| Previous changeset 1:98bd79bb98fe (2018-10-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e" |
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modified:
glimmer_glimmer_to_gff.xml macros.xml test-data/coordTest.txt test-data/glimmer.gff test-data/glimmer_w_icm_trans-table-11_genomic.dout test-data/glimmer_w_icm_trans-table-11_genomic.fasta test-data/glimmer_w_icm_trans-table-11_genomic.out test-data/streptomyces_Tu6071_plasmid_genes.fasta test-data/streptomyces_Tu6071_plasmid_genes.icm |
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| diff -r 98bd79bb98fe -r 891b330ffd94 glimmer_glimmer_to_gff.xml --- a/glimmer_glimmer_to_gff.xml Tue Oct 30 18:51:34 2018 -0400 +++ b/glimmer_glimmer_to_gff.xml Sun Mar 20 10:07:15 2022 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@"> +<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1"> <description></description> + <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> @@ -9,7 +10,7 @@ '$input' > '$output' ]]></command> <inputs> - <param name="input" type="data" format="tabular" label="Glimmer Output File"/> + <param name="input" type="data" format="txt" label="Glimmer Output File"/> </inputs> <outputs> <data name="output" format="gff"/> |
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| diff -r 98bd79bb98fe -r 891b330ffd94 macros.xml --- a/macros.xml Tue Oct 30 18:51:34 2018 -0400 +++ b/macros.xml Sun Mar 20 10:07:15 2022 +0000 |
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| @@ -7,7 +7,11 @@ <yield/> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">gemini</xref> + </xrefs> + </xml> <token name="@WRAPPER_VERSION@">3.02</token> <xml name="citation"> |
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| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/coordTest.txt --- a/test-data/coordTest.txt Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/coordTest.txt Sun Mar 20 10:07:15 2022 +0000 |
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| @@ -1,17 +1,17 @@ -00001 40137 52 +2 0.892 -00002 1319 1095 -3 0.654 -00003 1555 1391 -2 0.793 -00004 1953 2066 +3 1.078 -00005 2045 2146 +2 0.919 -00006 4463 4759 +2 0.985 -00007 6785 6582 -3 1.033 -00008 6862 7020 +1 0.915 -00009 7300 7488 +1 0.900 -00010 7463 7570 +2 0.912 -00011 8399 8527 +2 1.044 -00012 10652 10545 -3 0.895 -00013 12170 12066 -3 1.108 -00014 13891 13748 -2 0.998 -00015 14157 14044 -1 1.026 -00016 15285 15410 +3 0.928 -00017 15829 15704 -2 0.949 +00001 40137 52 +2 0.892 +00002 1319 1095 -3 0.654 +00003 1555 1391 -2 0.793 +00004 1953 2066 +3 1.078 +00005 2045 2146 +2 0.919 +00006 4463 4759 +2 0.985 +00007 6785 6582 -3 1.033 +00008 6862 7020 +1 0.915 +00009 7300 7488 +1 0.900 +00010 7463 7570 +2 0.912 +00011 8399 8527 +2 1.044 +00012 10652 10545 -3 0.895 +00013 12170 12066 -3 1.108 +00014 13891 13748 -2 0.998 +00015 14157 14044 -1 1.026 +00016 15285 15410 +3 0.928 +00017 15829 15704 -2 0.949 |
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| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/glimmer.gff --- a/test-data/glimmer.gff Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/glimmer.gff Sun Mar 20 10:07:15 2022 +0000 |
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| b'@@ -1,62 +1,70 @@\n ##gff-version 3\n \n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t897\t2918\t.\t+\t.\tframe=+3;score=3.19\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t891\t2918\t.\t+\t.\tframe=+3;score=3.28\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t144\t938\t.\t-\t.\tframe=-3;score=2.86\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t7237\t7368\t.\t-\t.\tframe=-1;score=2.50\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t4695\t5606\t.\t+\t.\tframe=+3;score=0.63\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t5833\t6183\t.\t+\t.\tframe=+1;score=1.21\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t7237\t7368\t.\t-\t.\tframe=-1;score=1.69\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t10347\t11945\t.\t+\t.\tframe=+3;score=2.93\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t12110\t12238\t.\t-\t.\tframe=-2;score=6.22\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t13067\t15088\t.\t-\t.\tframe=-2;score=2.95\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t15045\t16529\t.\t+\t.