# HG changeset patch
# User iuc
# Date 1663854674 0
# Node ID 1ae00120dd24e986b636de54047aed27c0457b05
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
diff -r 000000000000 -r 1ae00120dd24 integron_finder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integron_finder.xml Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,228 @@
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+ is a program that detects integrons in DNA sequences
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+ macro.xml
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+ gbk
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+ no_logfile == False
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+ pdf
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diff -r 000000000000 -r 1ae00120dd24 macro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macro.xml Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,40 @@
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+ 2.0.2
+ 0
+ 21.05
+ \${GALAXY_SLOTS:-2}
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+
+ hmmer
+ infernal
+ prodigal
+ integron_finder
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+
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+ topic_0085
+ topic_0798
+ topic_3047
+ topic_0091
+ topic_0080
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+ operation_0239
+ operation_3430
+ operation_3087
+ operation_0362
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+ integron_finder
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+ 10.1101/2022.02.28.482270
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diff -r 000000000000 -r 1ae00120dd24 test-data/covar.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/covar.txt Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,377 @@
+INFERNAL1/a [1.1 | October 2013]
+NAME attC_4
+STATES 145
+NODES 35
+CLEN 47
+W 895
+ALPH RNA
+RF yes
+CONS yes
+MAP yes
+DATE Mon Jan 19 20:03:31 2015
+COM [1] cmbuild --hand attc_4.cm attc_train_set_4.sto
+COM [2] cmcalibrate attc_4.cm
+PBEGIN 0.05
+PEND 0.05
+WBETA 1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA 1.52588e-05
+N3OMEGA 1.52588e-05
+ELSELF -0.08926734
+NSEQ 96
+EFFN 96.000000
+CKSUM 3931512547
+NULL 0.000 0.000 0.000 0.000
+EFP7GF -9.9186 0.72993
+ECMLC 0.63005 -4.33175 4.20996 1600000 260875 0.004600
+ECMGC 0.41832 -12.02668 0.81138 1600000 85985 0.004652
+ECMLI 0.58141 -4.10957 4.92170 1600000 228880 0.005243
+ECMGI 0.42824 -10.63745 1.38026 1600000 68728 0.005820
+CM
+ [ ROOT 0 ] - - - - - -
+ S 0 -1 0 1 6 1 2 895 1874 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983
+ IL 1 1 2 1 6 1 6 897 1875 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 2 2 3 2 5 1 7 897 1875 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 1 ] 1 141 G C [ ]
+ MP 3 2 3 7 6 2 17 896 1874 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -3.249 -1.316 -1.827 1.518 -2.413 -6.970 -1.008 -1.669 -6.771 3.266 -7.041 -1.135 -0.432 -6.231 -1.090 -5.342
+ ML 4 2 3 7 6 1 4 893 1872 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 5 2 3 7 6 1 4 893 1871 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 6 2 3 7 6 0 0 887 1865 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 7 7 5 7 6 1 6 895 1873 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 8 8 6 8 5 1 6 895 1873 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 2 ] 2 140 c g R m
+ MP 9 8 6 13 6 2 16 894 1872 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -4.164 -4.362 -2.109 -0.857 -0.435 -2.882 2.773 -0.766 -4.417 1.213 -4.988 -2.366 1.504 -1.682 -0.391 -1.681
