# HG changeset patch # User iuc # Date 1565797075 14400 # Node ID 7346619ad00509fc1fad2a7081d6d57806febec1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ commit d746438ee434696f2867394eca7a93d6ec704320" diff -r 000000000000 -r 7346619ad005 crispr_studio.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crispr_studio.xml Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,161 @@ + + + + facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect + + + crispr_studio + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputs and 'out_fasta36' in outputs + + + outputs and 'out_spacermatch' in outputs + + + outputs and 'out_spacermatch_mcl' in outputs + + + outputs and 'out_spacermatch_mcl_col' in outputs + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@UNPUBLISHED{moineaulab2018, +author = {moineaulab}, +title = {CRISPRStudio: Program developed to facilitate and accelerate CRISPR array visualization}, +year = {2018}, +url = {https://github.com/moineaulab/CRISPRStudio}, +} + + + diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,40 @@ +NC_010473 CRISPRDetect repeat_region 2994577 2994972 396 - . ID=CRISPR1_2994577_2994972;Note=GTGTTCCCCGCGCCAGCGGGGATAAACCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994577 2994606 29 - . ID=CRISPR1_REPEAT1_2994577_2994606;Name=CRISPR1_REPEAT1_2994577_2994606;Parent=CRISPR1_2994577_2994972;Note=TGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994606 2994638 32 - . ID=CRISPR1_SPACER1_2994606_2994638;Name=CRISPR1_SPACER1_2994606_2994638;Parent=CRISPR1_2994577_2994972;Note=GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994638 2994667 29 - . ID=CRISPR1_REPEAT2_2994638_2994667;Name=CRISPR1_REPEAT2_2994638_2994667;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994667 2994699 32 - . ID=CRISPR1_SPACER2_2994667_2994699;Name=CRISPR1_SPACER2_2994667_2994699;Parent=CRISPR1_2994577_2994972;Note=CTGTTTTCGCAAATCTATGGACTATTGCTATT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994699 2994728 29 - . ID=CRISPR1_REPEAT3_2994699_2994728;Name=CRISPR1_REPEAT3_2994699_2994728;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994728 2994760 32 - . ID=CRISPR1_SPACER3_2994728_2994760;Name=CRISPR1_SPACER3_2994728_2994760;Parent=CRISPR1_2994577_2994972;Note=GGGCGCACGGAATACAAAGCCGTGTATCTGCT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994760 2994789 29 - . ID=CRISPR1_REPEAT4_2994760_2994789;Name=CRISPR1_REPEAT4_2994760_2994789;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994789 2994821 32 - . ID=CRISPR1_SPACER4_2994789_2994821;Name=CRISPR1_SPACER4_2994789_2994821;Parent=CRISPR1_2994577_2994972;Note=TGGCTCTGCAACAGCAGCACCCATGACCACGT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994821 2994850 29 - . ID=CRISPR1_REPEAT5_2994821_2994850;Name=CRISPR1_REPEAT5_2994821_2994850;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994850 2994882 32 - . ID=CRISPR1_SPACER5_2994850_2994882;Name=CRISPR1_SPACER5_2994850_2994882;Parent=CRISPR1_2994577_2994972;Note=GAAATGCTGGTGAGCGTTAATGCCGCAAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994882 2994911 29 - . ID=CRISPR1_REPEAT6_2994882_2994911;Name=CRISPR1_REPEAT6_2994882_2994911;Parent=CRISPR1_2994577_2994972;Note=AGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994911 2994943 32 - . ID=CRISPR1_SPACER6_2994911_2994943;Name=CRISPR1_SPACER6_2994911_2994943;Parent=CRISPR1_2994577_2994972;Note=ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994943 2994972 29 - . ID=CRISPR1_REPEAT7_2994943_2994972;Name=CRISPR1_REPEAT7_2994943_2994972;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect repeat_region 2968265 2969028 764 - . ID=CRISPR2_2968265_2969028;Note=GAGTTCCCCGCGCCAGCGGGGATAAACCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968265 2968294 29 - . ID=CRISPR2_REPEAT1_2968265_2968294;Name=CRISPR2_REPEAT1_2968265_2968294;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGATGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968294 2968326 32 - . ID=CRISPR2_SPACER1_2968294_2968326;Name=CRISPR2_SPACER1_2968294_2968326;Parent=CRISPR2_2968265_2969028;Note=CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968326 2968355 29 - . ID=CRISPR2_REPEAT2_2968326_2968355;Name=CRISPR2_REPEAT2_2968326_2968355;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCTGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968355 2968387 32 - . ID=CRISPR2_SPACER2_2968355_2968387;Name=CRISPR2_SPACER2_2968355_2968387;Parent=CRISPR2_2968265_2969028;Note=TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968387 2968416 29 - . ID=CRISPR2_REPEAT3_2968387_2968416;Name=CRISPR2_REPEAT3_2968387_2968416;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTAACGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968416 2968448 32 - . ID=CRISPR2_SPACER3_2968416_2968448;Name=CRISPR2_SPACER3_2968416_2968448;Parent=CRISPR2_2968265_2969028;Note=GTAGTCCATCATTCCACCTATGTCTGAACTCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968448 2968477 29 - . ID=CRISPR2_REPEAT4_2968448_2968477;Name=CRISPR2_REPEAT4_2968448_2968477;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968477 2968509 32 - . ID=CRISPR2_SPACER4_2968477_2968509;Name=CRISPR2_SPACER4_2968477_2968509;Parent=CRISPR2_2968265_2969028;Note=CCGGGGGATAATGTTTACGGTCATGCGCCCCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968509 2968538 29 - . ID=CRISPR2_REPEAT5_2968509_2968538;Name=CRISPR2_REPEAT5_2968509_2968538;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968538 2968570 32 - . ID=CRISPR2_SPACER5_2968538_2968570;Name=CRISPR2_SPACER5_2968538_2968570;Parent=CRISPR2_2968265_2969028;Note=TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968570 2968599 29 - . ID=CRISPR2_REPEAT6_2968570_2968599;Name=CRISPR2_REPEAT6_2968570_2968599;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968599 2968631 32 - . ID=CRISPR2_SPACER6_2968599_2968631;Name=CRISPR2_SPACER6_2968599_2968631;Parent=CRISPR2_2968265_2969028;Note=AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968631 2968660 29 - . ID=CRISPR2_REPEAT7_2968631_2968660;Name=CRISPR2_REPEAT7_2968631_2968660;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCTCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968660 2968692 32 - . ID=CRISPR2_SPACER7_2968660_2968692;Name=CRISPR2_SPACER7_2968660_2968692;Parent=CRISPR2_2968265_2969028;Note=TAGTTTCCGTATCTCCGGATTTATAAAGCTGA;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968692 2968721 29 - . ID=CRISPR2_REPEAT8_2968692_2968721;Name=CRISPR2_REPEAT8_2968692_2968721;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968721 2968754 33 - . ID=CRISPR2_SPACER8_2968721_2968754;Name=CRISPR2_SPACER8_2968721_2968754;Parent=CRISPR2_2968265_2969028;Note=GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968754 2968783 29 - . ID=CRISPR2_REPEAT9_2968754_2968783;Name=CRISPR2_REPEAT9_2968754_2968783;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968783 2968816 33 - . ID=CRISPR2_SPACER9_2968783_2968816;Name=CRISPR2_SPACER9_2968783_2968816;Parent=CRISPR2_2968265_2969028;Note=GCGACCGCTCAGAAATTCCAGACCCGATCCAAA;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968816 2968845 29 - . ID=CRISPR2_REPEAT10_2968816_2968845;Name=CRISPR2_REPEAT10_2968816_2968845;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968845 2968877 32 - . ID=CRISPR2_SPACER10_2968845_2968877;Name=CRISPR2_SPACER10_2968845_2968877;Parent=CRISPR2_2968265_2969028;Note=TCAACATTATCAATTACAACCGACAGGGAGCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968877 2968906 29 - . ID=CRISPR2_REPEAT11_2968877_2968906;Name=CRISPR2_REPEAT11_2968877_2968906;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968906 2968938 32 - . ID=CRISPR2_SPACER11_2968906_2968938;Name=CRISPR2_SPACER11_2968906_2968938;Parent=CRISPR2_2968265_2969028;Note=AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968938 2968967 29 - . ID=CRISPR2_REPEAT12_2968938_2968967;Name=CRISPR2_REPEAT12_2968938_2968967;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968967 2968999 32 - . ID=CRISPR2_SPACER12_2968967_2968999;Name=CRISPR2_SPACER12_2968967_2968999;Parent=CRISPR2_2968265_2969028;Note=TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968999 2969028 29 - . ID=CRISPR2_REPEAT13_2968999_2969028;Name=CRISPR2_REPEAT13_2968999_2969028;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,36 @@ +>NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- +GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC +>NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- +CTGTTTTCGCAAATCTATGGACTATTGCTATT +>NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- +GGGCGCACGGAATACAAAGCCGTGTATCTGCT +>NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- +TGGCTCTGCAACAGCAGCACCCATGACCACGT +>NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- +GAAATGCTGGTGAGCGTTAATGCCGCAAACAC +>NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- +ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC +>NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- +CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC +>NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- +TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG +>NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- +GTAGTCCATCATTCCACCTATGTCTGAACTCC +>NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- +CCGGGGGATAATGTTTACGGTCATGCGCCCCC +>NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- +TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG +>NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- +AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC +>NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- +TAGTTTCCGTATCTCCGGATTTATAAAGCTGA +>NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- +GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG +>NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- +GCGACCGCTCAGAAATTCCAGACCCGATCCAAA +>NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- +TCAACATTATCAATTACAACCGACAGGGAGCC +>NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- +AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG +>NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- +TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36 Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,133 @@ +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- 100.00 32 0 0 1 32 1 32 1.4e-11 50.3 +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- 66.67 21 7 0 30 10 10 30 0.43 15.4 +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 100.00 8 0 0 23 30 4 11 0.65 14.8 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- 100.00 32 0 0 1 32 1 32 2.5e-15 62.7 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 100.00 8 0 0 24 17 2 9 0.079 17.8 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 88.89 9 1 0 13 5 23 31 0.22 16.3 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 100.00 7 0 0 13 7 11 17 0.28 16.0 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 80.00 10 2 0 7 16 13 22 0.61 14.9 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 80.00 10 2 0 1 10 23 32 0.61 14.9 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- 80.00 10 2 0 13 4 4 13 0.61 14.9 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 87.50 8 1 0 9 2 24 31 0.79 14.5 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 87.50 8 1 0 2 9 12 19 0.79 14.5 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- 87.50 8 1 0 27 20 14 21 0.79 14.5 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 100.00 6 0 0 11 16 15 20 1 14.1 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 100.00 6 0 0 8 13 24 29 1 14.1 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 69.23 13 4 0 3 15 20 32 1.3 13.7 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 73.68 21 5 2 3 23 3 21 1.3 13.7 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 63.16 19 7 0 5 23 12 30 1.7 13.4 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 85.71 7 1 0 3 9 4 10 1.7 13.4 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 64.71 17 6 0 17 1 1 17 1.7 13.4 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 100.00 32 0 0 1 32 1 32 3.9e-13 55.4 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 75.00 16 4 0 27 12 12 27 0.14 17.0 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 76.92 13 3 0 3 15 13 25 0.54 15.0 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 76.92 13 3 0 19 31 15 27 0.54 15.0 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 88.89 9 1 0 9 1 22 30 0.84 14.4 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 75.00 12 3 0 19 8 18 29 1.6 13.4 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 61.90 21 8 0 21 1 9 29 1.6 13.4 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 100.00 32 0 0 1 32 1 32 2e-12 53.0 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 66.67 21 7 0 23 3 1 21 0.28 16.0 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 63.64 22 8 0 3 24 7 28 0.66 14.7 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 65.00 20 7 0 12 31 9 28 0.82 14.4 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 88.89 9 1 0 28 20 19 27 1 14.1 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 75.00 12 3 0 23 12 21 32 1.9 13.2 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- 75.00 12 3 0 6 17 21 32 1.9 13.2 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 100.00 32 0 0 1 32 1 32 6.1e-13 54.8 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 66.67 24 8 0 24 1 9 32 0.056 18.3 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 87.50 17 2 1 10 26 4 19 0.088 17.7 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 70.59 17 5 0 32 16 2 18 0.34 15.7 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 88.89 9 1 0 31 23 12 20 0.82 14.4 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 71.43 14 4 0 32 19 18 31 1.3 13.8 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 80.00 10 2 0 10 1 6 15 2 13.1 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 80.00 10 2 0 23 14 14 23 2 13.1 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 100.00 32 0 0 1 32 1 32 1.1e-13 57.2 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 78.57 14 3 0 28 15 17 30 0.12 17.3 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 68.42 19 6 0 11 29 4 22 0.19 16.6 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 81.82 11 2 0 24 14 8 18 0.48 15.2 