\tframe=+3;score=3.36\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t12110\t12238\t.\t-\t.\tframe=-2;score=4.26\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t13067\t13564\t.\t-\t.\tframe=-2;score=2.78\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t13521\t16529\t.\t+\t.\tframe=+3;score=3.62\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t20276\t21385\t.\t-\t.\tframe=-2;score=2.90\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t21382\t23037\t.\t-\t.\tframe=-1;score=2.93\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t23031\t24797\t.\t+\t.\tframe=+3;score=2.92\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t27115\t27291\t.\t-\t.\tframe=-1;score=1.92\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t28556\t28960\t.\t+\t.\tframe=+2;score=2.51\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t29040\t30026\t.\t+\t.\tframe=+3;score=0.40\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t32942\t33151\t.\t-\t.\tframe=-2;score=1.06\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t34754\t38242\t.\t-\t.\tframe=-2;score=2.97\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglim'..b'sequence\tglimmer_prediction\tpredicted_gene\t123230\t123484\t.\t+\t.\tframe=+2;score=3.73\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t123689\t123925\t.\t+\t.\tframe=+2;score=4.44\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t124906\t126459\t.\t-\t.\tframe=-1;score=2.93\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t126704\t128992\t.\t-\t.\tframe=-2;score=2.95\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t129011\t129178\t.\t-\t.\tframe=-2;score=1.85\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t130337\t132172\t.\t-\t.\tframe=-2;score=2.94\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t129011\t129178\t.\t-\t.\tframe=-2;score=2.06\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t130337\t131737\t.\t-\t.\tframe=-2;score=2.92\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t131802\t132830\t.\t-\t.\tframe=-3;score=4.65\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t134324\t134983\t.\t+\t.\tframe=+2;score=0.80\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t134993\t136987\t.\t+\t.\tframe=+2;score=2.94\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137245\t137523\t.\t-\t.\tframe=-1;score=1.14\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137825\t140512\t.\t-\t.\tframe=-2;score=2.96\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137245\t137523\t.\t-\t.\tframe=-1;score=3.06\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137942\t139042\t.\t+\t.\tframe=+2;score=5.32\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t139202\t140140\t.\t+\t.\tframe=+2;score=5.82\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137825\t137941\t.\t-\t.\tframe=-2;score=2.04\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t140766\t142487\t.\t-\t.\tframe=-3;score=2.94\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t142484\t143056\t.\t-\t.\tframe=-2;score=0.89\n-gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t143099\t143578\t.\t-\t.\tframe=-2;score=0.42\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t142484\t143056\t.\t-\t.\tframe=-2;score=1.32\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t143099\t143545\t.\t-\t.\tframe=-2;score=2.75\n gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t144230\t147016\t.\t-\t.\tframe=-2;score=2.96\n' |
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| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/glimmer_w_icm_trans-table-11_genomic.dout --- a/test-data/glimmer_w_icm_trans-table-11_genomic.dout Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.dout Sun Mar 20 10:07:15 2022 +0000 |