+ ML 10 8 6 13 6 1 4 891 1870 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 11 8 6 13 6 1 4 891 1869 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 12 8 6 13 6 0 0 885 1864 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 13 13 5 13 6 1 6 893 1871 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 14 14 6 14 5 1 6 893 1871 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 3 ] 3 139 C G s i
+ MP 15 14 6 19 6 2 14 892 1870 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -1.807 -6.286 -6.486 1.123 -2.471 -7.327 3.283 -0.390 -6.409 -2.191 -2.297 -4.092 0.801 -6.656 -1.251 -2.606
+ ML 16 14 6 19 6 1 4 889 1868 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 17 14 6 19 6 1 3 889 1867 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 18 14 6 19 6 0 0 884 1862 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 19 19 5 19 6 1 5 891 1869 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 20 20 6 20 5 1 5 891 1869 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 4 ] 4 138 U A e r
+ MP 21 20 6 25 6 2 12 890 1868 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -1.567 -8.813 -8.434 -4.815 -1.986 -2.946 0.157 -7.792 -2.231 -2.356 -8.712 -6.694 3.739 -8.821 -4.591 -1.729
+ ML 22 20 6 25 6 1 3 888 1866 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 23 20 6 25 6 1 3 887 1866 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 24 20 6 25 6 0 0 883 1861 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 25 25 5 25 6 1 5 889 1867 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 26 26 6 26 5 1 5 889 1867 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 5 ] 5 137 A U c p
+ MP 27 26 6 31 6 2 10 888 1867 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -10.570 -9.997 -5.983 3.992 -11.330 -11.473 -9.053 -5.806 -10.659 -6.593 -10.896 -5.995 -9.154 -11.296 -10.137 -5.962
+ ML 28 26 6 31 6 1 3 886 1864 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 29 26 6 31 6 1 3 885 1864 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 30 26 6 31 6 0 0 882 1860 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 31 31 5 31 6 1 4 887 1865 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 32 32 6 32 5 1 4 887 1865 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 6 ] 6 136 A U = R
+ MP 33 32 6 37 6 2 8 886 1865 -12.592 -12.531 -0.012 -7.143 -11.588 -11.983 -10.505 -9.876 -6.003 3.989 -11.293 -11.472 -8.827 -4.132 -10.570 -6.478 -10.833 -5.957 -8.965 -11.262 -10.014 -5.977
+ ML 34 32 6 37 6 1 2 884 1863 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 35 32 6 37 6 1 2 884 1862 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 36 32 6 37 6 0 0 881 1859 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 37 37 5 37 6 1 3 885 1864 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 38 38 6 38 5 1 3 885 1863 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 7 ] 7 135 C G ] [
+ MP 39 38 6 43 4 2 6 884 1863 -11.730 -11.937 -0.002 -10.352 -9.944 -10.195 -1.983 -6.488 -7.012 -8.577 3.966 -8.587 -9.417 -6.461 -8.627 -8.589 -4.408 -9.819 -5.380 -8.218
+ ML 40 38 6 43 4 1 2 883 1861 -4.558 -4.740 -0.269 -3.470 -0.517 1.009 -1.262 -0.198
+ MR 41 38 6 43 4 1 1 882 1860 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 42 38 6 43 4 0 0 880 1859 -4.568 -4.250 -2.265 -0.520
+ IL 43 43 5 43 4 1 3 884 1862 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 44 44 6 44 3 1 2 884 1862 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 8 ] 8 - A - = -
+ ML 45 44 6 47 3 1 4 882 1861 -12.654 -0.001 -11.308 1.460 -0.087 -3.247 -2.301
+ D 46 44 6 47 3 0 0 880 1858 -6.174 -1.687 -0.566
+ IL 47 47 3 47 3 1 2 883 1861 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 9 ] 9 - A - = -
+ ML 48 47 3 50 3 1 3 881 1860 -12.654 -0.001 -11.308 1.392 -0.247 -1.648 -2.219
+ D 49 47 3 50 3 0 0 879 1857 -6.174 -1.687 -0.566
+ IL 50 50 3 50 3 1 1 882 1860 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 10 ] 10 - g - = -
+ ML 51 50 3 53 3 1 2 880 1859 -12.654 -0.020 -6.196 -0.298 -0.774 0.434 0.323