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- 100.00 7 0 0 17 11 7 13 0.77 14.5 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 75.00 12 3 0 24 13 11 22 1.2 13.8 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- 80.00 10 2 0 10 19 23 32 1.5 13.5 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 80.00 10 2 0 13 4 14 23 1.5 13.5 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 87.50 8 1 0 32 25 25 32 1.9 13.2 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 64.71 17 6 0 1 17 11 27 1.9 13.2 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 100.00 32 0 0 1 32 1 32 3.8e-12 52.1 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 66.67 24 8 0 32 9 1 24 0.086 17.7 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 83.33 12 2 0 23 12 12 23 0.31 15.9 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 100.00 8 0 0 6 13 6 13 0.47 15.3 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- 100.00 8 0 0 4 11 23 30 0.47 15.3 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 73.33 15 4 0 7 21 4 18 0.58 14.9 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 59.26 27 11 0 32 6 1 27 1.1 14.0 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- 75.00 12 3 0 30 19 19 30 2 13.1 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 75.00 12 3 0 22 11 13 24 2 13.1 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 100.00 32 0 0 1 32 1 32 6.5e-12 51.3 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 78.57 14 3 0 30 17 15 28 0.29 16.0 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 66.67 21 7 0 21 1 3 23 0.35 15.7 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 100.00 8 0 0 6 13 6 13 0.53 15.1 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 63.64 22 8 0 2 23 5 26 0.81 14.5 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 66.67 18 6 0 6 23 14 31 1.2 13.8 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 88.89 9 1 0 18 26 1 9 1.2 13.8 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 68.75 16 5 0 16 1 12 27 1.5 13.5 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- 71.43 14 4 0 32 19 12 25 1.8 13.2 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 100.00 32 0 0 1 32 1 32 2.8e-13 55.9 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- 100.00 8 0 0 9 2 17 24 0.22 16.3 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 81.82 11 2 0 15 25 15 25 0.44 15.3 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 75.00 12 3 0 29 18 4 15 1.1 14.0 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 80.00 10 2 0 29 20 7 16 1.3 13.7 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 80.00 10 2 0 15 24 18 27 1.3 13.7 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 80.00 10 2 0 15 6 1 10 1.3 13.7 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 64.71 17 6 0 11 27 1 17 1.7 13.4 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 100.00 32 0 0 1 32 1 32 7.3e-13 54.5 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- 90.91 11 1 0 17 7 1 11 0.095 17.6 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 81.82 11 2 0 26 16 2 12 0.7 14.7 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 88.89 9 1 0 20 12 23 31 0.88 14.3 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 88.89 9 1 0 27 19 20 28 0.88 14.3 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 88.89 9 1 0 30 22 1 9 0.88 14.3 +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- 100.00 32 0 0 1 32 1 32 2.6e-12 52.6 +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 100.00 9 0 0 25 17 2 10 0.2 16.5 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 100.00 32 0 0 1 32 1 32 1e-11 50.7 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- 100.00 9 0 0 10 2 17 25 0.19 16.5 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 73.33 15 4 0 4 18 7 21 0.65 14.8 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 81.82 11 2 0 18 8 14 24 0.98 14.2 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 88.89 9 1 0 1 9 18 26 1.2 13.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 100.00 32 0 0 1 32 1 32 1.6e-13 56.7 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 75.00 16 4 0 31 16 16 31 0.075 17.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- 78.57 14 3 0 32 19 1 14 0.094 17.6 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- 68.42 19 6 0 4 22 11 29 0.15 16.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 90.00 10 1 0 8 17 9 18 0.15 16.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 66.67 18 6 0 14 31 6 23 0.47 15.2 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 75.00 12 3 0 5 16 7 18 0.93 14.2 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 80.00 10 2 0 25 16 13 22 1.2 13.