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| b'@@ -1,8 +1,8 @@\n-Command: glimmer3 -o 50 -g 90 -t 30 -z 11 -A atg,gtg,ttg -l /tmp/tmpubrxoL/files/000/dataset_1.dat /tmp/tmpubrxoL/files/000/dataset_2.dat glimmer_output\n+Command: glimmer3 -o 50 -g 90 -t 30 -z 11 -A atg,gtg,ttg -l /tmp/tmp49ieyhkr/files/f/1/3/dataset_f1304d66-d689-4521-8be7-7b1770a35e64.dat /tmp/tmp49ieyhkr/files/8/e/9/dataset_8e96f649-243f-48f2-85d0-0c52f0e3ffb6.dat glimmer_output\n \n-Sequence file = /tmp/tmpubrxoL/files/000/dataset_1.dat\n+Sequence file = /tmp/tmp49ieyhkr/files/f/1/3/dataset_f1304d66-d689-4521-8be7-7b1770a35e64.dat\n Number of sequences = 1\n-ICM model file = /tmp/tmpubrxoL/files/000/dataset_2.dat\n+ICM model file = /tmp/tmp49ieyhkr/files/8/e/9/dataset_8e96f649-243f-48f2-85d0-0c52f0e3ffb6.dat\n Excluded regions file = none\n List of orfs file = none\n Input is NOT separate orfs\n@@ -26,1366 +26,1366 @@\n \n ----- Start ----- --- Length ---- ------------- Scores -------------\n ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC\n- +1 289 316 417 126 99 -12.44 0 0 0 0 - 0 0 99\n- +1 418 706 894 474 186 -12.50 0 0 0 72 - 0 0 26\n- +2 203 755 907 702 150 -7.78 0 - 0 4 - 0 5 89\n- -2 934 478 245 687 231 -16.05 0 - 0 0 - 0 0 99\n- -1 1005 960 808 195 150 -10.87 0 - - 0 0 - 0 99\n- +1 895 904 1029 132 123 -21.92 0 0 - 0 - - 0 99\n- +2 1211 1316 1450 237 132 -9.27 0 0 0 0 0 0 99 0\n- -2 1513 1462 1295 216 165 -13.99 0 0 - 0 0 0 99 0\n- -1 1587 1506 1006 579 498 -11.27 0 - - 0 0 - 1 98\n- +1 1132 1774 2016 882 240 -10.77 0 0 0 0 0 0 99 0\n- -2 2221 1633 1514 705 117 -17.27 0 0 0 0 - 0 0 99\n- +2 1451 2192 2287 834 93 -3.86 2 0 2 11 0 - 5 80\n- +2 2288 2414 2524 234 108 -14.85 0 0 0 0 0 0 98 0\n- +1 2386 2521 2676 288 153 -10.44 0 0 0 0 - 0 99 0\n- -2 2704 2332 2222 480 108 -8.27 0 - - 83 0 0 7 9\n- +1 2677 2713 2865 186 150 -16.16 0 0 0 42 - 0 4 53\n-0001 +3 174 183 2918 2742 2733 -2.60 0 - - 0 - - 99 0\n- +2 2525 2828 2947 420 117 -8.18 0 - 0 - - 0 0 99\n-0002 -3 3062 2777 144 2916 2631 -1.16 0 0 - - 0 - 0 99\n- -2 3301 2845 2705 594 138 -6.29 0 0 0 62 - 0 0 37\n- +2 2948 3149 3352 402 201 -10.20 0 0 0 0 0 - - 99\n- +1 2866 3262 3363 495 99 -8.25 0 0 - 13 0 - 3 83\n- -1 3396 3171 2995 399 174 -6.74 0 0 0 - 0 0 - 99\n- -2 3403 3400 3302 99 96 -10.07 0 - - 95 0 0 1 2\n- -3 3419 3407 3195 222 210 -5.41 0 - - 1 - - 0 98\n- -1 3810 3810 3553 255 255 -10.41 0 - 0 0 0 - 99 0\n- +3 3102 3750 3866 762 114 0.43 0 0 0 0 - 0 98 0\n- +3 3867 4098 4313 444 213 -6.66 0 0 0 0 - 38 0 60\n- -3 4343 3824 3420 921 402 -0.79 4 - 0 0 - - 4 95\n- +2 3353 3869 4357 1002 486 1.19 5 0 5 - - 94 - 0\n- +1 3754 4183 4413 657 228 -5.38 0 0 - - 0 0 - 99\n- -1 4416 4254 4105 309 147 -9.43 0 27 0 0 0 10 0 60\n- -2 4438 4'..b' 150 -13.67 0 0 0 0 - 0 0 99\n+ -1 141903 141825 141724 177 99 -12.67 0 - 0 2 0 0 0 97\n+ -2 141958 141406 141242 714 162 -21.67 0 0 0 1 0 0 90 7\n+ +1 141736 141769 142011 273 240 -11.25 0 0 0 0 - - 1 98\n+ -1 142218 142149 141982 234 165 -10.67 0 - 0 0 0 0 3 96\n+ +2 141086 142130 142381 1293 249 -9.21 0 - 0 0 - 0 0 99\n+ +3 141180 142302 142421 1239 117 -3.61 0 - - 0 - 0 72 27\n+ -2 142483 142222 141959 522 261 -13.90 0 - 0 0 - 0 0 99\n+0099 -3 142526 142487 140766 1758 1719 -6.47 0 0 - - - - 0 99\n+ -1 142713 142506 142321 390 183 -11.81 0 - - - 0 - 0 99\n+ +1 142357 142720 142821 462 99 -8.81 0 0 0 0 - 1 - 98\n+ +3 142539 142764 143033 492 267 -15.98 0 - 0 0 - 19 - 80\n+ -1 143058 142938 142801 255 135 -15.69 0 - 0 0 0 2 - 97\n+0100 -2 143098 143056 142484 612 570 1.52 99 - 0 - - 99 - 0\n+ -1 143415 143376 143248 165 126 -9.95 0 32 0 - 0 62 - 5\n+ -1 143571 143571 143458 111 111 -16.34 0 0 0 0 0 99 - 0\n+ +2 142460 143489 143683 1221 192 -7.71 0 0 0 0 - 98 - 1\n+ -3 143888 143816 143655 231 159 -14.02 0 0 - - - 0 0 99\n+ +1 143197 143746 143892 693 144 -15.45 0 0 0 - - 0 0 99\n+0101 -2 143938 143545 143099 837 444 3.02 99 - 0 - - 99 - 0\n+ +2 143750 143822 143944 192 120 -18.23 0 - 0 - - - - 99\n+ -1 143985 143970 143857 126 111 -17.05 0 - - - 0 - - 99\n+ +1 143893 143971 144120 225 147 -5.73 0 0 0 - - - 0 99\n+ -2 144229 144130 143981 246 147 -3.53 0 - 0 - - 0 0 99\n+ -1 144303 144111 143986 315 123 -10.51 0 0 13 - 0 56 0 29\n+ -3 144344 143981 143889 453 90 -18.94 0 0 - 0 0 - 0 99\n+ -1 144762 144504 144358 402 144 -16.74 0 0 3 0 0 29 0 66\n+ -3 144860 144584 144345 513 237 -7.61 0 - 26 0 - 27 0 46\n+ +3 144102 144816 144926 822 108 -19.73 0 0 90 0 - 0 - 9\n+ +3 144927 145053 145172 243 117 -11.87 0 0 88 0 0 0 0 10\n+ -3 145283 144956 144861 420 93 -6.74 0 0 44 - 0 0 0 55\n+ -1 145479 145422 144835 642 585 -16.32 0 - 99 - 0 0 - 0\n+ +3 145173 145734 145922 747 186 -22.07 0 0 99 0 0 0 0 0\n+ -1 145959 145836 145480 477 354 -23.56 0 - 99 0 0 0 0 0\n+0102 +2 143945 144212 145963 2016 1749 3.15 99 - 99 - - - - 0\n+ -3 145985 145880 145305 678 573 -2.77 0 - 99 0 - 0 0 0\n+ +3 146058 146082 146261 201 177 -28.88 0 - 20 0 - 0 - 78\n+ +3 146397 146721 146954 555 231 -22.21 0 - 0 0 - 0 0 99\n+ -3 146996 146627 146202 792 423 -7.95 0 - 97 - - 0 0 2\n+0103 -2 147025 147016 144230 2793 2784 -3.87 0 - 99 0 - 0 - 0\n+ -1 147072 147000 146782 288 216 -17.82 0 - 0 - 0 0 0 99\n+ +2 145964 146987 147097 1131 108 -18.22 0 - 0 0 - - - 99\n+ +3 146991 147033 147131 138 96 -20.67 0 - - 0 - - - 99\n+ -2 147346 147343 147062 282 279 -9.20 0 0 - - - 0 - 99\n' |