+ D 52 50 3 53 3 0 0 878 1856 -6.174 -1.687 -0.566
+ IL 53 53 3 53 3 1 1 881 1859 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 11 ] 11 - U - = -
+ ML 54 53 3 56 3 1 2 879 1858 -12.635 -0.032 -5.518 -1.914 -0.835 0.163 1.039
+ D 55 53 3 56 3 0 0 877 1856 -8.231 -3.744 -0.117
+ IL 56 56 3 56 3 1 1 880 1858 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 12 ] 12 - C - = -
+ ML 57 56 3 59 3 1 1 878 1857 -12.603 -4.129 -0.085 -3.211 1.629 -0.844 -2.053
+ D 58 56 3 59 3 0 0 877 1855 -9.376 -4.889 -0.052
+ IL 59 59 3 59 3 1 1 883 1861 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 13 ] 13 - A - = -
+ ML 60 59 3 62 3 1 3 881 1860 -8.488 -0.014 -7.142 1.871 -3.422 -2.956 -3.072
+ D 61 59 3 62 3 0 0 877 1855 -13.996 -9.509 -0.002
+ IL 62 62 3 62 3 1 1 882 1860 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 14 ] 14 - U - = -
+ ML 63 62 3 65 3 1 2 880 1859 -8.488 -0.014 -7.142 -2.483 -2.313 -3.251 1.813
+ D 64 62 3 65 3 0 0 877 1855 -13.996 -9.509 -0.002
+ IL 65 65 3 65 3 1 1 881 1859 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 15 ] 15 - U - = -
+ ML 66 65 3 68 3 1 1 879 1858 -8.850 -1.462 -0.656 -2.483 -2.313 -3.251 1.813
+ D 67 65 3 68 3 0 0 877 1855 -12.730 -4.483 -0.066
+ IL 68 68 3 68 3 1 1 882 1861 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 16 ] - 134 - C - =
+ MR 69 68 3 71 3 1 3 881 1859 -8.891 -0.013 -7.209 -3.099 1.851 -3.897 -2.265
+ D 70 68 3 71 3 0 0 877 1855 -13.963 -9.141 -0.003
+ IR 71 71 3 71 3 1 1 881 1860 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 17 ] - 133 - U - =
+ MR 72 71 3 74 3 1 3 880 1858 -8.891 -0.013 -7.209 -2.564 -2.382 -3.335 1.824
+ D 73 71 3 74 3 0 0 877 1855 -13.963 -9.141 -0.003
+ IR 74 74 3 74 3 1 1 880 1859 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 18 ] - 132 - U - =
+ MR 75 74 3 77 3 1 3 879 1857 -8.891 -0.013 -7.209 -2.564 -2.382 -3.335 1.824
+ D 76 74 3 77 3 0 0 877 1855 -13.963 -5.689 -0.028
+ IR 77 77 3 77 3 1 1 879 1858 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 19 ] - 131 - A - =
+ MR 78 77 3 80 3 1 2 878 1857 -9.245 -0.010 -7.562 1.210 -0.707 -0.713 -1.109
+ D 79 77 3 80 3 0 0 877 1855 -13.937 -0.765 -1.281
+ IR 80 80 3 80 3 1 1 878 1857 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 20 ] - 130 - C - =
+ MR 81 80 3 83 3 1 2 877 1856 -12.264 -0.001 -10.582 -2.570 1.571 -1.278 -1.160
+ D 82 80 3 83 3 0 0 876 1854 -12.663 -0.136 -3.476
+ IR 83 83 3 83 3 1 1 877 1856 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 21 ] - 129 - c - =
+ MR 84 83 3 86 3 1 1 876 1855 -12.905 -0.001 -11.223 -0.302 0.852 0.055 -1.536
+ D 85 83 3 86 3 0 0 875 1853 -9.257 -0.137 -3.487
+ IR 86 86 3 86 3 1 1 876 1855 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 22 ] - 128 - G - =
+ MR 87 86 3 89 3 1 1 875 1854 -12.951 -0.001 -11.268 0.549 -1.760 1.082 -2.997
+ D 88 86 3 89 3 0 0 872 1851 -6.390 -1.568 -0.620
+ IR 89 89 3 89 3 1 1 875 1854 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 23 ] - 127 - g - =
+ MR 90 89 3 92 3 1 1 874 1853 -12.951 -0.001 -11.268 0.377 -0.568 0.671 -1.199
+ D 91 89 3 92 3 0 0 871 1850 -6.390 -1.568 -0.620
+ IR 92 92 3 92 3 1 1 874 1853 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 24 ] - 126 - C - =
+ MR 93 92 3 95 3 1 1 873 1852 -12.951 -0.001 -11.268 -0.886 1.126 -0.297 -1.112
+ D 94 92 3 95 3 0 0 870 1849 -6.390 -1.568 -0.620
+ IR 95 95 3 95 3 1 1 873 1852 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000
+ [ MATR 25 ] - 125 - U - =
+ MR 96 95 3 98 5 1 1 872 1851 -11.595 -0.002 -11.410 -11.622 -12.514 -1.444 -0.765 -1.243 1.390
+ D 97 95 3 98 5 0 0 869 1848 -5.352 -0.707 -2.978 -4.409 -2.404
+ IR 98 98 3 98 5 1 1 872 1850 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 26 ] 16 124 G C [ ]
