJHIBDH#J##HFD=IG#HA#G8C?FE@>F?DEHA(?#->#;#CD:CA>@D\n+@NC_003198.1-82/1\n+CCGGGCACTGACCCAGCAGGCTGATACCATGCAAAACATGTTTGATGTGAGCGAATTTTTGTTCGACAACCATTTTCAACCGTGCAACCCAGTATCCCGG\n++\n+CC@+DFDFHHGDHHIIIJGIFJIAJ#I7JIIHDJHIIJAFHIIG:?#I#GFCB4F=:#AJGIDJIJDDHFIBADGADH@EAD#DECD#C##>#A:D@D?,\n+@NC_003198.1-80/1\n+ATAATCGCGAGCGACATTTGTTCGCCGCGGCAAATCAGCGCGGCGTTGATGCTATCCGGGCACTGATCCAGCAGTCTGATAACATGCAAAAAATGTTTGA\n++\n+C@CDBFFD:F#HH#BBGJI!JIIIBJ!GHDFCI>IJIFAIIAHDBIGII?HIIBCJ?BAHFGJ>HE(CJ@2ECE!DBCB=D#FB@;@CCC<#<2>#D@AC\n+@NC_003198.1-78/1\n+CAGAAAAAAGCCCGCACCTGAACAGGGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCCAGAGTTGAAGTTCGGCGGTACATCAGTGG\n++\n+@7@FFFFDFFFHDJJJIBJIJGIIA#IJIJJ*JE#IJJJDBBJGJICHJ<BIGJ?HJIFEHEFGIEBHD@#FD#=ADC#CDA<8>BD5>@C#D:CDD#B>\n+@NC_003198.1-76/1\n+GCGAAAATTACCAACTCTCTGGTGGCGATTATTTAAAATACTATCGGCGGCCAGGATGCTTTGCCGACTATCAGCGGTGCCGAACATTTTTGCTCTGTCC\n++\n+?<BFF<E?HHHHHJJ##II#IJ;<JJA<J#IJ:7JJ@D#IJIBJGJJGGGH?EHB4FE@BEI@FI(D#BDG>:##C!H>CBEDDB#F#B2<##BCDC##,\n+@NC_003198.1-74/1\n+GAGGTTACAACCATGCGAGTGTTGTAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGCTATTATGGAACGCAATTCCAGCC\n++\n+B1C(F#FBHHHHHJJGJGIEJ@JH#G1AC>BJAJJJJJJJHJIGIIJI<DJ#GIFF>GHDHJ@IH5FFIEDCD@H=#E#=(#?CDD(#?DA#DCDBDB#C\n+@NC_003198.1-72/1\n+CGCAGAAAACGTTCTGCATTTGCCACGGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTCGCCTCTGGTCACAAAAAAAGCTCGCTCAG\n++\n+BCCFFFDFHHHH:BIEIIJEJHJECI#GJI+FEI?BFGJE@IJCJDHGJGIJ#F;?)?GIIH;8CABGH?###I?F=F@;A##BC<CCB>B>#CA@#D#D\n+@NC_003198.1-70/1\n+CCCGGCTGCGCGCTGGCAAGACCTGGGAGCAGGTCAGAAAAAATACGTTCGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGACAGTTTTTTCAA\n++\n+@CC?FFDFH#DFHJF@JEF1#IHID#IGJJDCG#EEJIJHI<JGJBHHGJIGG9.I:I>JED:JDD@B=;J#@HC93#ED#B;CC?@D#CCC#DBB>DEB\n+@NC_003198.1-68/1\n+AAGTTCGGCGGTACATCAGTGGTAAATGGAGAACGTTTTCTGCGTGTTCCCGATATCCTGGAAAGCAATTTCAGGCAAGGGCAGAGACCGAATTCACTTT\n++\n+CB:FFFADDHF;>IJIHJJHJI#JIIJJ#JCJGEIDJJICGJDIGCBJ#AFIIFHD#GC3DFJIIF.HCG#JFBD:DF3D#CCE##;#DC:#####D#D,\n+@NC_003198.1-66/1\n+TAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACTACATCCATGAACCGAATCAGCATGACCTCCCTTACCTCGATCACCATTAC\n++\n+@B@DFFFDD@HGBEHI#+JIJIGIJIJ?+CIGJJJIIDJJGEFHIJAIJ#CIGHDEA9GCC=H8#DHHGEF;#(FCI#?F#CDC>##C(CDBDCC##ADD\n+@NC_003198.1-64/1\n+CCAGCAGGCTGATACCATGCAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCACGCGGGATTTCCGGCAGCGCGCTGGC\n++\n+@8CFFFF@GHF+HFIJIIBGII@I?IJJIIFJIDGI@DIIC#IJE@IJJJ@EFDJGJJCDEH?=JGH9#DG=DC(HDEECD#E#ADC>D#D9D#@CC3DC\n+@NC_003198.1-62/1\n+GCCTCCAGGAGTCCCGCCATAATCGCGATCTACATTTTTTGGTCACGGCAAATCAGCGCGGCGTTCAAGCTATCCGGGCACTGAACCAGCAGGCTGATAA\n++\n+C@=FFDDFHDGHHBHGEJC6JGDHBHEGJJ#I?AIIGJDF#I#JJGA9@F@'IEGJJICIGCDHE#C#HFBHABE;HJA,AC;5#D#FCBD+D5E@9?A,\n+@NC_003198.1-60/1\n+AGAATATCGGCAACACGGAGAAAACGTCCTGCATTTGCCACTGATGTACCGCCTAACTTCAACACTAGCATGGTTGTCACCTCGTGCTATCTGGTCGACA\n++\n+??#DFFFFDG@:HJIJ@2JEJJHJ*EI!HJJIAJ0<IJ6JBB#I>GICHGHD?#(AAIAIH.DJJE#FA7EDAD@B;#FECB.DB;#D#?ADAEC@AD#D\n+@NC_003198.1-58/1\n+GTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCGTGATGCGATGTCCACGAGCCTCCACGAGTCCCTCCATAATAGCGGTCGTCATTATT\n++\n+B@CFFDDFHHGFHJB<J;JHIG#J>ACAJ?JIGGD#JHJJFC?#BD?#F#HJEGIFIJHH#F@DJEDG#@DCDECE#DGBDBB8#5DD#AA5#DCD:#C<\n+@NC_003198.1-56/1\n+ACAGAGTACACAACATCCATGAACCGCATCAGCACCACCACCACTACCACCATCACCATTACCACAGGTAACGGTTCGGGCTGACGCGTACGGGATACAC\n++\n+C@CFDF?FD#HF?4"..b"GTGATCAATTCAAAAATTTATTGACTTACGCTGGCAGATACTTTTACCAATATAG\n++\n+C=CF=FDAGHDHHJGB?JIIFJIJJIEHFJI<JHJ0C?CI(HHJEJJGIG94CII#C#EHJ5IIFFJIH;DHE#D##DCE;DFCADCDD#AC#9BDDACC\n+@NC_003198.1-34/1\n+TTCAACACTCGCATGGTTGTCACCTCGTGATCTCTGGTCGGAAAAAAAGCCCGCACTGTCCAGGTGCTGGCTTTTTTCTGTGGTTCCTGTACGCGTCAGC\n++\n+;C@?BFFFHHHH?JIJ@JJG!EIDIHIJFIIGI;HJIDGG!GF9:J4BHJHH;>JIHFF!=@CHCIE#:#C8CG?CDAFA?C#BDE9@@D?C#D>>CD@D\n+@NC_003198.1-32/1\n+GCTATCCGGGGACTGACCCAGCAGGCTGATACCATGTAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAAT\n++\n+@@CFFBFFHH#HHJIJIGJGHJJIJG#HIIDJJJIG#IBH@B9IJIGH<EJHCJ?=B@HIIJHHHC?H#C@8ECHC;@;AD3H##6:@AE8:DE#C>;?;\n+@NC_003198.1-30/1\n+GGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCCAGACAAGTGCAGGTTGCGAACGAACTTTCCGCCCCCGCGAGAATTACC\n++\n+?C<D;FDFHG@DGABFHHJJ@IJJJGI3EIBGGFJHD:4CHBG#FIDJ9=IBIE#EIFF#.HDE(A#CC)E#@3#DE@CIC==>D<DAD<AD#D@#3ABC\n+@NC_003198.1-28/1\n+TTATCAACCATGTGGTGGCGATGATTGAAAAAACTATCGACGTCCAGGATGCTTTGACGAATATCAGCGATGCCGGACGTAGTTTATATGACCTCCTAGC\n++\n+?CC#FDFFHHC#HGEIJHIDCHGIJ>>GG>IIJ?IFHHJ#DJ'?FDJDIEHJJJGI#H8EIH#FIGJC>FCDECE#ECBCF#CDF#B#CCBA>B#43#C@\n+@NC_003198.1-26/1\n+TGTGCAAGCGGGAATCCCGGCTGCGCGCTGGCAAGTCCTGCGAGCACGTCAGAAAAAATACGATCGGCATCGCCGATATTCGGCAAAGCATCCAGGGCGC\n++\n+#CCF?FD>F-FHACBJJFHHI:#IHI?JGJGFIJJIJ#J(9@#BFA#BGGI2HII*BIIGG>#@8H#IHH#J##;@>>DEEBFB;CCCB@-#C#?C#?CD\n+@NC_003198.1-24/1\n+CGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGATAGGTTTTTCAATCATCGCCACTAGATGGTAGGTAATTCTCGCGTGGGTGGATATGACGGA\n++\n+@C=FFFFFFHFHH+JGGIJ8IIEFIJHJIJF?GGIAJFJBJ<#G@JJGGIH7CJEJIIICG#E#E@=DE#ED3E5>C#F#DC<#ADH#CDB#D##?>?D,\n+@NC_003198.1-22/1\n+CAGCAGTTTTTCTACCGGATCGATCACCGTGACGCGATGTCCACGCTCCTCCAGGAGTCCCCCTATAATTGCGATCGACATTTTTTCGTCACGGCAAATC\n++\n+@CCFFFBFDBHH2JJGEIJIJIJ#J<JIHFBJBJEIDGDGIDGI#D#CJIIGBIG:IFIBI#7#ICH9I#ED@6?>BAD@.BFB5BC##A?DAAE>DCBD\n+@NC_003198.1-20/1\n+CGACCGTACTTTCCGCCCCCGCGAAAATTACCAGCCATCTAGTGGAGATGATTGAAAAGACTATCGGCGGCCAGGATGCTTGGGCGAATAACATCGATGC\n++\n+?CCDDFDDHHCHHGFJA<JG>IAGJJJHICHJ9#9GHEI8#JJI??IDCDIEJJIGIF#CHF9IE?