Next changeset 1:402b67d1af7d (2019-01-23) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264 |
added:
macros.xml mash_screen.xml test-data/ERR024951_seqtk_sample_1000_1.fastq test-data/ERR024951_seqtk_sample_1000_2.fastq test-data/NZ_MYON01000010.1.msh test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv |
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diff -r 000000000000 -r bac720dc1948 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 07 15:09:58 2019 -0500 |
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@@ -0,0 +1,6 @@ +<macros> + <token name="@TOOL_VERSION@">2.1</token> + <token name="@INTYPES@"> + fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz + </token> +</macros> |
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diff -r 000000000000 -r bac720dc1948 mash_screen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mash_screen.xml Mon Jan 07 15:09:58 2019 -0500 |
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@@ -0,0 +1,74 @@ +<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01"> + <description>determines how well query sequences are contained within a pool of sequences.</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mash</requirement> + </requirements> + <version_command>mash --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$queries' queries.msh && + mash screen + $winner_takes_all + -i $minimum_identity_to_report + -v $maximum_p_value_to_report + queries.msh + '${ str($pool).replace(',', '\' \'') }' + > '$output' + ]]></command> + <inputs> + <param name="queries" type="data" format="msh" /> + <param type="data" multiple="true" name="pool" format="@INTYPES@" /> + <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/> + <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." /> + <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> + </test> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> + </test> + <test> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/> + <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> + </test> + </tests> + <help><![CDATA[ +Description: + + Determine how well query sequences are contained within a pool of sequences. + The queries must be formatted as a single Mash sketch file (.msh), created + with the `mash sketch` command. The <pool> files can be contigs or reads, in + fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from + standard input. The <pool> sequences are assumed to be nucleotides, and will + be 6-frame translated if the <queries> are amino acids. The output fields are + [identity, shared-hashes, median-multiplicity, p-value, query-ID, + query-comment], where median-multiplicity