+ MP 99 98 3 103 6 2 2 871 1850 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -6.582 -1.557 -6.411 1.191 -7.476 -1.489 1.101 -7.084 -6.836 3.115 -2.324 -2.899 0.456 -1.331 -4.597 -5.381
+ ML 100 98 3 103 6 1 1 869 1847 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 101 98 3 103 6 1 1 867 1846 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 102 98 3 103 6 0 0 863 1841 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 103 103 5 103 6 1 1 870 1848 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 104 104 6 104 5 1 1 870 1848 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 27 ] 17 123 u a = m
+ MP 105 104 6 109 6 2 2 869 1848 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -0.828 -4.312 -4.303 1.181 -4.254 -3.025 2.046 -3.077 -4.365 0.739 -4.937 -2.958 2.474 -1.830 -1.666 -0.703
+ ML 106 104 6 109 6 1 1 867 1845 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 107 104 6 109 6 1 1 865 1843 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 108 104 6 109 6 0 0 861 1840 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 109 109 5 109 6 1 1 868 1846 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 110 110 6 110 5 1 1 868 1846 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 28 ] 18 122 U A L i
+ MP 111 110 6 115 4 2 2 867 1846 -11.741 -11.948 -0.002 -10.362 -0.702 -9.034 -2.124 -0.041 0.340 -9.011 -1.841 -8.027 -8.700 -2.090 -8.930 -6.877 3.625 -9.170 -4.866 -7.506
+ ML 112 110 6 115 4 1 1 865 1844 -3.758 -3.940 -0.507 -2.670 0.368 -0.385 -0.191 0.094
+ MR 113 110 6 115 4 1 1 862 1841 -4.809 -3.838 -1.706 -0.766 0.368 -0.385 -0.191 0.094
+ D 114 110 6 115 4 0 0 860 1839 -4.568 -4.250 -2.265 -0.520
+ IL 115 115 5 115 4 1 1 867 1845 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000
+ IR 116 116 6 116 3 1 1 866 1845 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000
+ [ MATL 29 ] 19 - C - s -
+ ML 117 116 6 119 5 1 1 865 1844 -11.595 -0.002 -11.410 -11.622 -12.514 -2.365 1.152 0.068 -0.902
+ D 118 116 6 119 5 0 0 858 1836 -4.959 -0.803 -4.221 -2.596 -2.508
+ IL 119 119 3 119 5 1 1 864 1842 -2.408 -0.496 -4.087 -5.920 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 30 ] 20 121 A U e r
+ MP 120 119 3 124 6 2 2 864 1843 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -1.884 -7.244 -7.809 3.089 -6.922 -8.680 2.277 -2.136 -7.694 0.753 -8.160 -4.763 -1.577 -8.142 -4.435 -6.477
+ ML 121 119 3 124 6 1 1 856 1834 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 122 119 3 124 6 1 1 853 1831 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 123 119 3 124 6 0 0 837 1815 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 124 124 5 124 6 1 1 861 1840 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 125 125 6 125 5 1 1 861 1840 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 31 ] 21 120 A U c p
+ MP 126 125 6 130 6 2 2 862 1841 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -8.851 -7.764 -2.118 3.793 -8.437 -10.138 -0.570 -2.650 -8.525 -0.651 -9.020 -5.124 -1.428 -9.742 -6.081 -7.490
+ ML 127 125 6 130 6 1 1 850 1829 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 128 125 6 130 6 1 1 847 1826 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 129 125 6 130 6 0 0 831 1809 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 130 130 5 130 6 1 1 859 1837 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 131 131 6 131 5 1 1 859 1837 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 32 ] 22 119 G C = L
+ MP 132 131 6 136 6 2 2 860 1839 -12.592 -12.531 -0.002 -11.308 -11.588 -11.983 -6.681 -0.356 -6.503 0.360 -7.617 -1.551 1.417 -1.964 -6.924 3.364 -7.172 -2.953 -2.958 -6.355 -4.698 -5.467
+ ML 133 131 6 136 6 1 1 841 1819 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.368 -0.385 -0.191 0.094