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 80.00 10 2 0 22 31 13 22 1.2 13.9 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 87.50 8 1 0 32 25 14 21 1.5 13.6 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 100.00 6 0 0 26 31 1 6 1.8 13.2 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 66.67 15 5 0 23 9 18 32 1.8 13.2 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 66.67 15 5 0 29 15 10 24 1.8 13.2 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 100.00 33 0 0 1 33 1 33 4.4e-11 48.6 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 76.19 22 5 1 27 6 8 28 0.8 14.5 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 70.59 17 5 0 28 12 12 28 1.2 14.0 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 76.92 13 3 0 13 25 3 15 1.7 13.4 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 100.00 33 0 0 1 33 1 33 1.4e-12 53.6 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- 63.64 22 8 0 26 5 5 26 0.68 14.7 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 63.64 22 8 0 7 28 3 24 0.68 14.7 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 63.64 22 8 0 5 26 2 23 0.68 14.7 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 59.26 27 11 0 27 1 6 32 1 14.1 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- 68.75 16 5 0 27 12 1 16 1.3 13.8 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- 100.00 32 0 0 1 32 1 32 7.3e-13 54.5 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 90.91 11 1 0 11 1 7 17 0.074 17.9 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 78.57 14 3 0 14 1 19 32 0.14 17.0 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- 75.00 12 3 0 30 19 19 30 1.3 13.8 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- 80.00 10 2 0 29 20 15 24 1.6 13.4 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 63.16 19 7 0 2 20 12 30 1.6 13.4 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- 100.00 32 0 0 1 32 1 32 3.2e-12 52.4 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 70.59 17 5 0 18 2 16 32 0.44 15.3 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 65.00 20 7 0 9 28 12 31 0.83 14.4 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- 81.82 11 2 0 15 25 15 25 0.83 14.4 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 75.00 12 3 0 29 18 8 19 1.9 13.2 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- 75.00 12 3 0 32 21 12 23 1.9 13.2 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 75.00 12 3 0 7 18 5 16 1.9 13.2 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- 100.00 32 0 0 1 32 1 32 1.2e-09 43.8 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- 87.50 17 2 1 4 19 10 26 0.41 15.4 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- 76.19 22 5 1 28 8 6 27 0.82 14.4 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- 90.00 10 1 0 9 18 8 17 0.97 14.2 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- 76.92 13 3 0 15 27 19 31 1.6 13.4 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- 81.82 11 2 0 12 2 16 26 1.9 13.2 diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36.spacermatch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36.spacermatch Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,18 @@ +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,18 @@ +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.col --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.col Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,18 @@ +e92 e59 NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- +e83 a21 NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- +a41 ea0 NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- +5cc c33 NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- +165 34b NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- +aba 8b5 NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- +77b 31a NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- +4e4 f2f NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- +a8a f6e NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- +ea9 0b2 NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- +ebd 122 NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- +6dc 915 NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- +1e4 8c1 NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- +966 d0f NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- +be2 a25 NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- +986 6db NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- +608 00f NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- +609 0bf NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.final --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.final Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,18 @@ +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC 32 - e92 e59 cls_0001 