is computed for shared hashes, based + on the number of observations of those hashes within the pool. + ]]></help> + <citations> + <citation type="bibtex"> +@article{ondov2016mash, + title={Mash: fast genome and metagenome distance estimation using MinHash}, + author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M}, + journal={Genome biology}, + volume={17}, + number={1}, + pages={132}, + year={2016}, + publisher={BioMed Central} + } + </citation> + </citations> +</tool> |
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diff -r 000000000000 -r bac720dc1948 test-data/ERR024951_seqtk_sample_1000_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR024951_seqtk_sample_1000_1.fastq Mon Jan 07 15:09:58 2019 -0500 |
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b"@@ -0,0 +1,4000 @@\n+@ERR024951.882919 IL5_5116:1:14:7970:4622#4/1\n+AACGCCGAGCCACATTGACCAGTTGGCCGAAGTGGAGTCGTCCCAGTCGTCACGGCATTTTTCCCAGCGCGCCATA\n++\n+DCCDBBBDBBCCBBBCCCDCCDBCBBCCCBCB@BBBBBDB@BCBBB@CB@BB@BBCBBBB@BBB@B@B@@@@@@@4\n+@ERR024951.3404519 IL5_5116:1:58:6775:14230#4/1\n+CGCCGTCACCGTAGCCTACATGGTATTGGGTGCGCAGACGCACCACGTCAAATGAGAACTTCACTAACAATAACGC\n++\n+CCBBBCCCBBBBCCCCCCC@BCC@CBBBBB@BBBBBB@BBB@B@@B@BBC@BB@@B@B@CBB@BB@CC@@BBBBB;\n+@ERR024951.1794060 IL5_5116:1:29:11292:8612#4/1\n+TCGCCGACGATATCCGCAGCCATTATGAGGAGTATGATGGCTTTGTGATCCTCCACGGAACCGACACCATGGCGTT\n++\n+CCCBBBCCCC@BBB@CBBCBC9CCBBB@B@@@@BBB@@@B@B@B@@@@@B@@@B@B@@@@@BB@@@@B@@@@@@@B\n+@ERR024951.635976 IL5_5116:1:10:6111:8194#4/1\n+AATGTCAGCCCCGGCCTGCGGTACCGGAGCCACCGGCGCCGGTTCAGCCCATACCCGCCCACCGGTCATGGCCCCG\n++\n+CCCBBBCCBCBB@BCC@@@@B@BCB:@@@@@B@@@@;@@@@@@@@@@@@@8@@@@@4@@@@@@@@@@;;@@@@@@@\n+@ERR024951.6397248 IL5_5116:1:113:4294:7215#4/1\n+TTCCTCTAACGGCAAATCGCCGCTTTCCAGACGGTTAACGATCTGCTCCAGTTCGCCCAGAGCAGTTTCAAAGCTG\n++\n+DCCCCBBBCCBBCDCBBCCBBBBBCBBCCDBBCC@BCCCBB@CBBCBB@@B@@CBBB@@B@:@@B<@@@@@@@@@@\n+@ERR024951.2279751 IL5_5116:1:37:2007:18070#4/1\n+GTTAATTCAGGACGATAATTGATGCCATATACAAGTAATTTCATACTTAAAAGTCCTCAGCAACATCCATAAAATA\n++\n+DCCCCCCCDDCBCDB@BBBC@@DBCCCCBBBBBBBBCBCCBBBDBBDCBBBBB@B@5@@@BBB@BB@@CCB@@@BB\n+@ERR024951.1984739 IL5_5116:1:32:4982:14139#4/1\n+CCGACGCTCAACGCCCTGGAGAACGTCGAGCTGCCGGCGCTGTTGCGCGGCGCCAGCGATAGCCAGAGCCGGGGCG\n++\n+CCCDDDBBBBCCDBBBBDCCBBBBC@B@B@B@BBC@@BBBB@@@@@@@@@@@@@@@@@@@@@:@@@@@@@@:@@@<\n+@ERR024951.607606 IL5_5116:1:9:18645:19363#4/1\n+GCTGGCGATATCGTAGCCCAGCAGGCCGTGGCGATTGGCGCGGATGACGCCGCCCTGACGCTGCATCGTAAGCTGG\n++\n+<<<<<$<<88<<:<'CCCBB@@CCCBBB@BB@B@@BBC@@@BB8@@<4@@@@@@@8@@@@@5@@@@8@:@:53+*2\n+@ERR024951.1159044 IL5_5116:1:18:4496:14012#4/1\n+CATCCAGGCTATCAACTGAAAGTGGTTGACTGCCTGCTAACGAACTTACATCAGCCAAAAACGACGCATATGGTGT\n++\n+DDBDCCDCCDDBBDCCDBCCBB@BBBCCBCCDCBCDCCCCBC@B@CCCBBBBB@BBB@BBBB@B@BB@@@BB@@B@\n+@ERR024951.6522628 