>2DI=DF#>H>G>C;#H#FDDC:D##>(DD@##,\n+@NC_003198.1-18/1\n+TTAACCAATATAGGAATACAAGACAGACATATAAAAATCACAGATTACGCAACAACCATGAACCGCATCAGCACCACCACGTTTACCACGATCACCAATA\n++\n+@BCDFFFFGHDH?JII:#IFHJ<IGF5JJ#;GIJIGFC#JBCHE##J9#IFGFG#II0HG7IJHFF.JI:F(C@CA@BDB##FCCHA@###9D#EAC#AB\n+@NC_003198.1-16/1\n+GCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAAAAACCATGCTAGTGTTGAGGTTCGGCGGTACATAAGTGGCAAATGCAAAACGTCCTCTGCGTTTT\n++\n+?@1FDFFDHGFB2EIJ)CJHEIHJIJJHGGJIJJ?#IJFIFIIG#DB#G@GII#HB#DIDIEJE@-EJ#JDBE?FDC#E9>@##@C?@##DDCD@DD#DD\n+@NC_003198.1-14/1\n+AACGTTTTCTGCGTGTTGCCGATATACTCGAAGGCAATTCCAGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAGTTAGCAACCTCCTGGT\n++\n+?@CFFDDFDHDDHIDIGJIC+FG:3#HJ#I=B##@ICGIGDJI9EJIII@JJGDJGCDBC(DF.DHHG<B;C?HDCE>BDCAB#DAC#DDAE>##DDDB,\n+@NC_003198.1-12/1\n+ACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTCGCCGATATTCTGGAAAGCAATTCCAGGCAAGGGC\n++\n+BCCFFFFDH3HFGADGGEJJBJJIJHEGFIJJHIG#GECDFIIJJJBB?BJD6JJJC>CHJ=GDI-DACGEGC?D@;HDA7DD>CD>FECCDD=:C@D#D\n+@NC_003198.1-10/1\n+ACAGTGGAAATTGATTGAAAATAAAGATATCGCCAGCAGCACATGAACAAGTTTCGGAATTTGATCAATTTAAAAATTTATTGAGTTATGCCGCCAGATA\n++\n+@<CF#FFFDDGFDEIBIJJJGIJE##?EFEIJGIGG)FDDIIIJJA#GJJFEHFHHEIJI#EHD)5I9C,C#F#JD>#<?#DDC#>;C#(@#C#CD8@#C\n+@NC_003198.1-8/1\n+GGCCGGGTTCTGGCTGGCGGCGATACGGCGAGTCGATTCCGCGATACCGACGGTAGATTCGAGGTAATGGCCAACCGCCTGCAGTTTTTCTACCGGAGCG\n++\n+CC@7FAD#HHHHHII+AHIEJIGJEGJ:IIJGF?GCDIC<GAJ#JF4JJHBJBHHG#EGF#CJCECEH:HJD#FDG;EG#A5FDDC5D#D@#5?ADD#C,\n+@NC_003198.1-6/1\n+CTTCAACACTTGCATGGTTGTTACCTCGTGATCTCTGGTCGAAAAAAAAGCCCGCACTGTTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTGCACATCAG\n++\n+CCB=FFFFHD#AH<JJIJJJJ?IDIHI#ICIH46IJ0CIJGI9BJJJGJJFI)#JHFFH7H?FIB<ECCAAJ#C;HA:A>/EF<EDE@@CC#D#E#>BAD\n+@NC_003198.1-4/1\n+ATCGCCACCAGATGGTTGGTAATTTTCGCGGGGGCGGAAAGTACGGTCGCTACCTACGCTTGGCTGGAATTGCATTCTAGAATATCGACAGCATGCAGAA\n++\n+C@@FFFFF?HAHHE7BIICHJJJJDHEJEGHJJJJIIF@J?EFIHGJ@:;HJJDI#I#I#EB#B8IJH<6EAC#)#B#>D<FC#>?(#@##D>(2A##<,\n+@NC_003198.1-2/1\n+ACAACATCCATGAACCGCATCAGCACCACCACCATTACCACCATCACCATTACCACAGGTAACTGTGCGGGCCGACGCGTACAGGAAACACCGAACAGAG\n++\n+@@@+FFFFHFFF)JJAJIJJI@+IJGJJIJJ?GDAJ#<JJGA?GJ8IIIFGDHHJGJHBGG8I#CJJC)H@D#C##CDD@7>DDED>D@CA#D9##5#C>\n" |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_R2.fastq Wed Oct 16 16:57:55 2019 -0400 |
| b |
| b"@@ -0,0 +1,180 @@\n+@NC_003198.1-90/2\n+TTTCGCGGGGGCGGAAAGTACGGTCTCGACCTGCCCTTGCTTGGAATAGCTTTCCAGAATATCGGTAACAAGCGAAAACCATTCTGCATTTGACCCTGAT\n++\n+=@CAFDF+CHFFHHHEI,IEJJGJH#G#HIJJDI?9B??H#I3IBI*(JIDHI#HD&9DI#@HC#!E@;I!>D###H:#E#DCFD9>HADDB#A##@CAC\n+@NC_003198.1-88/2\n+GTGATTTCTGGTCGAAAAGAAAGCTCGCACTGGCCATGTGCGGGCTTTTTTCTGTGTGTCCTGGTCGCGCCACCATGCACAGGTAGCTCTGGTAATGGTG\n++\n+@:BFA!C0HFDHFJCBHJ#+<JJC#HJJHJE;##JF#?GIIJB0JHEGFFFHEE#F#!EHJJJ##ID#+#FI####ECC>#:#CD##D#CC#CC3CADCC\n+@NC_003198.1-86/2\n+TTTTTCGGACCTGCTCGCAGGACTTGCCAGCGCGGAGTCTGGATTCCCGCTTGCAAGGTTAGAATTGGTTGCCCAACAACTATGCTCGTGGATCACACTT\n++\n+CB1DFF!D?A8HHJFBI#JIAD@E9CI#F*JCIJ#GJ#J#@##8JFFFFE*HID;#IJ#=#!GI!FCIF?##@#).DDD##EH#:#####>(####CB#?\n+@NC_003198.1-84/2\n+CTGCCAAGTCCTGCGAGCAGGTAAGAAAAAATACGTTCGGCATCGCTGATATTCCGCAAAGCATGCTGGCGGGCGATAGTTTTTTCTATAATCGCCATCA\n++\n+@?+!DFFF<HCHHBCJHFJJHA#B#CJGIDE?HF@<D3<GJGEGJICF3BCHGF#HJ#;GCGJ##+=D@C#;#CGH;7@BCF59@<!9>#EDDDD###B<\n+@NC_003198.1-82/2\n+ATGCAGAACGTTTTCTGCGCGTTGCCGATATTCTGGAAGGCAATTCCAGGCAAGGGCAGGTAGCAACCGTAGTGTCCGCCCCCGCGAGAATTCCGAACCA\n++\n+@@BFFDDFFHGHHIHHDGI#HIEI>IGIGJ#0DI*DCI0JGIJ=FEJIJGHF?@<F#I;FI=H)#ID@DF:#B#>IC(DBDD##H<C##DCF#:###C@C\n+@NC_003198.1-80/2\n+GCCCCCGCGAAAATTACCAACCATCTGGCGGCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATCTCAGCGATCCCGATAGTAATTTTT\n++\n+BB@ADD<FHH@HH<:#FGI#?J3G<GI#!?IIJ?9DIDDIJHDIIGI='D<BCDJGJGGJJDHIHJ=C@E5?;D##3F>?;CDD#D=#>#!:AD#(C@D'\n+@NC_003198.1-78/2\n+AATACGTTTGTCCTCGCTGTTATTCGGCAAAGCCTCCTGGCCGCCGATAGTTTTTTCAATAATCGCCACAAGAGTGTTAGTAAGTGTAGAGGGGGCGGCA\n++\n+@B<FFDDD!H!H#AJDIJH#?A*:GJJFJGJCC#B)GJGGFG?GJ9JG#DF;HID@GCIE#GIAH6C=##HCE##C>J#>@DC#C#@#@,C@EBDCD:#D\n+@NC_003198.1-76/2\n+AGGAGTCCCGCCATAATCGCGATCGACATTTTTTAGCCACGGCAACTCAGCGCAGCGTTGATGCTATCCGGGCACTGACCCAGCAGGCTTATACCGTGCA\n++\n+BC@FFDEFFHDHH)I@1IAIJHHJ3@JJEJJ)HC!FJH@CGH??I!GIHICFB#FECBBI8AJIGJ@EDDJ#95AI5IEHD9C#?#CD@#CC>CB#BDC'\n+@NC_003198.1-74/2\n+TGTTCGACAACCATTCTGGTCCGTGAAAGCGGGAATCCCGGCTACGCGCAGGCACGTCCCGCGACCAGCTCGGAAAAACTACATTTGGCATTGATGATCT\n++\n+=C@F=?2D#:H<:JJ!I!##JG+H<#;)GFJID:HHFIJFJGI#GF#<F#>BGC#ID8J#HII##CGD.E##<E#F26#D>>#HD#D#<D0#C##CAD#C\n+@NC_003198.1-72/2\n+CGGAATGTGATCAATGTAAAAACTTATTGACTTAGGCGGTCAGATACTTTAACCGATATAGGAATACAAGACGAACAAATGATACTGGCAGAATACACGA\n++\n+;@C4=?+D,FHFFJJ#<HIIJ@#JJGEJDHJGJII@JJJ#?HGIGGJI9GB.ID#IJFIB;GJ9CGDBD@CG##DCDA;G#D#F#3D#DBB##A9C#D#D\n+@NC_003198.1-70/2\n+TGAACAGTGCGGGCTTTTTTTTCGACCAGACATCCCGAGTTAACAACCATGCGAGTGTTGAAGTTCGGCGGTCCACCAGTGGGAAATGCAGATCGTTGTC\n++\n+1CBDF8F#AFHAHJJHCAEEJ+JJJGGDFG#GFI#DJIE#?9D>5?JFF;IBAJBAEJHJDHDJCD@>;GBC!FE##DDCEC#(B?C#::HD#@CB##D'\n+@NC_003198.1-68/2\n+TTAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAATCCCGGCTGCTCGCTGGCAAGACCTGCCAGCAGGACAGAAAAAATACGTTCGG\n++\n+C#?FDFF>H:HHHGIJHJJCH>GIEGJ@IIGIIJE?IEFEGD>BJJ0FJ#HEBB@IJ##FJG>GDGJ7#AEFGH#DF;5D@#<D@CB<DCFC9+>D#9#'\n+@NC_003198.1-66/2\n+TTGCCTGGAATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGATCTGCATTTACTACTGGTGTACGGCCGAACTCCAACACTCGCATTGTATTTACC\n++\n+<@84FFFFH>G#H@I+AIIFGHJE:IEA<<:EIBHF?G1?IIAGJ!H;IAF=IHH#B#CF@F!#JFE.