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| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/glimmer_w_icm_trans-table-11_genomic.fasta --- a/test-data/glimmer_w_icm_trans-table-11_genomic.fasta Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.fasta Sun Mar 20 10:07:15 2022 +0000 |
| b |
| b'@@ -1,38 +1,38 @@\n >orf00001 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n-ATGGCGAATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAG\n-GCAATCGCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCT\n-GAGCCGGAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTG\n-CTTCAGACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTT\n-CATCAGCAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAG\n-CTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCC\n-GAGGTGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTG\n-TGGTCGCGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAG\n-TTCGCGAACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTA\n-CGGGTCCTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTT\n-GCCGACGCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAG\n-AACCCGGATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGGCCGGAC\n-GAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAG\n-GGCCTGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGG\n-GCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTG\n-TCGGACTCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAG\n-GACGGCGCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACG\n-GTCGCGGCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGG\n-TACGAGGCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCG\n-TACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCC\n-GCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGAC\n-GCGGAGGGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTT\n-CGCTCCTACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAA\n-GACGAGGGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGAC\n-GGACTCGGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGAT\n-GCGGACTGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTC\n-CTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGAC\n-GGGGATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTC\n-AGCACCGAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCG\n-GGGCGGGGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGA\n-ACGGCTTTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGG\n-AAACCCGTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTA\n-CGCCTCGGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAGGACGAA\n-CGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGA\n+GTGACGATGGCGAATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTG\n+TCCGAGGCAATCGCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACT\n+GATCCTGAGCCGGAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTT\n+GCGTTGCTTCAGACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTGCACCATGATG\n+ACGCTTCATCAGCAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCG\n+GCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCG\n+GCCTCCGAGGTGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCG\n+CGGGTGTGGTCGCGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTG\n+CGGGAGTTCGCGAACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCT\n+TCCGTACGGGTCCTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATC\n+TGCTTTGCCGACGCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTG\n+CGCCAGAACCCGGATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGG\n+CCGGACGAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTA\n+CTCCAGGGCCTGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGC\n+GTACGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGG\n+CTCCTGTCGGACTCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAG\n+GGCGAGGACGGCGCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCG\n+TCGACGGTCGCGGCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTG\n+GAGGGGTACGAGGCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCG\n+GTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGG\n+ACCGCCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTC\n+CTCGACGCGGAGGGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCG\n+GGGCTTCGCTCCTACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGG\n+GGCGAAGACGAGGGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGC\n+AAGGACGGACTCGGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCC\n+GTCGATGCGGACTGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTC\n+GTGCTCCTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGC\n+CTGGACGGGGATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCG\n+CGGCTCAGCACCGAGCAGCGGGCGCGGCTCGAAGCGCTCG'..b'7 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGCTTGCGGACGATGTCCACGCCGCCCGTGGTGCCCAGCTCCAGCGCGGTGTCGAGCCG\n+GGTCAGGGCCTCCCGCAGCCGCTTCTGAAGGGCCCCGATGAAGGACCCAGGGTCCTGCGG\n+CTGGCGGATCGCGTCGTAGTGGACATCGCGGTTGTCCTCGAAGTCGGGGGGCAGGTCGCC\n+CTCGGGGTTCTGCCACCGGCCCGCGCCCGGGACCCAGATCTCCCGGCGCCGCAGCGCGTC\n+CCGCAGGCTGACCAGCACGCACAGCTCGTACGGGATGCGCTCGACGCGGCCGCGCTCGTC\n+CACCACTGCCTTGCGCCACTCCTCGCGCACCACCCCGGCCAGCGGGATGTTCTCCGACTC\n+GTCGAAGAACGCGCCCTCCTTGGCGATGGGCTGGTCCAGGTACCGCTTCAGCAGGTCGAT\n+GGCGTCCATCACCGGCCGGTAAGCGGTGTTGTTGCACTTCAGCTCCACCGCCCCCAGCAG\n+CGGGGAGAGCATCCGCCGCCAGTGCCCCGAGTACGACGACCGCAGCACCGTGCGCACCCG\n+GGCCCGGTAGCGGGCCTCGTTCGCCGCGGCCTCCGCCGCCAGGGCCTTCAGCGTGGACTC\n+CCCGGCCACCGGGAAGATCACCTTGCGGACCGTGCCGCCCGGCTCCGCGACCGCGGCCTC\n+CGCCAGCCGCAGCAGAATCCCCTCCTTGCCACGGACCCGCTTGAGATCCTTGGTGAACTC\n+GCCCTCAACCTTCTTCTCCGCCCGCGTGTTGATCCGCTGCACCAGCTGGATGAACAGCTC\n+CACCAGCGAGTCGGTGATCTCCGTCTGCCGCACATGGCACAGCGCGGCCAGCAGCGTGTA\n+GCGCACCGGCCCGGCTGCCGCCCGCAGGTCCGAGGGGTACTCCTTCGACGCCCGCGCCCG\n+CCACGCCGCCACCAGCTTCTCCGACACGTCCCCGAATAG\n+>orf00098 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGAACCCGTACGGCCGGTTCGAGCTGGACATGAATTCCCACCTGGACCTCGTCGCCGCC\n+GTGGCGGCTTCGGTGCCCGGCCCGCGCAGCGGCGAGCCGGCCACGTCCCCGGCCTGA\n+>orf00099 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n GTGACTCGCGGGAGTGGCCCTCCCGGCGTCAAGGGACGGCGACCACGTTCAGGGCTCCGG\n GGGGCATCAGTGCAAGGGCCCCGGCGCGACGCCGTCGGTCGCCTCTTCATACACAACCCG\n CGAGGTGTCCCTCAGGGCGCCCGCGAGGGGGAGGCACGCGGCCATGACGGCGGCTACGAC\n@@ -1070,7 +1150,7 @@\n CGATGCCGGGCCGGTCCTCCTTGGACCACCGTCACCAGGACGTCGATCAGGTCTTCGCGC\n GATGCCACCTGGGTGAACAGGGCCTCATATTCGGCGGTGCGCTGTTCGACGTACCAGGCG\n AACGCCTGCGTGCACAGTTCGGTCAGGCTTGCGAAGTGGTAG\n->orf00094 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+>orf00100 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n TTGGAAGCCCAAGTGGTCGTGCATCAGCCGGTGCCAGAGGTCATGGGTCTGCTCGGCGTC\n GGTGAGGGCGGGGCGCTGTGGCGAGAAGGTGAAGCCGGGCAGGGAGGGGATGATGACGGT\n GAAGGCGTCGCGGGCGTCTCCTCCGTGGCGGGAGGGGGCGGCGAGTCGTTCGGCGAGCAT\n@@ -1081,16 +1161,16 @@\n CTCGGGCCAGCGAGTGGCGCGCAGCCGGGTGCGGAGGTCTTCCAGGTCGGCGTCGGCGAC\n CTGGATGACGGGTGTGCTGGTCGGCACGGTGTGCTCCTTCATGTGCGTGATGTGCAGGGG\n GACGGCGGCGGTGCGGTTCGTTCTCGTGCGTGA\n->orf00095 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n-GTGGTAGGTGCGCTCGGCCCAGCTCCGGGGCGGTTGGGCGAGGTCTGCGGGGAACAGGGC\n-GAGGGCGGTGGGGACGTCGACCCGCCGCACGCGCCGGGTGAGCTGGTGCGCGTACTCGTA\n-GTACGGGCGGAAGGACGTGGAGATCGTGCCGGTGAACCAGTAGAGCGATGCCTGGGTGAG\n-GAGGAAGTCGTCGCCGAAGCGGGTGGACAGGTCGCCGCCGCAGTCGGTCCACGCGCGGTA\n-CTTCTCGAGGATCCAGGAGAGCAGTCCGGCGGGCGAGTCGTTCAGTGCGGGCGCGAGGGT\n-GAGGGGACGGGTGTTCTGCTGGTGCATGTAGGCGCCCTCCTCTGCCTGCCAGGCCGCGGC\n-GGACAACAGGTGGGTCTTCTCCTCAGGGGTGAGCGAGGCCGGATCGTACTCTGCCGGGGC\n-CGCGGCAGCGAGCAGATGAATGCCGACGACGGCCTCGGGGTGGGCCTCGGCGAGCCGTGA\n->orf00097 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+>orf00101 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGGCGAGGTCTGCGGGGAACAGGGCGAGGGCGGTGGGGACGTCGACCCGCCGCACGCG\n+CCGGGTGAGCTGGTGCGCGTACTCGTAGTACGGGCGGAAGGACGTGGAGATCGTGCCGGT\n+GAACCAGTAGAGCGATGCCTGGGTGAGGAGGAAGTCGTCGCCGAAGCGGGTGGACAGGTC\n+GCCGCCGCAGTCGGTCCACGCGCGGTACTTCTCGAGGATCCAGGAGAGCAGTCCGGCGGG\n+CGAGTCGTTCAGTGCGGGCGCGAGGGTGAGGGGACGGGTGTTCTGCTGGTGCATGTAGGC\n+GCCCTCCTCTGCCTGCCAGGCCGCGGCGGACAACAGGTGGGTCTTCTCCTCAGGGGTGAG\n+CGAGGCCGGATCGTACTCTGCCGGGGCCGCGGCAGCGAGCAGATGAATGCCGACGACGGC\n+CTCGGGGTGGGCCTCGGCGAGCCGTGA\n+>orf00103 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAA\n CATCAGGTGGAGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGC\n GCCCGTTCGGGGCGGGGGGCGCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACG\n' |
| b |
| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/glimmer_w_icm_trans-table-11_genomic.out --- a/test-data/glimmer_w_icm_trans-table-11_genomic.out Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.out Sun Mar 20 10:07:15 2022 +0000 |
| b |
| @@ -1,61 +1,69 @@ >gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence -orf00001 897 2918 +3 3.19 +orf00001 891 2918 +3 3.28 orf00002 938 144 -3 2.86 -orf00003 7368 7237 -1 2.50 -orf00006 10347 11945 +3 2.93 -orf00007 12238 12110 -2 6.22 -orf00008 15088 13067 -2 2.95 -orf00009 15045 16529 +3 3.36 -orf00014 21385 20276 -2 2.90 -orf00016 23037 21382 -1 2.93 -orf00017 23031 24797 +3 2.92 -orf00020 27291 27115 -1 1.92 -orf00021 28556 28960 +2 2.51 -orf00022 29040 30026 +3 0.40 -orf00025 33151 32942 -2 1.06 -orf00028 38242 34754 -2 2.97 -orf00031 43300 43100 -2 6.70 -orf00032 43402 43497 +1 0.97 -orf00033 45157 44963 -2 1.68 -orf00034 47430 46852 -1 0.78 +orf00004 4695 5606 +3 0.63 +orf00005 5833 6183 +1 1.21 +orf00006 7368 7237 -1 1.69 +orf00009 10347 11945 +3 2.93 +orf00012 12238 12110 -2 4.26 +orf00013 13564 13067 -2 2.78 +orf00014 13521 16529 +3 3.62 +orf00018 21385 20276 -2 2.90 +orf00020 23037 21382 -1 2.93 +orf00021 23031 24797 +3 2.92 +orf00023 27291 27115 -1 8.70 +orf00024 28860 30026 +3 0.20 +orf00025 33151 32942 -2 3.88 +orf00027 36932 38236 +2 3.00 +orf00028 36949 34754 -2 2.95 +orf00029 43300 43100 -2 3.03 +orf00032 47445 46852 -1 2.60 orf00036 51314 48354 -3 2.96 -orf00037 55329 55069 -1 1.43 +orf00037 55290 55069 -1 3.18 orf00040 59457 56431 -1 2.96 -orf00041 59669 60169 +2 2.15 -orf00042 60516 60881 +3 0.34 -orf00043 62032 60959 -2 2.90 -orf00044 61997 62821 +2 3.73 -orf00046 66395 62922 -3 2.97 -orf00047 70996 71166 +1 0.90 -orf00049 81960 81835 -1 1.90 -orf00050 87355 89982 +1 2.96 -orf00051 90028 90390 +1 1.66 -orf00053 91917 92009 +3 0.65 -orf00054 93540 93307 -1 1.81 -orf00055 96379 94568 -2 2.94 -orf00056 96523 96383 -2 0.37 -orf00057 99628 100467 +1 3.23 -orf00058 99645 98455 -1 2.91 -orf00062 100811 102931 +2 2.95 -orf00065 103074 105521 +3 2.96 -orf00066 106200 105847 -1 0.32 -orf00067 108365 108069 -3 4.89 -orf00068 110498 109947 -3 0.90 -orf00069 110907 110791 -1 2.13 -orf00074 117071 116538 -3 0.81 -orf00075 117733 117443 -2 0.01 -orf00076 118776 118399 -1 3.59 -orf00077 119740 119582 -2 0.41 -orf00078 123152 123484 +2 2.86 -orf00079 123767 123925 +2 0.89 -orf00080 126459 124906 -1 2.93 -orf00084 128992 126704 -2 2.95 -orf00085 129178 129011 -2 1.85 -orf00086 132172 130337 -2 2.94 -orf00088 134993 136987 +2 2.94 -orf00089 137523 137245 -1 1.14 -orf00092 140512 137825 -2 2.96 -orf00093 142487 140766 -3 2.94 -orf00094 143056 142484 -2 0.89 -orf00095 143578 143099 -2 0.42 -orf00097 147016 144230 -2 2.96 +orf00041 59669 60169 +2 3.46 +orf00043 60516 60881 +3 1.56 +orf00045 60878 62821 +2 2.93 +orf00046 63564 66248 +3 3.14 +orf00047 63596 62922 -3 2.84 +orf00048 70422 70520 +3 0.07 +orf00049 75466 75654 +1 2.06 +orf00051 81960 81835 -1 6.45 +orf00052 87355 89982 +1 2.96 +orf00053 90028 90390 +1 0.39 +orf00055 91917 92009 +3 1.32 +orf00056 93406 93576 +1 2.94 +orf00057 93837 93998 +3 1.65 +orf00059 96379 94568 -2 2.94 +orf00060 99628 100467 +1 3.07 +orf00061 99645 98455 -1 2.91 +orf00063 100811 102931 +2 2.95 +orf00066 103074 105521 +3 2.96 +orf00067 106200 105847 -1 1.02 +orf00068 107401 106526 -2 0.12 +orf00069 108365 108069 -3 3.46 +orf00070 110498 109947 -3 1.27 +orf00071 111060 110791 -1 1.52 +orf00073 112883 113158 +2 0.43 +orf00075 115660 115022 -2 1.43 +orf00076 115768 115661 -2 0.06 +orf00077 116553 115729 -1 0.92 +orf00078 117080 116538 -3 0.58 +orf00080 118857 118399 -1 2.71 +orf00083 123230 123484 +2 3.73 +orf00084 123689 123925 +2 4.44 +orf00085 126459 124906 -1 2.93 +orf00089 128992 126704 -2 2.95 +orf00090 129178 129011 -2 2.06 +orf00091 131737 130337 -2 2.92 +orf00092 132830 131802 -3 4.65 +orf00093 134324 134983 +2 0.80 +orf00094 134993 136987 +2 2.94 +orf00095 137523 137245 -1 3.06 +orf00096 137942 139042 +2 5.32 +orf00097 139202 140140 +2 5.82 +orf00098 137941 137825 -2 2.04 +orf00099 142487 140766 -3 2.94 +orf00100 143056 142484 -2 1.32 +orf00101 143545 143099 -2 2.75 +orf00103 147016 144230 -2 2.96 |
| b |
| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/streptomyces_Tu6071_plasmid_genes.fasta --- a/test-data/streptomyces_Tu6071_plasmid_genes.fasta Tue Oct 30 18:51:34 2018 -0400 +++ b/test-data/streptomyces_Tu6071_plasmid_genes.fasta Sun Mar 20 10:07:15 2022 +0000 |