IL5_5116:1:115:4782:7623#4/1\n+CACAGATCGTGCCGTCTCAGACCTTAAACGGGGCGTCGGGCGCCCCGATATAGTATCAGTCCAGAGCCGCGTAAAT\n++\n+CCBBBBBC@C@BCCBC@BBCBBCC@CCBBBBBB@B@CB@@@@BB@@B@@@@@B@@@@@@@@@@@@@B@@@@@7@@;\n+@ERR024951.4182454 IL5_5116:1:74:8108:1011#4/1\n+NCGCACAATGAATACAAACTTTGCCCCCAGAAAAAGCAAAGAGCGCCACACCTGCAGGAGAAACATAAATGTCATC\n++\n+#9999<<<<8>=>>>>>>>=>=>>>>>>>>>>>=33>>=>>>>=>=>>>=>>==>=>==>>===>>>>=<=====9\n+@ERR024951.4084117 IL5_5116:1:72:10107:2705#4/1\n+CTTTAAGAGCTTTTTCGCCATGCTGGCGGTCAACGGCGACCTCTTTGTACCCGATTTTCTGGAACGGTTGGCGCGA\n++\n+CDCBBCCBBBCCBBBBDBBBCCCCCCCBB@B@BB@BB@@BB@B@@@@<@B@BB@@@@@@@@@@@@@@<@@@@@@*<\n+@ERR024951.5228707 IL5_5116:1:93:4560:9885#4/1\n+GTCTGCTTTGTGCCAGAAGCGGACACTGTTCACAATATCGAGTTAATCATTGGATATGTTGATCGCTCCCATTGAA\n++\n+DCDBBDDCBBBBBCCDBBBCBBBDBBBCBBBCBBBBBBBCBB@CCBCCBCCCBB@BB@@BB@@@@@BBBB@@B@@B\n+@ERR024951.4984369 IL5_5116:1:89:13014:2217#4/1\n+CCATTTGTGGCGTACAATCAAAACGCCTAACGGTACGCCGATGATAATCGCCAGACCGACGGCCAGCGCGACCAGC\n++\n+DCCDCBBBBBBBBDDBBBDDCBBBCBBBDCCCC@DCBBBBCCDCCBBBC@BBBCBBCCCC@@@@B@@@@BBB@@@C\n+@ERR024951.6386192 IL5_5116:1:113:15562:3629#4/1\n+AACCCGCTTATCGGTTCGGCGGGGGTCTCGGCGGTGCCGATGGCGGGCCGCGGATCGGAAAAAATGGGGGTGGGAT\n++\n+CCCCBBBBCCBBCCBCC@CCBBBBB@B@B@BB@B<@5@*-<'929<)8@240&-100(7(*89))5?<>*1)/+)'\n+@ERR024951.107949 IL5_5116:1:2:16582:11599#4/1\n+CCCGCATCCGCATAATCTGGCCCTGCGCACCTGGGTCAACGGCGAGCTGCGCCAGCAGGGCACCACCGCCGATCTG\n++\n+DCBB-BCDCCBBDBBBDBBCCCBBDDBBBBBBCCBBDCBCCBCBBBBBCBBBB@BB@@@@B@@@B@@@@@@9@@@@\n+@ERR024951.6798988 IL5_5116:1:119:10552:14383#4/1\n+TATTATTTCTGTCGAGATGAATATTGCTCAGGATAGCGCCAGCTTCCCGGTGATTGAGATCCTGCAAACGCATATT\n++\n+DDBBBBBBBBBBBDCBBBDDCCBBBBCCBBDCBCBBDBBBBCCCCCCBBC@BBCCCBBBBCBCCCBBB@CBBC@BB\n+@ERR024951.1312277 IL5_5116:1:21:12318:4085#4/1\n+GACCATCGCCGGCTGTCTCGCGATCCTCGCCGGACTGTATCTGTGCTGGCGGCTGCGCGATCGCCCGCAGGCGGTG\n++\n+CCCCCCCCBBBCCCC@BB'B@:@@@CBBBBBBC@@BC@@BBB@@:B@@@B@@7:@-::0-4/114;*-*5;-59(;\n+@ERR024951.6120272 IL5_5116:1:108:6383:16466#4/1\n+GCCAAACCTGCAGCGCCAGGTGATCGCCGATATGCTCCGCGACTGGGACAAGCGTTATCCTGGGCGCATTGAAACC\n++\n+DDCCCBBCCDDDDDBBBBDB@BBCCDBBBBCBBBCCBBBBBBBDCCB@BB@BBB@BBB@@@@@@@:B@@@B@@@@<\n+@ERR024951.1713237 IL5_5116:1:2"..b"@BBB@@@@@@B@@@@@@@<@@@@@@-@@@@5@5;7@@;;:B&-5;'(;\n+@ERR024951.2271366 IL5_5116:1:37:15192:15096#4/1\n+CTGTGGGGACGTACGGAGGCGGGCTACCAGCGCCGGGTGCTCGGCGGCCTGCGCCGTGTCGCAGTGATGATGGGCG\n++\n+DCDBBBBBBDDBDDC@C@BBBBBBBBBBB@B@BBB@B@@B@@@B@@@9@5@@<:@6#8$6<4*2-A(>>+@@@@<7\n+@ERR024951.2406425 IL5_5116:1:40:8349:3633#4/1\n+CGCCATTGTGTAAATAATGGAATCAAAGCGCCAACGGCCTGATGCGCTGCCGCCATATAGTTGGGCAGCGCAATCA\n++\n+DCBBBDCCBB@BCBBBBBCCCCCDDCBBCBBBBBCB@BCC@@@@@BB@BB@B@@@@@@@@@@@@@@@@@@@@@<B@\n+@ERR024951.2423944 