#FBHCEBBE#DCA?D>#BA@CD#FA##?CCCD\n+@NC_003198.1-64/2\n+GCAAATGCAGAACGTTTTATGCGTGTTGCCGATATTCTGGAAAGCAATTACAGGCAAGGGCAGGTAGCGACCGTACCTTTCGCCCCCGCGAAACTTAACA\n++\n+BBCB=2DFHAFGCDII?C#JDJ<+JIJGJI?IG??IDIIBJ9J?GG#IJ#G=JJCIG=@G#FCGIGC;@6D>ACCJ#CD!DA5C@C>#ECC#:#C#D#@'\n+@NC_003198.1-62/2\n+TCCGCCCCCGCGAAAATTACCAACCATCTGGTTGCGATGATTGAGCAAACTATCGGCGGCCAGGATCCTTTGCCGAATATCAGCGATGCCGAACATAGAC\n++\n+:C1DBFFDHAFAHJGJGHJ33ID#JCG?I#EJ#GFFD@J?GCGD*#BIG?HHJ;IJFC7@DG8D)F!DJHHC.@I?@=##CGDC#CBD#D#C?8#C###'\n+@NC_003198.1-60/2\n+ACTTAGGCGGGCAGATCCTTTGACCAATAGAGGAATACAAGACAGACAAATAAAAATGACACAGTACACAAGATGGGTGACCCGCATCAGCACCACCGCC\n++\n+CC@BDFFF#HGHBIFI#GG#J!JDJHJGE#EDJJICII)JHIFJEJIED=D@=CH<JFICF.IC#EHIBIF#D.###ECC##F>BCCA#>DDBC#C:#BD\n+@NC_003198.1-58/2\n+ATATCAGAGATGCCGAACGTATTTTTTCTAAGCTTCTCGCAGGACTTGCTATCGCGCAGCCGGAATTCCCTCTTGTAGGGTTGCGAATGATTGTCGAACC\n++\n+@?C+FDF#:HFHDJ:F:JACCIGCG@AJF#@#@41?G)?I#IIDIJJJI#9#IICD#H@FHFF#HH=AID#I>F>#D##A<3B)#FC#C#C>C7??#CD!\n+@NC_003198.1-56/2\n+GTTGGTAATTTTCGCGGGGGGGGAAAGTACAGTCGCTACCTGCCCTTGCCTGGAGTTGCTTTCCAGGATACCGGGAACATGCACAAAACGTTCTGCATCT\n++\n+@C@BBFDB:HDCH2"..b"CTCATGAGCGGTCTTTTTTCTGTGTTTCCTGTACGCGTCCGCAAGCATCTTTCCC\n++\n+B?BDACED2?;DH)JDJG0HGHAIJJGIE@H;GAIJID@JGF8GG#JBG#I#G9ID#C?EHJH=5D2IICFCII#B#HECHDDB#B##!:CC#>#?E#;D\n+@NC_003198.1-34/2\n+AAATATATCGCCAACAGCACATGAACAAGTTTCGGAAGGTGATCAACTTAAAAATTTAAAGACTTAGGCGGGCAGATACTTTAACCAATATAGGGATACA\n++\n++C+DFC;FH+#1G#HAJJIDH#JHJCJGBFDCFFJBJ#JH*JII#B!J'H@GH@?GH>##HDB8J=DH@CBCC57CC8CDGF@C(D5E#>EDD:#DCAC'\n+@NC_003198.1-32/2\n+ATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAATCAATTCCAAGCAGGGGCAGGTAGCGAGCGTACTTTCCACTCCCGCGAAAGACACCAACCA\n++\n+BC@D=D=DHEHGGJHI+J+GJDJICJCI?I*#GIHJ9JD!??GJ08G>#HHI#GFCFJ#IG;I>JD##?D#DGEA#H!9!D#EDD@#3;###@D:>>@AC\n+@NC_003198.1-30/2\n+AGGCTGATACCATGCAAAACCTGTTAGATCTGAGCGAATTCTTGTTCGACAACCATTTTCACGCGTGCAAGCGGGAATCCCGGCTGCTCGATGACAAGCC\n++\n+@?B#BFFA4EAHHGJCJIIH#>G#3!>EGI04#J9FHJIIBJFJFE@?4#I8?D?DDEJJA##BI@HD>D>DCFD#8H=A#/C;CGD#AC#DC##BB##D\n+@NC_003198.1-28/2\n+CACGCGCCTCCAGGTGTCCCGCCATGATAGGGATCGAACTATTTTCGCCACGGCCAATCAGCCCGGCGTTGATGCTATACGGGTACTGACCCAGGAGGCC\n++\n+B=1DFFFED2<B6I#,IG3F?IJH?#JG#G#JI)CGJ!#B(@G?#HCI8F9C20#D8JJ=EJ#=#DH#CI@D.JH2D;!EE05#?;@C->DD<##@AD@'\n+@NC_003198.1-26/2\n+TTTTTGCGACCATAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGCCGGTACATCAGTGGCAAATACAGAACGTTTCCTGCGTGTTGCCAATAT\n++\n+?BCAF)F2DGH<#JICG@JJH#0?AG#@JI/AFJI@#GDD0BG;:?GIFCG#EICICD#B/4GG(BJ3J@D#E(?IAGDH;@#D6ACCFC##DDD##D#'\n+@NC_003198.1-24/2\n+GAAACACAGAAAAAAGCCCGCACCTGAGCAATGCGGGCTTTTTTTTCGACCAAAGATCACGAGGTAAGAACCATCCGAGTATTGTAGTTCGGCGGTACCT\n++\n+@BBDBFF+HH?HDGIJ<IJIEGJAH#I!FH#J?IGIHGIGCJ9IFJGHFGBI#@8HCJHJEHIID@D#H;E5;H!EECA8#E#,#?EB;C@D>0CDC##@\n+@NC_003198.1-22/2\n+CTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGGCGCCGAACGTAATTAATCTGACCTGATCGCAGGACCTGCTAGTCCGTAGTCGGGATTCCCGCA\n++\n+B?@4DFDFA?CDH@JJIGJIJAHEIHJIDEH<I9E1#!*B;FIJIGID#H3!!IDIE=FJG<#BCDDDDEGF#CDG#A<0#B1#>C!DFBDCDD#3>BD'\n+@NC_003198.1-20/2\n+AATCGCGATAGACATGCTTTCGCCACGGCAAATCAGCGCCAGGTTGATGCTATGCGGAGACTGACCCAGCAGGTTGATACCATGCAAAACATCTTTGTTC\n++\n++@BFDFFFH#C++C>##JIBIIC#J<#FC)GDF9:J*JI!#!##B@#C;IGJG##G:##F3FJFH'DJ#9I#9#9C>?IC(CCDCC?EC@AD#@BDC#DD\n+@NC_003198.1-18/2\n+CCCTTGCATGGAATTGCTTTCGAGGATATCGGCAACACGGAGAAAACGTTTTGCATTTGCCTCTGATGTACCGCCGAACGTCAACACTCTCATGGTTGGT\n++\n+?@CFD>C#HHFHHGFHFJJH##JJ#JFIJJD?@*#JCCJ#@FJ?JBJD:I!;II1JGGHFG#IJ=JIE;IED@DF?HDE#CD@@CC?:4#DD:DDCCD#'\n+@NC_003198.1-16/2\n+TCGTGCAAGCGGGAATCTCGGCTGCGCGCTGGCAAGTCCTGCGTGCCGTTCAGTAAAAATCCGTTCGGCATCGCTGATATGCGCCAAAGCATCCTGGGAG\n++\n+#@@FF=DDBCGGHHI#A#GC3A?I#IHJIGJIJ?GHF##ICGB#:J#F#GH-I#JJIGJE#H@##IFCIE5;=C>CCB#C#ED#FCFD9D6?CC@C@##>\n+@NC_003198.1-14/2\n+CGTTGATGCTAACCGGCCGCTGACCGAGCAGGCGGATACCATGCGAAGCTAGTTTGATCTGAGCGCATTCTTGTTAGATAACCATTTTCCCCCGTGTACG\n++\n+?B@DF?CDFH2#:H#J#I!JHGJJG!IEJCG?**JIC?BJ#EJ2####H##=GJ8)JJGI@##D=#=E>DC>#BC#BC##D)@3#C?#C#!###@?#D#@\n+@NC_003198.1-12/2\n+TCTTGTTCGACACCCATTTTCACCCGTGCAAGCGGGAATCCCGGCGGCGCGCTGGCAAGTCCTGCGAGCAGGCCATAAAAAATATGTTCTGCATCGGTGA\n++\n+@BC++DDBDEHG#GJI<<I3JC!IIBG1*H#ICJIF?EIHIF;JJ#G4@6?/FAJ5GDAH#CDC;>IDFE(C#A@#CH>E#D#C#FDC?#>ACDFD#D>D\n+@NC_003198.1-10/2\n+CGCATGGTTGTTACCTCGTGTTCTCTGGTCGACAAAAAAGCCCGCACTGTTCAGGTGAGGGCTTTTTTGGGTGTATCCTGTATACGTCAGCCCGCAACGT\n++\n+@@CBDF?FHF>H<JHC?JJC#EGIG)GJGGH:#GHHDJGBCI@GHJJJII5H;HFII#GBH<EHH8C)#!CCEF#@DG;@DB###DDFD?;ACD8@#CC'\n+@NC_003198.1-8/2\n+CAGGACATTCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCTGACCAGAATTCGCTCAGACTAAGCATGTTTTACAGGATATGAG\n++\n+#BB+BC#F2HHF3I=JEEJGAAIGI;BGCJHCG@F#HGIIFG@G?FGHJC63HIHC##JC!FHEI<EDG>=7GDF##@D#EH-BDFEE!D>!A#B>?#D'\n+@NC_003198.1-6/2\n+TCGCCGGCAGCACATGAACAAGTTTCCGCATCTGTTCCATTAAAAAATTTATAGACTTAGGCGGGCAGATACTTCAACGCTTAGACGAATACAAGCCTCG\n++\n+CCC+D##FAF<DC,IAJGIC,?GJEF#I#HH#GF##G#JIG#0J7I#(CICE#JDDDE=D#JDGBEGIEDE5EF#HD6###BC#A#CEBD?CDE>#A##'\n+@NC_003198.1-4/2\n+AACCGCATCAGCACCACCACCATTACCAACATCTCCATTACCCCAGGTAACGGTGCAGGCTGACGCGTACAGGAAACACAGACACAACGCCGCACCTCTA\n++\n+@+BF4FFFHAD<<JBG?GHIGJGJ#ID)#IEEI(BJJBHJGJ#IJD?#JJGBHA>I#GI)C=F<BJ7@;H;HH@DEEHFDEC#C!>:###9A@DDDD##'\n+@NC_003198.1-2/2\n+ATTGTTTTTTCAATCATCGCCACCAGATGGTTGGTCATTTTCGCGGGGGCGCAAACTACGGTAGCTACCTTCCCTTGCCTGGAACCGATTTCCAGTAAAT\n++\n+C#!+D+*<HHF##@JJJ4JBIADHGFIJGF?GF?G#CH:9EI>FJ#EJ9=8#FGG##CJFI.#ACFBH=D!E?55>;D3BHABA##C#BAC?CDD#?#EC\n" |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_bracken_report.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Salmonella enterica 28901 S 40 2 42 1.00000 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_003198.1_simulated_kraken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_kraken_report.