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- CTGTTTTCGCAAATCTATGGACTATTGCTATT 32 - e83 a21 cls_0002 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- GGGCGCACGGAATACAAAGCCGTGTATCTGCT 32 - a41 ea0 cls_0003 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- TGGCTCTGCAACAGCAGCACCCATGACCACGT 32 - 5cc c33 cls_0004 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- GAAATGCTGGTGAGCGTTAATGCCGCAAACAC 32 - 165 34b cls_0005 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC 32 - aba 8b5 cls_0006 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC 32 - 77b 31a cls_0007 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG 32 - 4e4 f2f cls_0008 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- GTAGTCCATCATTCCACCTATGTCTGAACTCC 32 - a8a f6e cls_0009 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- CCGGGGGATAATGTTTACGGTCATGCGCCCCC 32 - ea9 0b2 cls_0010 +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG 32 - ebd 122 cls_0011 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC 32 - 6dc 915 cls_0012 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- TAGTTTCCGTATCTCCGGATTTATAAAGCTGA 32 - 1e4 8c1 cls_0013 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG 33 - 966 d0f cls_0014 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- GCGACCGCTCAGAAATTCCAGACCCGATCCAAA 33 - be2 a25 cls_0015 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- TCAACATTATCAATTACAACCGACAGGGAGCC 32 - 986 6db cls_0016 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG 32 - 608 00f cls_0017 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG 32 - 609 0bf cls_0018 diff -r 000000000000 -r 7346619ad005 test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test.gff.fasta_fasta36.spacermatch.mcl.svg Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,39 @@ + +NC_010473 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 7346619ad005 test-data/crispr_test_adv.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test_adv.gff Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,40 @@ +NC_010473 CRISPRDetect repeat_region 2994577 2994972 396 - . ID=CRISPR1_2994577_2994972;Note=GTGTTCCCCGCGCCAGCGGGGATAAACCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994577 2994606 29 - . ID=CRISPR1_REPEAT1_2994577_2994606;Name=CRISPR1_REPEAT1_2994577_2994606;Parent=CRISPR1_2994577_2994972;Note=TGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994606 2994638 32 - . ID=CRISPR1_SPACER1_2994606_2994638;Name=CRISPR1_SPACER1_2994606_2994638;Parent=CRISPR1_2994577_2994972;Note=GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994638 2994667 29 - . ID=CRISPR1_REPEAT2_2994638_2994667;Name=CRISPR1_REPEAT2_2994638_2994667;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994667 2994699 32 - . ID=CRISPR1_SPACER2_2994667_2994699;Name=CRISPR1_SPACER2_2994667_2994699;Parent=CRISPR1_2994577_2994972;Note=CTGTTTTCGCAAATCTATGGACTATTGCTATT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994699 2994728 29 - . ID=CRISPR1_REPEAT3_2994699_2994728;Name=CRISPR1_REPEAT3_2994699_2994728;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994728 2994760 32 - . ID=CRISPR1_SPACER3_2994728_2994760;Name=CRISPR1_SPACER3_2994728_2994760;Parent=CRISPR1_2994577_2994972;Note=GGGCGCACGGAATACAAAGCCGTGTATCTGCT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994760 2994789 29 - . ID=CRISPR1_REPEAT4_2994760_2994789;Name=CRISPR1_REPEAT4_2994760_2994789;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994789 2994821 32 - . ID=CRISPR1_SPACER4_2994789_2994821;Name=CRISPR1_SPACER4_2994789_2994821;Parent=CRISPR1_2994577_2994972;Note=TGGCTCTGCAACAGCAGCACCCATGACCACGT;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994821 2994850 29 - . ID=CRISPR1_REPEAT5_2994821_2994850;Name=CRISPR1_REPEAT5_2994821_2994850;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994850 2994882 32 - . ID=CRISPR1_SPACER5_2994850_2994882;Name=CRISPR1_SPACER5_2994850_2994882;Parent=CRISPR1_2994577_2994972;Note=GAAATGCTGGTGAGCGTTAATGCCGCAAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994882 2994911 29 - . ID=CRISPR1_REPEAT6_2994882_2994911;Name=CRISPR1_REPEAT6_2994882_2994911;Parent=CRISPR1_2994577_2994972;Note=AGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2994911 2994943 32 - . ID=CRISPR1_SPACER6_2994911_2994943;Name=CRISPR1_SPACER6_2994911_2994943;Parent=CRISPR1_2994577_2994972;Note=ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2994943 2994972 29 - . ID=CRISPR1_REPEAT7_2994943_2994972;Name=CRISPR1_REPEAT7_2994943_2994972;Parent=CRISPR1_2994577_2994972;Note=CGGTTTATCCCCGCTGGCGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect repeat_region 2968265 2969028 764 - . ID=CRISPR2_2968265_2969028;Note=GAGTTCCCCGCGCCAGCGGGGATAAACCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968265 2968294 29 - . ID=CRISPR2_REPEAT1_2968265_2968294;Name=CRISPR2_REPEAT1_2968265_2968294;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGATGCGGGGAACAC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968294 2968326 32 - . ID=CRISPR2_SPACER1_2968294_2968326;Name=CRISPR2_SPACER1_2968294_2968326;Parent=CRISPR2_2968265_2969028;Note=CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968326 2968355 29 - . ID=CRISPR2_REPEAT2_2968326_2968355;Name=CRISPR2_REPEAT2_2968326_2968355;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCTGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968355 2968387 32 - . ID=CRISPR2_SPACER2_2968355_2968387;Name=CRISPR2_SPACER2_2968355_2968387;Parent=CRISPR2_2968265_2969028;Note=TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968387 2968416 29 - . ID=CRISPR2_REPEAT3_2968387_2968416;Name=CRISPR2_REPEAT3_2968387_2968416;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTAACGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968416 2968448 32 - . ID=CRISPR2_SPACER3_2968416_2968448;Name=CRISPR2_SPACER3_2968416_2968448;Parent=CRISPR2_2968265_2969028;Note=GTAGTCCATCATTCCACCTATGTCTGAACTCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968448 2968477 29 - . ID=CRISPR2_REPEAT4_2968448_2968477;Name=CRISPR2_REPEAT4_2968448_2968477;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968477 2968509 32 - . ID=CRISPR2_SPACER4_2968477_2968509;Name=CRISPR2_SPACER4_2968477_2968509;Parent=CRISPR2_2968265_2969028;Note=CCGGGGGATAATGTTTACGGTCATGCGCCCCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968509 2968538 29 - . ID=CRISPR2_REPEAT5_2968509_2968538;Name=CRISPR2_REPEAT5_2968509_2968538;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968538 2968570 32 - . ID=CRISPR2_SPACER5_2968538_2968570;Name=CRISPR2_SPACER5_2968538_2968570;Parent=CRISPR2_2968265_2969028;Note=TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968570 2968599 29 - . ID=CRISPR2_REPEAT6_2968570_2968599;Name=CRISPR2_REPEAT6_2968570_2968599;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968599 2968631 32 - . ID=CRISPR2_SPACER6_2968599_2968631;Name=CRISPR2_SPACER6_2968599_2968631;Parent=CRISPR2_2968265_2969028;Note=AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968631 2968660 29 - . ID=CRISPR2_REPEAT7_2968631_2968660;Name=CRISPR2_REPEAT7_2968631_2968660;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCTCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968660 2968692 32 - . ID=CRISPR2_SPACER7_2968660_2968692;Name=CRISPR2_SPACER7_2968660_2968692;Parent=CRISPR2_2968265_2969028;Note=TAGTTTCCGTATCTCCGGATTTATAAAGCTGA;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968692 2968721 29 - . ID=CRISPR2_REPEAT8_2968692_2968721;Name=CRISPR2_REPEAT8_2968692_2968721;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968721 2968754 33 - . ID=CRISPR2_SPACER8_2968721_2968754;Name=CRISPR2_SPACER8_2968721_2968754;Parent=CRISPR2_2968265_2969028;Note=GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968754 2968783 29 - . ID=CRISPR2_REPEAT9_2968754_2968783;Name=CRISPR2_REPEAT9_2968754_2968783;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968783 2968816 33 - . ID=CRISPR2_SPACER9_2968783_2968816;Name=CRISPR2_SPACER9_2968783_2968816;Parent=CRISPR2_2968265_2969028;Note=GCGACCGCTCAGAAATTCCAGACCCGATCCAAA;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968816 2968845 29 - . ID=CRISPR2_REPEAT10_2968816_2968845;Name=CRISPR2_REPEAT10_2968816_2968845;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968845 2968877 32 - . ID=CRISPR2_SPACER10_2968845_2968877;Name=CRISPR2_SPACER10_2968845_2968877;Parent=CRISPR2_2968265_2969028;Note=TCAACATTATCAATTACAACCGACAGGGAGCC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968877 2968906 29 - . ID=CRISPR2_REPEAT11_2968877_2968906;Name=CRISPR2_REPEAT11_2968877_2968906;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968906 2968938 32 - . ID=CRISPR2_SPACER11_2968906_2968938;Name=CRISPR2_SPACER11_2968906_2968938;Parent=CRISPR2_2968265_2969028;Note=AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968938 2968967 29 - . ID=CRISPR2_REPEAT12_2968938_2968967;Name=CRISPR2_REPEAT12_2968938_2968967;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect Spacer 2968967 2968999 32 - . ID=CRISPR2_SPACER12_2968967_2968999;Name=CRISPR2_SPACER12_2968967_2968999;Parent=CRISPR2_2968265_2969028;Note=TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG;Dbxref=SO:0001459;Ontology_term=CRISPR +NC_010473 CRISPRDetect direct_repeat 2968999 2969028 29 - . ID=CRISPR2_REPEAT13_2968999_2969028;Name=CRISPR2_REPEAT13_2968999_2969028;Parent=CRISPR2_2968265_2969028;Note=CGGTTTATCCCCGCTGGCGCGGGGAACTC;Dbxref=SO:0001459;Ontology_term=CRISPR diff -r 000000000000 -r 7346619ad005 test-data/crispr_test_adv.gff.