IL5_5116:1:40:7356:9851#4/1\n+TGATTAACAAGAAAGTGGCGCCGTATTTTTTCCTCGGTTTTGTGCTAATGGCCTATTTGAAAATCCCGGTGACCGG\n++\n+DDDDCCCCBBBBBBB@BBBBBBB@BBBBBBBBBCBBB@CBBB@BBBC@BB@B@BBBB@@@B@@@@@@@@@@@@@@@\n+@ERR024951.963405 IL5_5116:1:15:14263:10597#4/1\n+ATCCGAGCGNACGTAAAATCGGTTCCTATCTGATGTGGGTAGCGATCACCGCCGCCTGTATTACCAGCTCGATGTT\n++\n+DDDCCDBBB$DDCBDCBBBDDCBCCCCCBBBBBCC@BBB@CBB@@B@CBB@BB@@BB@@BBB@@BB@@@@<@@@@@\n+@ERR024951.2142254 IL5_5116:1:35:1189:9353#4/1\n+AGTATCTGCTGGATCAGGGGTATCACGTTATCCCGGTTTCGCCGAAGGTGGCGGGCAAGACGCTGCTGGGACAGCA\n++\n+@@@@@@@@-@@@@:@@8@@@2-;;?@@;97@@@;@@<;;85@@@@@@@@;@@@@@@9@@@@@@5:2@@59'22=94\n+@ERR024951.5016495 IL5_5116:1:89:12666:13682#4/1\n+GAAGTCGAGGCTGTAACCCGAGGCCAGCCAGAACACCGAGTTATTACGTACCAGGTACTGGTAGCGCTTACTGATG\n++\n+CCCC@C@CBBB@C@B@BCBBBBBBBB@@C@@@B@@@BB@B@@BBB@@@@@@B@@@8@@@@@@@@@@@:@@@@@@8@\n+@ERR024951.1509728 IL5_5116:1:24:8476:12109#4/1\n+CATCGACCACAGCCAGCCGAAACGCACCAGCATCAGCGCGGCATAGATCAGGATAATGTCGGTAAACAGCATCCAG\n++\n+DDDDDDDCCBBBDCCDDC$CCBBDBBBBBDCBDCCCCB@BBBBCBBB@BBC@@BBBBB@B@@@@@@@B@@@@@B@@\n+@ERR024951.3926293 IL5_5116:1:68:10190:20292#4/1\n+CGAAATAAGACGACGAGGGTTTATTTGTACAGCTCAGCGGTGGCGTGCCAGCTATCGCCGGTACGTGCTTCAATAA\n++\n+DDBCBBBBBBBCBCDBBBB@CBBBBBB@BBBBBBBBBBB@@@@@@@@@@@@@@@@@@@@@@@@@:8@@@@@;@@@@\n+@ERR024951.4937927 IL5_5116:1:88:12469:5363#4/1\n+ACGGAGGGCTTGTAGTTGAGCATAGCCTGGTGCGAAGTGAATTCAAGCTGGGGAAACGCGGACATAAAAAAGCCGT\n++\n+DDDCCB;BBDCCBBCCCCBBBDCBBDCCDC@BBBBCC@BBBCCCCBCCDCBBBBBBB@BBB@CBBBB@B@@BCB@@\n+@ERR024951.5925702 IL5_5116:1:105:3270:10599#4/1\n+AACATATGCACATGATGGTGACTGTCGAGATGCGTTGGCTCGCTGCCAAATACGTCGATGAAACGCTGATACTGAC\n++\n+DCCBBBBBD@BBB7DCCC@BBDDDBBCDBBBBDBBBBBCCB8@@@@C@@B@@@@@@@@@@@@@@@;@@@@@9@@@@\n+@ERR024951.425152 IL5_5116:1:7:15424:4386#4/1\n+AAATATTTCAGTCGTCTTAAGTTCATTTTGCCTCCTGTAAGGAACGCCAGCGTCAACGCTGGGAGTATGATGCACT\n++\n+DCBBBBBBBDDCDDCDBBBCCDCCCDCBBBCCCBBBDBBCCCBCBCBB@@C@@CBCBB@@BB@@B@B@@@BB@@@8\n+@ERR024951.1231222 IL5_5116:1:19:12205:17292#4/1\n+ATGACCCTGTCAGGTATCAGCTGATTATTATCTGCCTGTGCCAGGAACAGCATATCGCTGACCATTTTGGTCATCC\n++\n+DDDDDCBBDBBDDC@CBBDDCDDBDCCBBBBBBBDCCC@BBCCBBBCCBBBCCBBBBBBCB@CBBC@BB@@BB@@B\n+@ERR024951.3813054 IL5_5116:1:66:15592:15150#4/1\n+CGTCTGTCGGGTATCGCGCCGCTGGATCAGATAATAGGTGGCGGTGGGTAACACTTCACGGATGGGGATCATCACC\n++\n+DDCDBBBBDCB@DBBCBBBBBBBDC@CCBC@BBBBBBB@B@BBB@BBB@@B@@@B@BBB@@@@@@@@@@@@@@@@@\n+@ERR024951.3743468 IL5_5116:1:65:6095:7731#4/1\n+GTGATGCTGATGGTCAACCCGAGCGTGATTGCCGCCTTCACCATGATCACCACGGTGTCGGCGATCCTGTTTATGT\n++\n+DCBBDCDDD@CDCBCCCCCBBCBBB@BBCCCBBCB@BCB@BBBBBBB@@B@@BBB@B8@B@@B@@@@@@@@@@@@@\n+@ERR024951.4977094 IL5_5116:1:88:12105:19442#4/1\n+GCATCCTGCCAGCTCAGCTCGGTCTTTTCCATTTGTGCGCGGTAGCGGTCGCTGGCGTTAAATACCATCAGCTCCG\n++\n+DDDDDCCDDCCCDDBBDCDBBC@CBBBBBCBDCBB@BBBBBB@CCCBB@BBBBBBCB@BCB@B@B@@@B@@@@@@8\n+@ERR024951.502181 IL5_5116:1:8:12994:7502#4/1\n+AGGGCTATTATGGCTGGGGCTTCATTAACGATACCCAGATCCTAACGCCGCGCCTGAAAACCCCCATGATCCGCCG\n++\n+CCCBBCCBBBBBCCCCCB**9=929?4=*79:90?