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,13 @@ + 6.67 3 3 U 0 unclassified + 93.33 42 0 R 1 root + 93.33 42 0 R1 131567 cellular organisms + 93.33 42 0 D 2 Bacteria + 93.33 42 0 P 1224 Proteobacteria + 93.33 42 0 C 1236 Gammaproteobacteria + 93.33 42 0 O 91347 Enterobacterales + 93.33 42 2 F 543 Enterobacteriaceae + 88.89 40 0 G 590 Salmonella + 88.89 40 0 S 28901 Salmonella enterica + 88.89 40 0 S1 59201 Salmonella enterica subsp. enterica + 88.89 40 0 S2 90370 Salmonella enterica subsp. enterica serovar Typhi + 88.89 40 40 S3 220341 Salmonella enterica subsp. enterica serovar Typhi str. CT18 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_1kb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_1kb.fasta Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome +GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCT +TCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAAT +ATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCA +TTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGC +CCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGT +TCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG +GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAA +AAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGA +CGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGC +CCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG +ATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTA +CCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA +GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCC |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_R1.fastq Wed Oct 16 16:57:55 2019 -0400 |
| b |
| b"@@ -0,0 +1,180 @@\n+@NC_011750.1-90/1\n+TAAAATTTTATTGACTTAGGTCACTAAATACTTTAAGCAATATAGGCATAGCGCATAGACAGATAAAAATTATAGAGTGCACCACATCCATGTAACCCAT\n++\n+CB@D#FFDFBHFDJHJJIEHJJIFIJGJFIJ#?EG?#DGFGCII0?FJJIDIGJ*#GEIJ#IJ?)BC5EHD##>F8A;#@FA#A>;BDD>DD#C#8#@?C\n+@NC_011750.1-88/1\n+TGGCGCAACTGAAAACTATCGTCGATCAGGAATTCGCCCAAATAAAACATATCCTGCATGGCACTAGTTTGTTGGGGCAGTGCCCGGATAGCAGCAACGC\n++\n+CC1FFFF=D2D+HGIHJ#3JFIIAIIAIGJJFEJ#JGJJIJ?IIGC@BDB#HIHIB<JJGHGJ#DJHIHFCEH8A@BCDEFDBD>;FA5D#DA#D#FCDC\n+@NC_011750.1-86/1\n+CTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCAAGCGAGTGTTGACGTTCGGCGGTACATCGGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA\n++\n+5C>FAFAFHD<FHGJFIJJIJHH,JJIJJJJJI6IJ#JIJ#IFI#/JI#JDJDI#=HH#DFJ?7#II#FD#E>CA=C@#D<@DC#DDD>D:DDA#D?ED,\n+@NC_011750.1-84/1\n+GAAAACGTTCTGCATTTGCCACTGATGTACCACCGAACTTCAACACTCGCCTGGTAGTTACCTCGTTACCGTTGGTCGAAAAAAAAGGCCGCACTGTCAG\n++\n+@C=DFDFFFHGDCGEIIIJD?#JAIIDBHJ?#JEGGIBFJIJ=J>FGIJD##DI?!EE=JBBJ#FBD=DI#?E;<FCDDC#DDACD@#>CECDDCB53DD\n+@NC_011750.1-82/1\n+TGCTTTACCCAATATCAGCGATGCCGCACGTATTTTTGCCGAACTTCCGACGTGACTCGCCGCTGCCCAACCGGGCTTCCGGCTGGCGCAACTGAATACT\n++\n+@@?A#FDDHGHF<>JJ4GAIIICCD0###EEIIHIIJ#JHGJJHJIB#'FHH#IJCJJCJ8GEG7??-?>EF(C?#;C7?#DH#CDABDDAD?DBA#DC@\n+@NC_011750.1-80/1\n+TGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTTGTTTGGTGGGCCAGTACCTGGATAGCATCTACGC\n++\n+@C=DFEFFDHHHH#CHEEIICIJHJJJJ#JGGGHJFJIJBED=?DEIHH>BJI#CGIBEI#I>DC#HBGED)HE?:##ED5#CE#EAE2EC5DDC##BAC\n+@NC_011750.1-78/1\n+GTCCCGTCAGAAGTTCGGCAAAAATACGTTCGGCATTGCTGACATTGGGTAAAGCATCCTGGCTGCTTGTGGTTTGTTCAATCATCTCCACCATGTGAAT\n++\n+@@CFFFFFFHHH#JJJIJJHJHFAJJI#J#I:HIJG#JBGH@#H3JEII@?IIFIHBFH9EC@#J=D##FCEIC;#@CD4EFECAD#D3DDC8#C+>##@\n+@NC_011750.1-76/1\n+GCAGAACTTCAACACTCGCATGGTTGTTAACTCGTTACCTTTGGTCGAAATAAGAGCCCGCACTGTAGGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGC\n++\n+C?!DD#;FC7FHAHI2JJEI=HJ?IIJJI#HICHJGHJ8IJGI;JD@H*FB@J#CGI@EBA#JEEG##E#GDCCE?DHJFA<#>>AD#C>?E>8AD#ADB\n+@NC_011750.1-74/1\n+AGAACGTTTTCTGCGTGTTGCCGATATTCTGCAAAGTAATGCCGGGCAGGGGGAGGTGGGCATCGTGCTCCCTGCCCCCGCGATAATCACCATCCACCTG\n++\n+??CFFDF1HFH<FBJ?IIGDEIJHGI;IJ)J#DIHJ)AJHIHI!ID:DJGHB#GIC=I##JH#<CE#CGI#@CD@7HBCHH)9#DF?ED?ED##DABD#3\n+@NC_011750.1-72/1\n+TGCCAGGCAGGGGCAAGTGGCCACCGTCGTCTCTGCCCCCGCCAAAACCACCAACCAGCTGGGGGCGATCATTTAGAAAAACATTAGCGGCCAGGGTGCT\n++\n+@+@DD?FFHHHHGIA#E?IGHBJIJG9I#GJHGBJIEJH#E@IIIJJ#JFFEH3JEF#JFDI#I(IDCE#CJ>#E#FC(E#C;CD:#,>#CDDCC#B#?,\n+@NC_011750.1-70/1\n+ATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGAAGCTTCTGCACTGGTTCCCTTACGCGAGTAAAGTAAAATGTTATTGGCGTAGTTCTCAAA\n++\n+CCCFFBFFHA@HCJIHJGGGBJJJJJIJFA1>J#IHBAD#FG#HAH#@#FH@BC1##IJD!#FH#7@?AD@E!A>:I@B#D#;#??#A##D##@D#B#?D\n+@NC_011750.1-68/1\n+CCGCTAATGGTTTTTTCAATCACCGCCACCAGGTGGTTGGTGATTTTGGTGGGGGCAGAGAGGACGGCGGCCACCCGCCCCTACCTGGCATGGCTTTCCA\n++\n+@CCDFFEDHDHH=#EIIJIJHH#JJIB:EGJIFI096HGJIEFJFIGJE#JIGJIBHJDJCBFGJGH#;?HID;E#F>I=@F#EDD5BDC@#D#DDCCDD\n+@NC_011750.1-66/1\n+CTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTGACGAGGTAACAACCATGAGAGTGTTGAAGT\n++\n+@@@FF+FFHFHHHIJ<JFIIJI@CGIJ*JJGEGIJCIGJGJI>I?/IJECGEJHHB;FC(EHCJD?5;F#EDEF=EH#D?@<D>E>C#DF#>CB5#D??A\n+@NC_011750.1-64/1\n+AAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACGATTACCACCACCATCACCAGTACCACAGGTAACGGTGTGTGGTGACGCGTTTTG\n++\n+?@CDDDFADH?HHJG#JBGJ@BJJAJHEGJIIFGJIIIJJBJIJI##IAEHDGCAIBH#HGFAJJ#GFHDD#D;#;=#GCBCE#D#D#DDDA>#@<###,\n+@NC_011750.1-62/1\n+TCAACACTCGCATGGTTGTTGCCTCGTTACCTTTGGTCGAAAAAAAAGCCCGGACTGTCAGGTGCGGGCTTCTTTCTGTGTTTCCTGTACGTGTCACTCC\n++\n+C@+FFFFD<?HFGIHFCFFI#GGIJFH#CJIBAIIJ?HFCIJH.G)EIEIAF#H#JJFJ)CFBE=JDBCIE#F;9=>C#D=>#?E,;DC5D#D,BE##<C\n+@NC_011750.1-60/1\n+GTGTGGATTAAAGAATGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGCAAATTAACATTTTACTTACTTAGATCACTAAATAGTGTACC\n++\n+B@?