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test_adv.gff.fasta Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,36 @@ +>NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- +GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC +>NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- +CTGTTTTCGCAAATCTATGGACTATTGCTATT +>NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- +GGGCGCACGGAATACAAAGCCGTGTATCTGCT +>NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- +TGGCTCTGCAACAGCAGCACCCATGACCACGT +>NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- +GAAATGCTGGTGAGCGTTAATGCCGCAAACAC +>NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- +ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC +>NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- +CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC +>NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- +TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG +>NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- +GTAGTCCATCATTCCACCTATGTCTGAACTCC +>NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- +CCGGGGGATAATGTTTACGGTCATGCGCCCCC +>NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- +TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG +>NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- +AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC +>NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- +TAGTTTCCGTATCTCCGGATTTATAAAGCTGA +>NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- +GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG +>NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- +GCGACCGCTCAGAAATTCCAGACCCGATCCAAA +>NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- +TCAACATTATCAATTACAACCGACAGGGAGCC +>NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- +AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG +>NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- +TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG diff -r 000000000000 -r 7346619ad005 test-data/crispr_test_adv.gff.fasta_fasta36.spacermatch.mcl.final --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test_adv.gff.fasta_fasta36.spacermatch.mcl.final Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,18 @@ +NC_010473||CRISPR1_SPACER1_2994606_2994638:32:- GACAGAACGGCCTCAGTAGTCTCGTCAGGCTC 32 - cc8 3d2 cls_0001 +NC_010473||CRISPR1_SPACER2_2994667_2994699:32:- CTGTTTTCGCAAATCTATGGACTATTGCTATT 32 - e4b 34d cls_0002 +NC_010473||CRISPR1_SPACER3_2994728_2994760:32:- GGGCGCACGGAATACAAAGCCGTGTATCTGCT 32 - 878 92b cls_0003 +NC_010473||CRISPR1_SPACER4_2994789_2994821:32:- TGGCTCTGCAACAGCAGCACCCATGACCACGT 32 - 9fc 5d4 cls_0004 +NC_010473||CRISPR1_SPACER5_2994850_2994882:32:- GAAATGCTGGTGAGCGTTAATGCCGCAAACAC 32 - 5ca 262 cls_0005 +NC_010473||CRISPR1_SPACER6_2994911_2994943:32:- ATTACGCCTTTTTGCGATTGCCCGGTTTTTGC 32 - bbb 654 cls_0006 +NC_010473||CRISPR2_SPACER1_2968294_2968326:32:- CAGCGTCAGGCGTGAAATCTCACCGTCGTTGC 32 - 9ff d71 cls_0007 +NC_010473||CRISPR2_SPACER2_2968355_2968387:32:- TCGGTTCAGGCGTTGCAAACCTGGCTACCGGG 32 - 37d 0e9 cls_0008 +NC_010473||CRISPR2_SPACER3_2968416_2968448:32:- GTAGTCCATCATTCCACCTATGTCTGAACTCC 32 - 349 b3e cls_0009 +NC_010473||CRISPR2_SPACER4_2968477_2968509:32:- CCGGGGGATAATGTTTACGGTCATGCGCCCCC 32 - 210 c94 cls_0010 +NC_010473||CRISPR2_SPACER5_2968538_2968570:32:- TGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAG 32 - c06 56c cls_0011 +NC_010473||CRISPR2_SPACER6_2968599_2968631:32:- AAGCTGGCTGGCAATCTCTTTCGGGGTGAGTC 32 - bfb 89d cls_0012 +NC_010473||CRISPR2_SPACER7_2968660_2968692:32:- TAGTTTCCGTATCTCCGGATTTATAAAGCTGA 32 - f25 372 cls_0013 +NC_010473||CRISPR2_SPACER8_2968721_2968754:33:- GCAGGCGGCGACGCGCAGGGTATGCGCGATTCG 33 - 686 4d5 cls_0014 +NC_010473||CRISPR2_SPACER9_2968783_2968816:33:- GCGACCGCTCAGAAATTCCAGACCCGATCCAAA 33 - fbb 296 cls_0015 +NC_010473||CRISPR2_SPACER10_2968845_2968877:32:- TCAACATTATCAATTACAACCGACAGGGAGCC 32 - d33 650 cls_0016 +NC_010473||CRISPR2_SPACER11_2968906_2968938:32:- AGCGTGTTCGGCATCACCTTTGGCTTCGGCTG 32 - fb9 3c0 cls_0017 +NC_010473||CRISPR2_SPACER12_2968967_2968999:32:- TGCGTGAGCGTATCGCCGCGCGTCTGCGAAAG 32 - 8e0 5aa cls_0018 diff -r 000000000000 -r 7346619ad005 test-data/crispr_test_adv.gff.fasta_fasta36.spacermatch.mcl.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crispr_test_adv.gff.fasta_fasta36.spacermatch.mcl.svg Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,57 @@ + +NC_010473 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +32 + + +33 + + +33 + + +32 + + +32 + + +32 + \ No newline at end of file diff -r 000000000000 -r 7346619ad005 test-data/test_isolates.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_isolates.txt Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,1 @@ +nothing useful