@2:@59@7@@)59=6;5:=:4@@@@;@@BB:25@@2@@@@2\n+@ERR024951.5261665 IL5_5116:1:94:4048:1573#4/1\n+CAGGCCAGATGCGTACCTTCCTGGATCAAACCGGTGGACTGTGGGCATCCGGCTCGCTATACGGCAAGCTCGGCAG\n++\n+DDCCCCCDBBBDBBDCCCCCCCDBB@DCCBBCCB@BB@BBB@@@@BBBBBB@C@B@B@@@@B@@@@@@@@@@@@@@\n+@ERR024951.5800706 IL5_5116:1:103:10685:8400#4/1\n+TTCATGTAAACTGAAAAATGCCGGATAGCCCGTATCCGGCATGGGCTGTACCTATACCGCAAGCAGCCGATCCATC\n++\n+DCCDDD-BCBBCDDCBBBBCDCCCBCBBBBBB@CBBBBBBBB@@@BBB@@B@BBBBB@BBB@@B@@@@@@@@@@@@\n+@ERR024951.2073767 IL5_5116:1:34:8966:5387#4/1\n+TTCAGTCGTGTAGTTGCTCACTACGCCGTATCGCCAATAGAGCTACTGAGTGTCCCGTTGACCATGTTCTGGATGC\n++\n+DCCBDBCC@B@BBBBC@BB@B@BB@BBB@BBB@BBB@@@@@@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@8@@@\n" |
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diff -r 000000000000 -r bac720dc1948 test-data/ERR024951_seqtk_sample_1000_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR024951_seqtk_sample_1000_2.fastq Mon Jan 07 15:09:58 2019 -0500 |
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b"@@ -0,0 +1,4000 @@\n+@ERR024951.882919 IL5_5116:1:14:7970:4622#4/2\n+ATATGCAAGCGTTGGGACGATATGCGCCGTCTGGCTAAAAAGGCGAAAGAGCAGGTGGCGGCGCGTGTCGGTTTTT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BB@B<@@BB@B@@BBA@@BB\n+@ERR024951.3404519 IL5_5116:1:58:6775:14230#4/2\n+TGGCGAAGTGGCATCAGTCGGGGACCCCGTGGTTGTTCCTGCATACTCCGGACATTGCCTTCGCCCCGGCACTGGT\n++\n+BBBB@BBBBBBBBBBBA@BBBB@:BBBBBB@BBBB@BBBB@B@BBBBBB@BBB8BABBBBBB<@BB@BBB@B9B1&\n+@ERR024951.1794060 IL5_5116:1:29:11292:8612#4/2\n+TAAATCGTCACCACGCCAATCGGCTGCGGAGTGATGGGGTGCACGATAAGATCTCCGCTGCCCTGCGGCGCCGGCG\n++\n+BBBBBBBBBBBBBB5BBBBB<BBBABABB@B@B1B:B@B8B@B@B@@9B3@@@@@@@@=9@@@8@@@@>@::@@4=\n+@ERR024951.635976 IL5_5116:1:10:6111:8194#4/2\n+AGCCGCCGGTATCTGGCTCAGCCCGCTGACCGATCGGGACGGACGGCTGGAGGCTATCGGCGGAGAGGGACGAATT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBB@@BB@@@B@B@@@@68@<@@:@<@@(@-8:3%'.%+.,\n+@ERR024951.6397248 IL5_5116:1:113:4294:7215#4/2\n+CCTGGGCGCGGAGTATATCACCATTGCGCGTTATTTGCTTACACGCGTGACTTCGTTACCATACCCGGTATTGCCG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBB@B@@@<@B@B@@@9B@B@B@@B@@A;=50>:%\n+@ERR024951.2279751 IL5_5116:1:37:2007:18070#4/2\n+TAAAAATGATACGAAATGAAAGTACTTTTCTTGGTGTCTTTCAACATTTCTATGATGACAATTTTTTTAATACTGA\n++\n+BBBBBBBBBBBBBBBBBABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBA@B@BBBBBBBB@B@BBB@\n+@ERR024951.1984739 