=DFFFHHHD#JJ#IEJGJJHHJI1IBI?JJGJ?CJ:JJIAJEJJJ?HCJHICDAD#EJ>AIF>!I7#GJE#F#HD#.>@#E#A;@D>DDB#C#@C#B\n+@NC_011750.1-58/1\n+CTCAGTAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCGACCAGTTTTTCGACAGTATCGATAACGGTAACGTTGTGACCGCGCGCTTTTAATACG\n++\n+@@@F8#FFHDHDH#GGJJIHHECIJFIJ?@JGICJICJFJ:##J#F?JEIFIJHCIJ#H#;DEHGDCI@GFCHF>G8BFC2>A#EDEDDCED#@CCD#C,\n+@NC_011750.1-56/1\n+GTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGGGCGCTTCTAATACGCCGGCCATAATGGCGGTCGACATTTGCTCGCCACGGCAAATCAGGGC\n++\n+@@CAFDFBCHFHDE"..b"GCCGGACGTATTTTTGCCGAACTGCTCATGGGGCTAGCTGCTGCCCAACCTGGAT\n++\n+@C?FFF?FFHFHHGGGGHJIBJIJJH)?J:GHIIDFIGDJJIGJJJ?ED#JGJGFIJGJJGBCBJFFD#JD#D#GBG#H<#ED#A=D@DD=B#CD#>AC>\n+@NC_011750.1-34/1\n+TTCTCGCCACGGCAAATCAGCGCAGCGTTGATGGTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGATATGTTTTATTTGGGCAAACGCCTGAT\n++\n+@@@?F+DFHHA8+JJJIJJJGJI2EJJJI#I#H#?F#GDIFGIG?G=JCJIIGBII:IIHIEH?DJEDCI<G@#=ABA@E>#CEA<DC#B=D###A#C#@\n+@NC_011750.1-32/1\n+GTATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAACTGAATACTTTCGTCGATCAGGACTTTGCCCAAATTAA\n++\n+?C?FFF,FCHFHH@G?IBEDI>JJJJJIIGIJCJG?HHJIFAH?EJCJ?G0JIJGGGF+7JHI=EBB#H;G;B@AD@DDC=DAFD#B<CC@B>:CDC#D@\n+@NC_011750.1-30/1\n+TGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGCTCGACATTTTATCGC\n++\n+@C=FFFFFFGHBDIIJJGI?IG,JFCHJJ#JFIJ;IHIHJ@E*FJHEIJJJGBJ>G4GE#G@D@<EIF?BDCEDHB=>?;<(DC#E#(CC:#DC@#19CA\n+@NC_011750.1-28/1\n+AAAAAAGAGTGTCCGATAGCAGCTTCTGAACTGGTTACCTGCCGCGAGTAAATTAAAATTTAATTGACTTAGGTCACTTAATACTTTAACCCATATAGGC\n++\n+@@CAFDFFHHFH<#FIAJAGFEJ=IJJIJJJFEIHI7#IHJJ3J#EG=AIGGJDHEAE74A'DFHJAIJJCGIDEHH>#;HCDEFA?:DA?#CDC?D#:C\n+@NC_011750.1-26/1\n+AATGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGACGAAGGCGGCCACCGTCCTCTCTGCCACCTCCAAAATATCCAACCACCCCGT\n++\n+=B#FDFAFDHGGBJF@JGIJIJJIHHIIGI0H<0#GIAJJIFFJCI###I!GEJ#JDGGI=GAAGAGCDFB;#F#?B#ACEA#:>##CDDAE>C9###AB\n+@NC_011750.1-24/1\n+CGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATTTCGGTAACACGCAGAAAACGTACTGCATTTGCCACTGATGTACCGCCTAACTTCACCCC\n++\n+CC?FFFFFH3HHHJJJJJH<IJ@IJJHGJJBIJG1GBJJI#IDII!GGJJHDIIJDHDIECJ#7C9EE.D?58DGECA@BAHD#DDB@#:D?4EBC###,\n+@NC_011750.1-22/1\n+TGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGGGGTTCGTGATTTTGGCTGGGGCCGAGAGGACGGGGGCCACCTG\n++\n+#CBFFFDFH1HHF@GJJJE9GJEBBJIJJJGJJJCIGHDFHJ@J9HHJEJJIG;JI#FGID#FA#HICA=HI;#F>CA2#;#DD:DC<5(#C3CD0ADCD\n+@NC_011750.1-20/1\n+TAATGGCGATCGACATTTTCTCGCCACGGCAAATCCGAGCAGCGTTGATGCTATCGGGGTACTGCCCCAACAAACTAATGCCATGCAGCTCATGATTAAT\n++\n+?@CAFFFFFHHDHJJJ@EJDG@JIHAF@#J?CFJG#I#J#JIBIH'HIDFJIHJ=##F=#DC@H=FHJFEJD><@F?GDD@C@FBCFB##B@AD#C@#C,\n+@NC_011750.1-18/1\n+CGATGCCGAACGTATTTTTGACGAACTTCTGACGGGACTCCCCGCTGCCCCACCGGGATTCCCGCTGCCGCAACTAAAAACTATCGACGATCAGGAAGTT\n++\n+@@CDFFFF?G<HHJIIEJJ;#ACGJ2:F?JJI?HJ)BHJE#JJHIG:J@*#@BBG=CHFED@>FH:F#GC@F@;@#CBIFC##D>D#C@B#DD>ABA#B,\n+@NC_011750.1-16/1\n+GCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCCACAACCACCTGGTGGCGAGGATTGAAAAAACCATTAACGGCCAGGACGCAT\n++\n+BCCFFFDFFDAH>GIIICHGHIIDJEJJDJFJJJEIEHGIJICJJJHH##JGHGIFIFE#BIJ7G=G#G7EDFICCE#?F#>@DD#1CCCCDAC##DD#B\n+@NC_011750.1-14/1\n+GAAACACAGAAAAAAGCCCGCACCTGACAGTTCGGGCTTTTTTTTCGACCGAACGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGTCGGTACCAC\n++\n+@@@DDDAFHB+HF@JFIJH:IIJ?HH#JIHA#JHDCJG#II7)JBJ@JII#EA#GIEFG8JH<J?D78I<FC@GBBDDCC@CECCA>FED#DC:DDD##C\n+@NC_011750.1-12/1\n+CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTTCCATGAGTATATTAAAATTTTATTGACATTTGTCCCTAACTACTTCA\n++\n+;C>F-FFFDHHHHGJG?JJJJEJJJJJDAIGDGIJGGJ4IIJAID0#FJJ;G#ID#G8@IIH#@A#GGIHBDED:#D;CC#D##BB##C@D@#DC?D?#D\n+@NC_011750.1-10/1\n+TTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTTACCGCGCGCTTCTAATACGCCGGCCATCATAGCGATCGAC\n++\n+C<?F44FFHHHGHEHGIJHGIJJHJJGJJHIHIJDIJ1HJ#7@IEH9JCHDJD>B5=HI#)DFGAH@:IHJIJ3E>DF?#BDFDE9E#DD#E7CCBAEC>\n+@NC_011750.1-8/1\n+TTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGTGCACAGACAGATCAAAATTACAGAGTACACAACACCCATGAAACGCATTATCACCACC\n++\n+@CCFDFDEGHHHFFJI77CJ:HIJJJGIJI?GH3JJ)DBGJ#A=D8JF?#DBGJ.BIFJG(.#F=#C?AEF7DJ?H#5@>:DCDDDIB+E#;#3D:93BC\n+@NC_011750.1-6/1\n+ACTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGAAGTTTTTCGATCGGATCGATAACGGTAACG\n++\n+BC@FF=FFHHDHHGDAJ>GIIIGGJGAJI?I@J)II?GFJ?IIIJJJJJCDHIHJG#0FG@<I#?DGCI#>#EHFCDDBD#E=DB8AC>E4C##C>B>D@\n+@NC_011750.1-4/1\n+TGCCACTGATGTACCACCGCACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGGAAAACAAGCCAGCTCTGTCAGGTGCGGGCTTGTTTCT\n++\n+CC?FFDFFDF=HDI+#EJ>#IJH?JFDFJGDIDGE?JJI9@JJGGJGIJHIGE9H/EJDCCH#F8AG#7C4A@#GD#@BGH2B@>#BD#E#?C##D@CDC\n+@NC_011750.1-2/1\n+CCTGCCTGCCATTGCTTTCCAGAATATCGGTAACACGCAGAAAACGTTCTGCATTTGCCAGTGATGTACCGCCGAACTTCAACGCTCACATGGTTGTTAC\n++\n+@@CFF8FF#HHAHH7@JIBG@JIHJF2BFJ#IDIB@IIIIB@J;IJCGHGIIEB>/GABJ#BFBJHDED6@F@8H#(:BDD<B#CC)-EB##DC>CAD>,\n" |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_R2.fastq Wed Oct 16 16:57:55 2019 -0400 |
| b |