| [ |
| b'@@ -290,1648 +290,3 @@\n AACGGCGTCGTCGCCGCCGTCATCGGCGCCCTCACCGCCCACAACAGCTTCACCACCGCCCTGACCGTCC\n TCACCGCCTGCGCCGCCCTCGGCCTCCTGACCGCACTCCTCCTCCCCGCCCCCGAGAAGAGCACCGTGCC\n CGAAACCTCCCCACACGTGCCCGCCAACGACGCACCGGCCACGACCGCGTGA\n->lcl|NZ_CM001166.1_gene_26 [locus_tag=STTU_p0026] [location=complement(22689..23459)]\n-ATGGTTGATGTCGCGTTCACCGCGCTCTACCCGTGGAGCCTGCCGCCCGACAAGCCGCGTACCGACCGGG\n-CGGCCGCCCGGTCGGAGCGCGACCTGTACGCGGCGCATTTCCGGCACGCGCGGATCGCCCGGCTGCCCGC\n-GGACTGCCCGCCGTGGGCGCTCGGCCAGGATCTCGGCTGGGTGGTGCGCTCCCCGGTCACCGCGACCCTG\n-ACGCCGCTGTCGGACACGGACGTCGCCGTGCCCGAGGACGAGGACGTCAGAGCGGTGAGCCGCCGCGCGG\n-GCGGCGGGCAGATGTGGCGCCGCGGCCCCGACTGGATCGCCGTTCCCGACCAGGGCGGAAGCTGGCTGCG\n-CCGCTACGACTTCCGCAACTCCAGCGGGCAGTGGGAGGCGATGTTCCTGCCCAACGGACAGGGCACCGTG\n-GAGTGGCATCTCGGCGTCGCGGTCCGCCTCCCGCAGCCGTACTTCCTCATGGTCCTGCCCCTGGACCCGC\n-CCCTGCCCGGCCTCCACGTCCCCGTCGGGATCATCGGCGCGAAGACCGTGAACACCATGACGGACATCAG\n-CATCGCCATCCACCCCACCCACCCCGTCGCCGTCCGCCGCGAGCAGCCCGTCGCGCGCCTCGTGCTGCTG\n-CACCCCGACACCCTCCGCGCCACCAGCACCACCACCCCCCTCACCGCCGCGCCCCCCGCACCCGCGTCGA\n-GCCCACCCGACCCCGCCGGGCCGGCCGCACCGGTCGCTGCGCCCAACACCACGATCCTGGACGCCTCATG\n-A\n->lcl|NZ_CM001166.1_gene_27 [locus_tag=STTU_p0027] [location=complement(23592..24644)]\n-ATGGCACGTAACGTCGAGTTCTTCTCGACCGACACCGACGACGGCACGATCTCGGTCGTGGCGAAGGCCG\n-GGCCTGGCGAGCACCGGCGGATCGACCAGATCCGGGTCGGCAACGCGCCGCGCGGCGGCGTGAAGTTCAC\n-GAGGTCCGGGCGCGGGTTCGTGTGCAACACCTCGCAGAACACGATCAGCGAGATCGACCCGGTCGCCCAC\n-ACCGAGGTGCGGCGGATCGAGGTCGGGCACGGCCCGCGCGGCCAGGGGCTGCTGCCCGGCGACACGTACC\n-TGCTCGTCTCCAACTCCGGCTCCGACACCGTCAGCATCGTCGACCTCGAGCTGAACGTCGAGATCCACCA\n-GGTGCCGGTGGGCCGCGACCCGCGGCACATGGGGATCAGCGCGGACGGCCGGAGTGCGTGGGTGTGCGTG\n-TGGGGCGCCGGCTACGTGAGCAAGCTCGACCTCACGGCGCTGGTGGAACGGCAGGACGCCGCCGGGGTCA\n-CCGAGGTCGCGCGGATTCCCGTCGACGCGAAGGCCCACCCCTACAGCCTCGGCATCGACCCCTCCGGTCG\n-CAGGGTGTTCGTCGCGAACACGCAGGCCACCTACGTGACGGTGATCGACACCGCCACCCACGAGACCCAC\n-CGTGTCGACGTCGGCTTCATCGGCGGCCGTGGGGTGGCCTTCTCCCCGGACGGGCGCCACGCGCTGATCA\n-CGGTCGAGTCCATCAGCCGGGTCTACGTCATCGACGTCGACACCCTCGCCGTTACCCGGCACATCCCCGT\n-CGGCGGCGGCCCCCGCGGCCTCGTCGTCGACCCCGCCGACTCCACCGCGTACGTCACGAACTTCTCCCGC\n-ACGAACCTGCGCGCGGTGGCCCCGGAGCTCGACTACGACCCCAACACCCTCACCGTCATCGACCTCGGCA\n-GCGCGCCTCTCGACCGCGAGGAGGGCGTCTTCGACACCGAGCCCCTCTACGTCGGCTTCGGCCCCTGCTC\n-GGTGACGATGTTCGACCTCGACACCCTGCCCGAGCAGGAACGCCAGCGCCGCACCGAGCGCCTCACCACC\n-TGA\n->lcl|NZ_CM001166.1_gene_28 [locus_tag=STTU_p0028] [location=complement(24697..25320)]\n-ATGCAGGCGTTCGCCACGCCCGTGGCGCGGTGCCCGTACCCGGAGGCCGCAGCCGTGCGGGATGTCCTCA\n-CCGAGGCGGTCCTCTCCCGCCTGGGGGAGGGGAAGGTGTTCGGCTACAAGCAGGAGACCTCCCGGGACCT\n-GACCACATGGGGTGTGGCGGAGCTGGACGCGCTGACGGGCTGGGTCGGCCGGATGACGCGTCAGCTGGTG\n-GAGAAGCTGGCCGGCGTCCCGCTGGGGGAGGCGTTCGCGCGCTCGGCGGGCCGGGAGGGCGAGGGTGCGG\n-GGGTGCGGGCGGCGGGGATCGTGGCGTCGCGGAGCTGGGCGAGCGTGTACCGGGCGGGTGACCGGCATGC\n-GGCGCACTTCCACCCGAACACGGCCTGGTCGGCGATCTACTACCTGACCGCTCCCGGTGTGTGTGAGCTG\n-GACCTGCTCGATCCCCGCCCCGTGGGCTACTTCGATGCGGGGATCGTCTTCGCGGGGGAGGACCAGCGGA\n-TGCGGCTCTCCTGCTCACCCGGCGACCTCGTGATCATTCCGGGGTGGCTGCGTCACGAGGTGCCCGAATT\n-CCAGGACGACGAGGTGCGTATTTCCCTTTCCTGGAACCTGAACTACTCGCTCCATCGCGGCTGA\n->lcl|NZ_CM001166.1_gene_29 [locus_tag=STTU_p0029] [location=complement(25613..25759)]\n-GTGCGGGCTCGCGCGGGGCGGCGGCGGTGCGGGGCCGGGGACCTTGCGGGTGCCGGTGCTGTGCGCCTGT\n-GGCTGCGCCGCTTCTGCTCCCGTGCGGGGCAGGTTTTCTCTGTGGTGCTGCAGGTGGGGGTTGCGTTTTG\n-GTGGTAG\n->lcl|NZ_CM001166.1_gene_30 [locus_tag=STTU_p0030] [location=complement(25840..26139)]\n-GTGGATTGGGACGCTCACACCGAAGAGGTGCGCCTCGCGACCATCGCGCTGCCCACGGTGGTCTCCGATC\n-TCCTCGGGCGCCTCACGGACGAGATCGAGAAGCTGACCAGGTCGTCACCACTCGCTGCGGCACGCGCCGC\n-GCACCTCATGCAGGTCGCTGCGAAGCAGGCCGGCCGGTGGCCCGCGCAGAAGGCCCTGAACGACACCGAC\n-CGACACGATGCGGCCGTTGCGCTGGTCGTCAGCGAGAACGGCGCGCGCTCGTTGCTGGCGCATCTCGGTG\n-ATGTCAGCCTGTACGGCTGA\n->lcl|NZ_CM001166.1_gene_31 [locus_tag=STTU_p0031] [location=complement(26139..26732)]\n-GTGTCTCACAGACGAGGCAGCGGCCCGGGCACTGAGGCCGCGCTTGCCCACGAGTTCTCCCAGCGGATCC\n-TGATCGCCATCTCCAACGGCACCAACGCCGTCGCGGCGAAACAGTCATCCGCCGACGCGGTCGTCGCCTC\n-TGGTGCGCTCGCCTGTTCCCTCGAGAGCGGCGTGCGGGCTCGGAGCGGGCGGCGACTTTCTGGTTTTTGG\n-GGCGGCGGCGGCTGGGAGGGGGCATTGTCGGAGCACCGTATCTGTAGCGCGGGT'..b'ATCTGCTCGCTGCCGCGGCCCCG\n-GCAGAGTACGATCCGGCCTCGCTCACCCCTGAGGAGAAGACCCACCTGTTGTCCGCCGCGGCCTGGCAGG\n-CAGAGGAGGGCGCCTACATGCACCAGCAGAACACCCGTCCCCTCACCCTCGCGCCCGCACTGAACGACTC\n-GCCCGCCGGACTGCTCTCCTGGATCCTCGAGAAGTACCGCGCGTGGACCGACTGCGGCGGCGACCTGTCC\n-ACCCGCTTCGGCGACGACTTCCTCCTCACCCAGGCATCGCTCTACTGGTTCACCGGCACGATCTCCACGT\n-CCTTCCGCCCGTACTACGAGTACGCGCACCAGCTCACCCGGCGCGTGCGGCGGGTCGACGTCCCCACCGC\n-CCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGGAGCTGGGCCGAGCGCACCTACCACCTCACG\n-CGTTACACCCGTATGCCTCGCGGCGGCCACTTCGCCGCGCACGAGGAACCGGCCTTGCTTGCCGACGACA\n-TCACCGCGTTCTTCGGCGACCTCCGTTAG\n->lcl|NZ_CM001166.1_gene_174 [locus_tag=STTU_p0174] [location=complement(143857..143970)]\n-GTGGATGGACTGCATGGGAGCCCACTTCATAAGAGGCTCGACGAACACTGCGCTGGCCGATTCGGGATCG\n-CACCACCGCTAACCGGGGAAATCACCACGAAGATCAACCACTGA\n->lcl|NZ_CM001166.1_gene_175 [locus_tag=STTU_p0175] [location=complement(143981..144157)]\n-ATGCCCACCGAGACCCTGCCGCCCGAGGTGCGGAATTTCATCGACGATGCGCGGCGTCACCTGGCTTTCT\n-GCGCCGGGCTGCGCGCGGGCGAGGACCCGGCGTACGCGACCGTGCTCCTGGCCGCCGCCGAGCAGGGAGA\n-AGAAGTCCTCGCCCGGTACGAAGGCCGCGTAGCTTAG\n->lcl|NZ_CM001166.1_gene_176 [locus_tag=STTU_p0176] [location=complement(144230..147016)]\n-TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAACATCAGGTGG\n-AGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGCGCCCGTTCGGGGCGGGGGGC\n-GCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACGATCAGCGCGGCTGTTGCGGCGTTGGAGTTG\n-TTCCCTTCGGGGCGGGTTCTCGTGATGGTGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGC\n-GGGCGGTGGGGCACACGGCGCCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTT\n-GCGGGTGCGGACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n-GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTGGCGGGCTCGG\n-GGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAGGCGCACCGTACGGCGGGCAG\n-CGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGTATCCCGGCGGCGCACCGGCTCTACCTCACC\n-GCCACCCCGCGCGTCCTCGCGCCCGCCCGCCCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGG\n-CGCCGGCACTCGTGACGATGGCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTT\n-GTCCGAGGCGATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n-CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTCCAGACTGCGT\n-TGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCATCAGCGGGTGGAGGAGGCGGC\n-GGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATCTT\n-GCCCTAGCCGAGGAGCTCCCGGCCTCCGAGGTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATG\n-TGCGGCCGGAGCGGGTGTGGTCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCT\n-GCGGGAGTTCGCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n-GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCCGACGCGCGCG\n-GGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAACCCGGACGGGCAGACGAAGAC\n-GGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAGGACGGGGAGGGGATGGTCGCGAGCGAGGCG\n-TACCGGCCGCTCGTGGCCGTGCTCCAGGGGCTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGC\n-TCCGGGCCCGGGTGCGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCG\n-GGTCCTGTCCGACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n-GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCGGAGTCGGTGT\n-TGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTGCGGACGCGGGTGTACCAGCC\n-GGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGCGCGGC\n-TTGTGCGCGGTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGA\n-CCACCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGA\n-GGGCATGGTGTGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n-GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGACGTCGTACGCG\n-TCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGACGCGGAGCGGGCCGCCGCGCG\n-CGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGCCCCTGGCCGCTGGACTGGCAGCGCTGCTGT\n-CGGCAGCTCGCGCTCCTGGCCGCCGACGAACCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCA\n-TCGACGGGGACGACCTCGGCGCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCAC\n-CGAGCAGCGGGCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n-GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGCGGCCTCGCGG\n-CGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGCAAACACACCGAGACCGTGAG\n-CGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGGGTCTCGAACGTGAAGAGCCGCTTCGACGGG\n-ATGGGCGAGGACGAGCGCGGCCAGCTCACCGCGCTCGGAGTGCCCTGGGCGGTGTAG\n-\n' |
| b |
| diff -r 98bd79bb98fe -r 891b330ffd94 test-data/streptomyces_Tu6071_plasmid_genes.icm |
| b |
| Binary file test-data/streptomyces_Tu6071_plasmid_genes.icm has changed |