IL5_5116:1:32:4982:14139#4/2\n+GGATCGTGAGTGACGAGGATCAGGGCGGTGCCGTGTTCGCGATTAAGCGAGAACAGCAGATCGGCAATTTTGTCCC\n++\n+BBB@BBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBBBBBBBBBBBB@BBBBB@BBBB@B@@B@@B@B@B@@@@@@\n+@ERR024951.607606 IL5_5116:1:9:18645:19363#4/2\n+GAGACCGCACGCACCAGATTGTGCAGGGTCTGCGCCGGCAGCTCCCAGTCCAGCCGGCCATCTTCCGGGGTACGAC\n++\n+BBBBBBBBBBBBBBBBBBBBABBBABBB@BBBBBBB@@B@B@@@BB@@3@@=@@@@@/@@;@@@@@@92:37<;(<\n+@ERR024951.1159044 IL5_5116:1:18:4496:14012#4/2\n+AAGGTTATTGCCCGAATCCCCTGATGCTTATTCTCGGTAAAACCGGTAGCATTATATGTACCGGTTTTATTTTATT\n++\n+BBBB@BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB=BBBBBBBBB@BBBBBBBBBBB@BBBBB@BBBBBBBBBBB\n+@ERR024951.6522628 IL5_5116:1:115:4782:7623#4/2\n+TGAACGCGGTGATGCTGCCCTGACACGCCACCTGATGCTGCGGGAATCGCAGCTGTGGAATTTCATTGACTCTCAT\n++\n+BBBBBBBBB@BBB@BABBBBBBBBBBBBBBBBBBBBBB@BBBBBBB@BAB@B@@B@BB@@@B@@@@@@@@<@@@9@\n+@ERR024951.4182454 IL5_5116:1:74:8108:1011#4/2\n+TATGACCGGTAATCAAACGCTTGCGTGTTTCGTTATCAATTTCTTGTACTGGCGCACGCATCGGCGTCTCCAGCCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBB=BBBBBBBBBBBBBBBBBBBBBBB@BB@BBBBB@@B@B@@B@@@@A@@@@7\n+@ERR024951.4084117 IL5_5116:1:72:10107:2705#4/2\n+GATGACGCGAACGCCGGGCCTCGTCAAGCTCGGTGATGTCGGTATGCAGGCTGACAATCCCGCCATCCGCCAGCCG\n++\n+B@BBBBBBBBBB@BB@BB@BBBBBBBBBBBBBB@8BB@@BB@@BBBB@B@@8B@B@BA@B@@@@@@@B@@@@@@8.\n+@ERR024951.5228707 IL5_5116:1:93:4560:9885#4/2\n+TGTAATCAGGGTATAAATAAGACATATATACCCTGAATTTTTTATTTCCCTGTAGATTTACTAGGCTTTAGTCCCG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@ERR024951.4984369 IL5_5116:1:89:13014:2217#4/2\n+CCCATCAATTTTTGCAGGACAAAGGTCTGCTGTAAGGAGCGACTATGGATACGATACATTATATGCTGGATAACGC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBAB@@BBBBBBB=B@@B@B@B@@=\n+@ERR024951.6386192 IL5_5116:1:113:15562:3629#4/2\n+ATTTGGATGAAAATGGGATACGACATGCGTATCCCATCCACTATTACATCGCCAGCACGTATTTCAGCATCACGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@@BBBB@<@BBBBB@BB\n+@ERR024951.107949 IL5_5116:1:2:16582:11599#4/2\n+CAGGCGGCCCACGCCCTCGACTTCAACGATCACCTCGTCGCCCGGTACCACGTCGGATAGCCCTTTCGGCGTGCCG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBBBBB@BBBB@BBBB@B@BBBBB@@B@BB\n+@ERR024951.6798988 IL5_5116:1:119:10552:14383#4/2\n+CGCCAAAGTTTTCCGGTACGCTGAAGCGACTCTGGTCCTTATTATGTTCCAGAAGCAGTACGCTAAAATCGTAATC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBB@BB\n+@ERR024951.1312277 IL5_5116:1:21:12318:4085#4/2\n+CAGATCGACGCCTAGCGTCTCCGACATATACAGATTGCCCCAGTCGTTAATCGCCGCCCGCACCACGTACACCAGC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBB@@B@@B@=@@@@@BB@@@@@@@@B\n+@ERR024951.6120272 IL5_5116:1:108:6383:16466#4/2\n+TCACTTCCACTACGTTCAGACGCAGCTCATCGAGACGGGCGTCTTCTTCTTCCGGCTGCCAGCCGGCGGGCTGCAG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBB@BB@@@@@@@@@@@@@@@=@@.