| b"@@ -0,0 +1,180 @@\n+@NC_011750.1-90/2\n+ATCGGCAACACGCAGAAAACGTGCTGCGTTTGCCACTGTTGTACCGCCAAACTTCAACACTCGCTTGGTTGTTACCTCGTTACCGTTGGTCCAAAAAAAA\n++\n+?CCB=FFFHH2H<AAGGIC?#,#?J#G!GJIJJHA?CJ#?I0#JDCCJ#I04I7DH=JHIJDGJ#J5CI:FDAHCF7HE>D#CB##5@##5!AFDCE##D\n+@NC_011750.1-88/2\n+CAGCACCATGTGATCAGCCGGGATACGGCTTGCCGCAATACGGCGGGTGGACTAAGCTAGATACACGGTAGATTTGAGGTAAAGCCCCAATGCCATCAGT\n++\n+@@@ADFF,FFHD<E#GH#JJJ#IE#IE#EAJJICBB@0EJHC>JIABCB@9=A!HCH#D#C?##G@CJDIG);###?A?DDC##CCA:D!?(5@>#DDF:\n+@NC_011750.1-86/2\n+ACGAAAGTTTTCAGTTGCGCCAGCGGGAATCCCGGTTGGGCAGCGGCGAGTCCCCTCAGAAGTTCGGCAAAAATACGTTAGGGATCGAGGATATCGGAAA\n++\n+@1CFD?3<G8HHFGFI<AGG1IEJ?FIHEIIJJHIEJJHE#E?GJI;#JHF#C##HEIBJF#JCHFIEDC#EI<9F#BH!#C#CC#:##C#CD##BC##'\n+@NC_011750.1-84/2\n+GTTACCTGCCGTGAGTAAATTAAAATTGTATTGATTTAGGTCACTAAATACTTTAACCAGTAGAGGCACAGCGCACAGACAGATAAAAACTACAGAGTAC\n++\n+=C;F4CFF2GF:C#HJJJJAHJJGIH+#JJJ)J###FJJHG@IJCBI@AGEIEED@#FC#E@#BC5CI#=DED>CID;8#GEF@;=D@E#@@ABDFD(D'\n+@NC_011750.1-82/2\n+TCGAGGTAATGCCCCCCTGCCAGCAGTTTTTCGACCGGATCAATAAGGGTAACGTTGTGACCGCGCGCTTCTATTACGCCGGCCATAGTCGCGATCGACA\n++\n+:@?:FDD:<GF<DGB!BIG#GJJJJFE,C)HFFJIDF)GHI#J#F0#IJGHBGH?F)HGEI>J>)GFEH5>C7#DD>DB6>9CHHFA#C#CA@CDC:@3'\n+@NC_011750.1-80/2\n+ATCAGCCTGAATACGACTTGCGGCGATTCGGCGGGTTGACTCAGCGATATCGTCGTTGCATTCGATTTAATGCCCCACTGCCAGGAGTTTTACGTCCGGA\n++\n+=<C+FAD#A<HFAEEFAJCGI#IG!FI!#@I:EIBD#IFBJ?I3H#GJJJBH!#?#G##F?IIHE##EHDJFHEHCFCBEAFCA#DACDB5#>#!###C'\n+@NC_011750.1-78/2\n+CAGTGCGGGCTTTTTATTCGACCAACGGTAACGAGGTAACAACCATGCGAGAGTTGAAGTTCGGCGGTACATCAGTGGCACATTAAGAACGTTTTCAGCG\n++\n+CB;F=CFFHHHHHIC#EGIHCHAHI#J4A1H@JI<19:I3JHJGA?GHIB;##FHIGFJJHG)FCBHEDDGC5F#C#D4E#BH##CFC5EA#BCC##>CC\n+@NC_011750.1-76/2\n+TAGCAGCGTCTGAACTGGTTACATGCCGTGAGTAAATTAAATAGCTTTTGAGTTAGGTCACTGAACACTTTAAGCAAGATAGGGATAGAGCAGATAGAGT\n++\n+BB?4=FD#HGHDHJI2FG:)JG#?JH+I+#FIJIJ#IG*H1##!#I#D;?D#IGBG7EDAFJ#CF#D@FE#HE#HED#)I<D##>ADC!7EB###D#A#!\n+@NC_011750.1-74/2\n+ATTGCCCCAACAAACTAATGCCATGCAGGACATGTTTGATTTGGGCAAATACCTGATCGCCGGAAGTGTTTAGTTGAGCCAGCGTGAATCCCGTATGGGC\n++\n+C#BAF#DFF3GFBJG#IJJH@JCEJAJG?JJ0JGGHH#@1:JIFI9GF#F#ADDICHHJ!GI#EBF:#FD#IAGB###C#BDBH#5>EE:EB###AC>A?\n+@NC_011750.1-72/2\n+ACATTATCTCGCCACAGCAAATCAGCGCAGCGTTGATGCTATGGGGGCACTGCCCGAACAAACTACTGCCATACAGGACATGTTTTAATTGGGCAAATGC\n++\n+?C=DF!FFGHHHDJA#<CAGCJB?IJ?B;IGGHI)HIIGCH;!#4?#CGBIJB98#8DCC)JJHG#BCHIHC#GC<#DDD#CD?DFA#?D@CD>>B@D#5\n+@NC_011750.1-70/2\n+CTCGTTCCCTTGGGTCGAAAAAAAAACCCGCACTGTCAGGTGCGGGCTTTTTTCTGTATTTCCTATACGCTTGAGCCCGCACCATTACCTGTGCTAATGA\n++\n+BBBF4F#;CF<#FF)JI,BJ,9+:H#C<?I9#GJJIJJJ3D#<JFAI?D#7F<@IJA##GI=GC#E##C##I#AFDDDF#D#D!@ADDBF>?(#D>C#>'\n+@NC_011750.1-68/2\n+CACCTTCACCATTACCACAGCTAACGGTGCGGGCTGACGCGTACTTGAAAAACGGAAAAAAGCCCGTACCGGACAGTGCGGGCTTTTTTTTCGACTAGAG\n++\n+CCCD+FFFHH?BFA<E+EJJ!BJJCII)EI#CGJJHHHGG?IJI##4.D##DB!CHI4I9JJFDID#C(F#BCH5DH@D?BDEED1CC@@D>;?D###C'\n+@NC_011750.1-66/2\n+ATACGTTCGGCATCGCTGATATTGGGTATATCATCATGGACGCTGATGGTTGTTTCAATCACCGCGACCATGTGGATTGTGATTTTGGAGGGGGTAGAGA\n++\n+@::4FD#FFH>H+J+J@IJ+I1FEIIHG+##G3:I(HJJ#I9JI#JIBHHCAIJIFGC#HD#AF=#GIJF!DJHA#F#ACEFEDDC5@#9#B>B#CC#BC\n+@NC_011750.1-64/2\n+TGATTTTGGCGGTGGCAGAGAGGACGATGACCACCTGCCCCTGCCTGGCATTGGTTTCCCGAATTGCGGCAAGAGGCAGAAAATGTTGTAATTTTGCTAC\n++\n+BB:?F=D;AFHH#GIJIGJGAIJHJE!)G#1CH@IGF@IIIDEJJ-IGHI#IF#FDDFE#FGC<!#HCAD75#D#IFFCBCC?#CFB#A###DB<DC#3'\n+@NC_011750.1-62/2\n+TGGATTAAAAAAAGAGTGTCTGATAGCAGCTGCAGGATTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTAACTTAGGTCACTAAATGATTTAACCGA\n++\n+##CF=F;DG?BHFF;FHF?AI2BFCJEGJI<#I#J###IG>JEICG8J#D9HFF2JCGECDHC=H=AG=#?C#F=A@C?BHC+B#?AC#!#AC>D@C##'\n+@NC_011750.1-60/2\n+GTTACCTCGTTAGCTTTGGTCGAAAAAAAAGCCCGCACTGACAAGTGCGGGCTGTTTTCTGTGTTTCATGGACGCGAGAGCCCCCCCCGTGACCTGTGGT\n++\n+BC@DFDDF2H+F#<C:HHHFJG?FIJH1GII?HDIHIBGJ!HC#IH9D=IH.?#HJJ@#D#JHH=D@#HI#GC@G>##D>FCB#D##CA5#C#D<?;CA'\n+@NC_011750.1-58/2\n+CCGAAGTTCTGACGGGACTCGCCGATGACCAACTGGGATTCCCGCTGGGGTAACTTAAGACTTTCCGCGATTAGAAATTTGCCTAAGAGAGACATGTCAT\n++\n+C@CF:#FDFHHHHEJJ+IIJDHID+G##HICH*#FB2=IIJIDI#=H5!B#AJII#@I#JFDFGE##G?GC/CH#C#DD##DB#C9#!#4!CDC>>C@#'\n+@NC_011750.1-56/2\n+CCATTAGCGGCCAAGAAGCTTTAACCAATATCAGCGATGCCGAACGTATTTTAGCCCTACTTCTGAAGGGACTCGTCGCTGACACACCTGGATGGCCGCT\n++\n+@CC#+FCAFCHHH!"..b"TAATGGCGGTGGACTTTTTCTCGCGCCGGCAATTGAGCGCAGCGTTGATGCTGTC\n++\n+@=@+=CF:FHDGF<HJGFCC?HJDCIFI?+1IBHJG#HIG?*#IBIII/#.BG#I!H=H!CIHHDG?D?##D1)@CH#@##CBDC;D;CA;#>#CDD#@'\n+@NC_011750.1-34/2\n+GGCAGGGGCAGGTGGCCATCGTCCTCTCTGCCCCCGCCAACATGACCAACCACCTGGTGGCGATGATTGAAAAAACCAATAGCACCCAGGATGCATTACT\n++\n+@@@FADDFHHHAH92FFJ!GECAEECJG##JHDAHIJ*GJ!<*!C?DI#D=EHGJ2JJHJJGGAJ=#HBEFBIHA<#F#:<@D#!D5ECFDCCB#CD#@'\n+@NC_011750.1-32/2\n+ACGGCGGGTGCACTTAGCAATATCGACGGTAGATTCGAGGTAAGGCCCCACTGCCAGCAGATTTTCGACCGGGTCGAGAACCGTAACGTTGTGGTAGCGC\n++\n+?BCF4;DDH<#3HG#HGHJ#>AGGHAE?DDII+GF?IJIG*JI#BIHICFHGIC6DHGH##DI(#>CG;7>A##C@F#(:D#EBA#I#DC8D##!#?>DC\n+@NC_011750.1-30/2\n+TTGACCCAATATCACCGATGCGCAACGGATTTTTTGCGAACATCTGACGGGACTCGCCGCGGCCCAACCGTGATCACCGCTCGCGCAACTGCAAGAATTC\n++\n+B@+D1F0DAEHFGD#HA3JJI##HIFI#IGGGJH!#G#EJG#A#DBIHEFC;GEJBJGCH'J<#E;#.@D#HD>##DDD#7#@EC;,CFC?#CC##!;?5\n+@NC_011750.1-28/2\n+TACTCGCATTGTTGTTACCTCGTTGCCTTTGGTCGTAAAAAAAGCCCGCATTGTAAGGTGCGGGCTTTGTGCTGTGTTTCCGGTACGCTTCATCGCGCAG\n++\n++CBFBDFDH#HHHEHHJJJIE<JJ#HDJHIHIGAI!IHEFH#1@FIJ@HI!#JI#JDDI#)DIHHDGD#(#F:4#EIH#CD#CCFCC>#@A9!<#DDD<'\n+@NC_011750.1-26/2\n+CACTGCCCGAACAATCAACTGCCATACAGAACATGTTCGATTTGGGCACATACCTGATCGACGAAAGCTTTCAGTTGCGCCAGCGGGAATCCCAGGTGAT\n++\n+BCCFFFAA#HHH+J+E#A#JJGICA#FC1#JJJIIII##IIJHJII>I#AF#IDC#FIEHIDFI;CF!DFF>DB&@+A)3DE4C;CDDA5B>D###CD#'\n+@NC_011750.1-24/2\n+AATTACAGAGTATACAACATCCATGAAACTCATTAGCACCACCAATACCACCACCATCACCATTACCACATGTAACGGAGCGGGCTGACGCTCCCAGAAA\n++\n+B@@F4CFFH+B2#+?JII?JJ,?<+IJ@J#GHH#GID>H*BJ?D!F9I9DF1FICHG;JF@D8JEGHJJB#=?@D?HG##=D;ECDC,FAD8##1CD#BD\n+@NC_011750.1-22/2\n+TCACCATTTCCACAGGTAAAGGTTCGGGCTGACGAGTACAGGAAACACAGTAAACGGCCCGCACCTGACAGTACGGGCCTTTTTTTCGACCATAAATAAC\n++\n+:@CAFEFB#HDAH2*;JIF#JGI#?IBIG#HIHG#B0IH:HJFG#GIJ9<!