@\n+@ERR024951.1713237 IL5_5116:1:2"..b"B@BBBBB@B@@@@@@@B@@@A@@@@@@@@@@@@@A@@@>@A@@@@@@2\n+@ERR024951.2271366 IL5_5116:1:37:15192:15096#4/2\n+CGGTGAAAATGACATCGGTATTGGCTTTCTCTTTGGTGAGGAACCAGTCGGTCACCTGGCGGCGCACCTCGGCGGT\n++\n+BBB@BBBBBBBBBBBBBBB@BBB@BABBBBBBB@BB@BBB@BBBBBB@BBB@BBBB@B@B@:B@B@@B@@@;@@@A\n+@ERR024951.2406425 IL5_5116:1:40:8349:3633#4/2\n+CTGACCATTGCATAGTGGGATTCTTGTCCTCACGCACCAGTAAGATTGATCCTTTGGTACTGTGCAGTGAGAATGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BB@BBBBBBBBBB=BB@BBBB@BB@A@B@B@@BB@\n+@ERR024951.2423944 IL5_5116:1:40:7356:9851#4/2\n+GAACACCCGGCGTAAATCGCGCGGCGTAATCCGGGTTTCTTCCTGCGCCTGCGGCTGCAGGGGCTCTTCAGAAATC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBB@@BBBBBBBBB@BBBBBBB@BBBBB@@BB@B@@@;@@@+@@@@@@&@7@@@;\n+@ERR024951.963405 IL5_5116:1:15:14263:10597#4/2\n+CAGCGGCATAGCCAGAATCAGCAGGATACCCAGCGGCAGGAAGGCGATGAACCAGGTGCCCCAAGAGATATTGATG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@@<@B<B=BB@@<@ABBB6B@@B<@@@B@@@@\n+@ERR024951.2142254 IL5_5116:1:35:1189:9353#4/2\n+CCCCCAGCTGCAGCCATAGCGTTTTCGCGCCGATGGCTATCGCTTCCTGCGCTACGCCCCACGCCGCTTCTGAATT\n++\n+BABBB@@9@B@B<@BB=:B7BBBBBBBBBB@B3BBBBB@B<@A@BBBBB<BB@9B@@@@BBB@@:B%3>=>B3BB@\n+@ERR024951.5016495 IL5_5116:1:89:12666:13682#4/2\n+CAGCGATTCGCGTTATATCGACGGCCTGAACATCGTGGTGGAAGCGCCGGAGGCGGGGTCGCTTGGCATCGGTACG\n++\n+BBBBBBBBBBBBBBBBBBBABBBBBBBBBBBBBBBBBB@BBBBBBBBBB@9BBBBBBB@@@<@@:@@0=@@@7@@@\n+@ERR024951.1509728 IL5_5116:1:24:8476:12109#4/2\n+GATTGTCCTGCTGTTCCTGCTGCCGTTTGCCTCCTATCTGATTGCCGAACATATCGGTGTCTCCGGCATCCTGGCG\n++\n+BBBBBBBABBBBBBBBB@BBB<BB@BBBBBBBBBBBBBBBBABBABB@B@@B@@B+B8?<=>B==@@@@@@@@@@<\n+@ERR024951.3926293 IL5_5116:1:68:10190:20292#4/2\n+ATGCCACTGCTGAGCTGTATAAATAAGTTTTAGACGTCAACGATTAACCTGACAAAAATTCTCTACCGCGGCCCGG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBABABBBBBBBBBA<B=@@@@A@\n+@ERR024951.4937927 IL5_5116:1:88:12469:5363#4/2\n+CTGGAAAATCGAAGTGGAAGATTTTCCGGCGTTTATCCTCGTCGATGATAAAGGCAACGACTTCTTCCAGCAGATC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBB@BBB@B@@@@B\n+@ERR024951.5925702 IL5_5116:1:105:3270:10599#4/2\n+ATTACGGCATTGTTGAAGCATATCGCAACGGCGTTGTGACCTCCACGACGGCGCTGGTCAATGGCGAGGCTATTGA\n++\n+BBBBBBBBBBBBBBBBABBBBBBBBBBBBBBBBBBB@BBBBBBBBB@BB@@=@@=@@A@@@@@@@@>:<;.//7'&\n+@ERR024951.425152 IL5_5116:1:7:15424:4386#4/2\n+ATCGCCATCCATGCGCTGTTTTTTTCACCATGTTGCACCGTTGTAGTGCGAATGTACCCCTAATGGGGCATACCAC\n++\n+BBBBBBBBB1BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BB@BBBBBBB@BBBBBBB@BB@@@B@@@@@@B\n+@ERR024951.1231222 IL5_5116:1:19:12205:17292#4/2\n+ACCAATCTGGTGACGCAGACTGAAATCGCACTGAGTCAGGATCGAACACAGAGGGAACTTGAGGATGTCCTCTATT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBBBBBBBBBBBB@BB\n+@ERR024951.3813054 