#IH##CDIJEEG##GC3D#A)#HF)BC#DE#DCEED8>C2D#E##CA>'\n+@NC_011750.1-20/2\n+CACCGTCCGCTCTGCCCCCGCCACAATCACCAACCACTTGGTGGCGATGATTGAAAAAATGATTAGCGGCCCAGATGCTTTACCCAACACAAGCGCTGCT\n++\n+@BCFF;FA+FHF,CEHJC+JGHD#FGIJGF1?1J9#)#D;GBHHH#<FBABIJIJDCHC!#E;>DCBECGH##CDFCH>H:DD6CDD#@##BC#D#C(D'\n+@NC_011750.1-18/2\n+GTAGATGCGAGGTAATGCCTCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTAGGACCGCGCGCTTCTAGTTCGCTGGCCTCAATGGCGA\n++\n+@C+F4C!FHHHF#JCCHCJ!J0JHGC<#GIC:IE9JI:II9G9;EFG#IF#GHJB.?F:IBF###9#HBHDDBEGH:@I#J#DCH#D4D###C#9C><@D\n+@NC_011750.1-16/2\n+ACATTTTCTCGCCACGCCAAATCAGCGCAGCGTTGTTGCAATCCGGGCTCGGCCCCAACAAACTAAGGCCATGCAGGACATGTAATATTTGGGCAACTCC\n++\n+CC=FFFDFHHGH2JGJ#IHIE@HJJI#IFABF;G?#?II!HBJI@BHB#<#CEG@B>C#HHC;JJD#8<G9H##D@A>DBCDH#?9@CCB@>HC:E#:#@\n+@NC_011750.1-14/2\n+GGGCAGCGGCGAGTCCCGTCAGAAGTACAGCAAAAATATATCCAGGAGCGCTGATATTGGGTAAAGCACACTGGAAGCAAATGGGTTTTTAAAGCACCGC\n++\n+=C?DFF>DDHHH?JCIAII<GJ32+##J##HCJJJHH8##J#I#J#J#IG?;BECEECCFE#JC#J#E##E##A##CI#3BBAE#E>B:D#DD#3D#:A'\n+@NC_011750.1-12/2\n+GTTTCCTTGTTACCTTTGGTCGAAAAAAAAGCCCGCACTGTCAGGTGCGGGCCTTTTTCTGTGTTTCCTATTCGCGTCAGCTCGCACGGTGACCTGTGGT\n++\n+=@@#=F,!HHGHBI+J2?JIHI<IHJ2GCBEHJJH:GI:GCIFHEGDGIA?C#F0ID@@IGHCEG#H;H#F#F6F5E8ECC##CD3?#CD#+A?D#AC@4\n+@NC_011750.1-10/2\n+ATGCTTTACCCAATATCAGCGATGCCGAACGTATTCTTGCCGAACGTCTGATGGGACTGGCAGCTGCCCATCCGGGATTCGCGCTGGCGCCACCGATGAC\n++\n+BB@FF0=FHFHF?I@+J4:JJAI:JEIFEFJ@<@*#DCIDJGI#<#9*5CI#HH@H*##FF#IHA#IG@E#:4J?B#CC#!C<C;C<ADA#9B##E##C<\n+@NC_011750.1-8/2\n+CCCTGCCTGGCATTGCTTTCCGGAATATCGGCAGCACGCAGAAAACGTTCTGCCTTTGCTACTGATGCACCGACGAACTCCAACACTCGAATGGTTATTA\n++\n+C@CDA;DDDHHGHBADJAJ;?#GCACHHH<?GG#.J@IBHG#9=BEGBIDDJE#@ICJC#)GFHHHE#CJE##H=@?GD#>:#E;?CD>#DBD?5A#EBC\n+@NC_011750.1-6/2\n+TGCCCAACCGGGATTCCCGCTGGCGCATCTGAAAACTTTCGTAGATCAGGAGGTTGCCCAAAGTAAACATCTCGTGCATGGCATAAGGCTGTTGGGGCAG\n++\n+@1B4FDFF=CD?2I#IJF<<EFIGFFJ#JIGBJ<GIICGJHJ#IF*DBGGE##BGFIEGH>8##CDJ#HB#C=#>F=D#G@DHA#B#!#CC<DC@<#?A'\n+@NC_011750.1-4/2\n+TGGTTACCTGCCGTGAGCAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCACTATGGGCATAGCACACAGACAGATAAAAATCACAGACT\n++\n+?##D+FD;@H+<#HHEI#4IJA8HE9EJJ?G??HJCGCGI?HJB8FIJGJFF(I7G#GEJJ#;)G#D3C#JFEH#H@EEJDBCD;D@<>E;9#B@CC#!'\n+@NC_011750.1-2/2\n+TTTATTGCCTTAGGTCACTAAATACTTTAACCAATACATCCATAGCGCACAGACACATAAAAATTACAGAGTACACAACATCCATGAAATGCGATAGCAC\n++\n+8BCDFFD)HHHH>AIIJJJJE*J<JBJC?CEC#?J##B##@JIF0D>#A9JH@JJ#9JDD=JIA)FA:#C==?#FCA#DD9CBCBADD?#(C###9D?BD\n" |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_bracken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_bracken_report.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Escherichia coli 562 S 42 1 43 1.00000 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/NC_011750.1_simulated_kraken_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_011750.1_simulated_kraken_report.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ + 4.44 2 2 U 0 unclassified + 95.56 43 0 R 1 root + 95.56 43 0 R1 131567 cellular organisms + 95.56 43 0 D 2 Bacteria + 95.56 43 0 P 1224 Proteobacteria + 95.56 43 0 C 1236 Gammaproteobacteria + 95.56 43 0 O 91347 Enterobacterales + 95.56 43 1 F 543 Enterobacteriaceae + 93.33 42 0 G 561 Escherichia + 93.33 42 0 S 562 Escherichia coli + 93.33 42 42 S1 585057 Escherichia coli IAI39 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/bracken_databases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracken_databases.loc Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +test_entry "Test Database" ${__HERE__}/test_db/database100mers.kmer_distrib |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/reproduce_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reproduce_test_data.sh Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,29 @@ +#!/bin/bash + +# This script produces a small kraken2 database containing only a ~1kb portion each of a salmonella and ecoli genome +# It requires kraken2, art and entrez-direct (all available on bioconda) +kraken2-build --db test_db --download_taxonomy +mv test_db/taxonomy/nucl_gb.accession2taxid test_db/taxonomy/nucl_gb.accession2taxid_full +grep -e 'NC_003198.1' -e 'NC_011750.1' test_db/taxonomy/nucl_gb.accession2taxid_full > test_db/taxonomy/nucl_gb.accession2taxid +esearch -db nucleotide -query "NC_003198.1" | efetch -format fasta > NC_003198.1.fasta +esearch -db nucleotide -query "NC_011750.1" | efetch -format fasta > NC_011750.1.fasta +head -n 14 NC_003198.1.fasta > NC_003198.1_1kb.fasta +head -n 14 NC_011750.1.fasta > NC_011750.1_1kb.fasta +kraken2-build --db test_db --add-to-library NC_003198.1_1kb.fasta +kraken2-build --db test_db --add-to-library NC_011750.1_1kb.fasta +kraken2-build --db test_db --build + +# Simulate 100bp reads from ~1kb portions of genomes +art_illumina -sam -i NC_011750.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_011750.1_simulated_R +art_illumina -sam -i NC_003198.