IL5_5116:1:66:15592:15150#4/2\n+AGCTGGGACGGGAGCCAAAGGTGGGGATCGTCTGCGAAACGTTCTCATCCTGCATCAGCCTGGTGGTGAAAAGTGA\n++\n+BBBBBBBBBBBBBBBBBBBBB@BBBB9BBB@BBBBB@BBBB7BBBBB@BB@@BB@B@@BB@@@@@@@B@@@@@AB@\n+@ERR024951.3743468 IL5_5116:1:65:6095:7731#4/2\n+CACGGGTATCGTCTTCCAGGGTCAACAGCACCAGCACAAAGACGAAGAAGGCCATGCACACCCAGCACATGACTTT\n++\n+BBBBBB@BBBBBBBBBBBBBB@BB@@BBB@BBBBBBBB@BB@BB@BB<B@A@BBB@=@B=@@BBB@A@@@B@@@B@\n+@ERR024951.4977094 IL5_5116:1:88:12105:19442#4/2\n+GGTCGTCACCTGCGGATTAAGTCTGCTCGACGTCACCCTCGCGCTGACGCTCGGCGGTATCATGCTGGCGACCCTG\n++\n+BBBBBBBBBBBBABB@BBBBABBBBBBB@BBBBBBBBBBBBBBB@BBBBB@B@B@BB@@@@@@@@:@@@@:@@@A8\n+@ERR024951.502181 IL5_5116:1:8:12994:7502#4/2\n+GAGCGCAGCAGTCGACGTTATTGGTACCAATAACGGCGCGCGCGAATTTTTGCATCACATAGTTGCTTTCATTACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBB@@BBBBBBB@@BB@@@@@@B@@@BBB@BB@@@\n+@ERR024951.5261665 IL5_5116:1:94:4048:1573#4/2\n+TAAGGCGTGCCGCCGCGAACCTGGGAGACGTCAAAGAGTTCCTGTGCGGCATAGCATATCGGGACGATCACCATCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBBBBBBBBBBBBB$7BBBABBABBB@B<B@B@BB\n+@ERR024951.5800706 IL5_5116:1:103:10685:8400#4/2\n+GCATGGCGATCTATGGTCGGCGAACTGCGCGCTTGGCCCTGACGGCCCCTATATCTTCGATCCAGCCTGCTATTGG\n++\n+BBBBBBBBBBBB9BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB@BBBBB@B@BBBB@@BB@@<B@@@@@@@7B\n+@ERR024951.2073767 IL5_5116:1:34:8966:5387#4/2\n+CTCAGACGCTTGCTGGTCGCATTTAGTCTGGTGTTCATTCCACCAAGAGAAGTAGTGGCACCCTTGATCTCAGTCT\n++\n+BBBBBBBBABBBBBB<@BBB@BBBBB@BBBB@B@BB@B@BB@@@@@B@@@@:@@@=@=@@@>@@@<8@@42-0%;'\n" |
b |
diff -r 000000000000 -r bac720dc1948 test-data/NZ_MYON01000010.1.msh |
b |
Binary file test-data/NZ_MYON01000010.1.msh has changed |
b |
diff -r 000000000000 -r bac720dc1948 test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv Mon Jan 07 15:09:58 2019 -0500 |
b |
@@ -0,0 +1,1 @@ +0.768798 4/1000 1 9.64626e-22 NZ_MYON01000010.1.fa NZ_MYON01000010.1 Salmonella enterica strain BCW_4905 NODE_10_length_152932_cov_1.77994, whole genome shotgun sequence |
b |
diff -r 000000000000 -r bac720dc1948 test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv Mon Jan 07 15:09:58 2019 -0500 |
b |
@@ -0,0 +1,1 @@ +0.799067 9/1000 1 1.6653e-47 NZ_MYON01000010.1.fa NZ_MYON01000010.1 Salmonella enterica strain BCW_4905 NODE_10_length_152932_cov_1.77994, whole genome shotgun sequence |
b |
diff -r 000000000000 -r bac720dc1948 test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv Mon Jan 07 15:09:58 2019 -0500 |
b |
@@ -0,0 +1,1 @@ +0.777011 5/1000 1 2.58497e-27 NZ_MYON01000010.1.fa NZ_MYON01000010.1 Salmonella enterica strain BCW_4905 NODE_10_length_152932_cov_1.77994, whole genome shotgun sequence |