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_003198.1_simulated_R + +# Generate kraken reports +kraken2 --db test_db --report NC_011750.1_simulated_kraken_report.txt --paired NC_011750.1_simulated_R1.fastq NC_011750.1_simulated_R2.fastq +kraken2 --db test_db --report NC_003198.1_simulated_kraken_report.txt --paired NC_003198.1_simulated_R1.fastq NC_003198.1_simulated_R2.fastq + +# Build bracken kmer distribution files using default kmer-len=35 and read-len=100 +bracken-build -d test_db + +# +# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_003198.1_simulated_kraken_report.txt -o NC_003198.1_simulated_bracken_report.txt +# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_011750.1_simulated_kraken_report.txt -o NC_011750.1_simulated_bracken_report.txt |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database.kraken --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database.kraken Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +C NC_003198.1 220341 910 220341:169 A:67 543:23 220341:9 A:42 220341:9 543:65 220341:134 543:2 220341:356 +C NC_011750.1 585057 910 585057:11 A:41 585057:116 A:67 543:24 585057:7 A:42 585057:10 543:64 585057:134 543:2 585057:358 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database100mers.kmer_distrib --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database100mers.kmer_distrib Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +mapped_taxid genome_taxids:kmers_mapped:total_genome_kmers +0 220341:2:811 585057:2:811 +543 220341:23:811 585057:24:811 +220341 220341:786:811 +585057 585057:785:811 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/database100mers.kraken --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/database100mers.kraken Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +NC_003198.1 220341 220341 910 0:2 543:23 220341:786 +NC_011750.1 585057 585057 910 0:2 543:24 585057:785 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/hash.k2d |
| b |
| Binary file test-data/test_db/hash.k2d has changed |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/9C7DdW7GAD.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/9C7DdW7GAD.fna Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,17 @@ +>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome +AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATAT +CGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGG +CGGGCAGATACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTAC +ACAACATCCATGAACCGCATCAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGT +AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGAACAGTGCGG +GCxxxxxxxxCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT +ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC +AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTG +GCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAA +CGTATTTTTTCTGACCTGCTCGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCA +CGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAACATGTTTTGCATGGTATC +AGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTGGCGAAAAA +ATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGGTGATC +GATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG +GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCG +GGCTTTACTG |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/cWk1IBlK73.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/cWk1IBlK73.fna Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,17 @@ +>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome +GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTxxxxxxxGAGTGTCT +GATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGT +CACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACA +CAACATCCATGAAACGCATTAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGTA +ACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGC +xxxxxxxxCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC +ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG +GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGC +GATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACG +TATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCA +ACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAG +TTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAAT +GTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGA +TCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA +GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGG +TTTCACCGCC |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +ACCNUM NC_011750.1 NC_011750 +ACCNUM NC_003198.1 NC_003198 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ACCNUM NC_003198.1 NC_003198 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ACCNUM NC_011750.1 NC_011750 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/opts.k2d |
| b |
| Binary file test-data/test_db/opts.k2d has changed |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/seqid2taxid.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/seqid2taxid.map Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +NC_003198.1 220341 +NC_011750.1 585057 |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 test-data/test_db/taxo.k2d |
| b |
| Binary file test-data/test_db/taxo.k2d has changed |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of bracken database in the required format --> + <table name="bracken_databases" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/bracken_databases.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r b7b1c8bf7ae0 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Oct 16 16:57:55 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of bracken database in the required format --> + <table name="bracken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/bracken_databases.loc" /> + </table> +</tables> |