+ MR 134 131 6 136 6 1 1 838 1816 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.368 -0.385 -0.191 0.094
+ D 135 131 6 136 6 0 0 825 1803 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319
+ IL 136 136 5 136 6 1 1 856 1834 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000
+ IR 137 137 6 137 5 1 1 856 1834 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000
+ [ MATP 33 ] 23 118 c g ] [
+ MP 138 137 6 142 3 2 2 858 1837 -0.007 * -7.643 -0.812 -0.317 -2.510 -0.729 -4.140 -1.090 2.981 -4.503 -4.225 0.880 -1.072 -2.070 0.595 -1.518 -0.284 -3.425
+ ML 139 137 6 142 3 1 1 821 1799 -1.000 * -1.000 0.368 -0.385 -0.191 0.094
+ MR 140 137 6 142 3 1 1 821 1799 -1.000 * -1.000 0.368 -0.385 -0.191 0.094
+ D 141 137 6 142 3 0 0 820 1798 -1.000 * -1.000
+ IL 142 142 5 142 3 1 1 857 1835 -0.027 * -5.744 0.000 0.000 0.000 0.000
+ IR 143 143 6 143 2 1 1 13 28 -1.823 -0.479 0.000 0.000 0.000 0.000
+ [ END 34 ] - - - - - -
+ E 144 143 6 -1 0 0 0 0 0
+//
+HMMER3/f [i1.1 | October 2013]
+NAME attC_4
+LENG 47
+MAXL 899
+ALPH RNA
+RF yes
+MM no
+CONS yes
+CS yes
+MAP yes
+DATE Mon Jan 19 20:03:31 2015
+COM [1] cmbuild --hand attc_4.cm attc_train_set_4.sto
+NSEQ 96
+EFFN 81.594727
+CKSUM 3931512547
+STATS LOCAL MSV -8.0165 0.72993
+STATS LOCAL VITERBI -8.5470 0.72993
+STATS LOCAL FORWARD -2.8542 0.72993
+HMM A C G U
+ m->m m->i m->d i->m i->i d->m d->d
+ COMPO 1.36592 1.36257 1.42708 1.39094
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 0.00000 *
+ 1 1.47847 2.74840 0.46402 2.53536 1 G [ - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 2 2.80092 0.67279 1.80861 1.32771 2 C R - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 3 1.85804 0.41549 3.36842 1.90005 3 C s - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 4 3.69371 2.33806 3.58381 0.16154 4 U e - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 5 0.00512 6.50309 6.16068 6.50100 5 A c - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 6 0.00672 5.72139 6.25551 6.50195 6 A = - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 7 4.27255 0.02200 6.25809 5.13253 7 C ] - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 8 0.37524 1.45216 3.61000 2.96117 8 A = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 9 0.42348 1.56183 2.52300 2.89563 9 A = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 10 1.58522 1.91861 1.09174 1.16265 10 g = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.01535 6.88959 4.25350 1.46634 0.26236 1.09861 0.40547
+ 11 2.67081 1.96038 1.27856 0.67029 11 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.02368 6.87631 3.79983 1.46634 0.26236 2.77000 0.06471
+ 12 3.57863 0.25850 1.98007 2.78364 12 C = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 2.83122 6.85473 0.06187 1.46634 0.26236 3.60115 0.02767
+ 13 0.11057 3.55402 3.24839 3.29069 13 A = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03515 4.05867 4.05867 1.46634 0.26236 6.83206 0.00108
+ 14 2.90925 2.82331 3.43701 0.15793 14 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03515 4.05867 4.05867 1.46634 0.26236 6.83206 0.00108
+ 15 2.90925 2.82331 3.43701 0.15793 15 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03515 4.05867 4.05867 1.46634 0.26236 0.00216 6.13892
+ 16 1.79396 1.85607 0.57562 2.16230 16 G [ - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 17 1.68938 1.29005 2.11445 0.86890 17 u = - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 18 2.17270 2.31497 4.10529 0.26023 18 U L - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 19 2.98995 0.59134 1.34531 1.99756 19 C s - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 20 0.60908 1.14694 2.20721 3.55669 20 A e - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 21 0.12915 2.93836 3.14908 3.67645 21 A c - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 22 2.02391 1.59657 0.43035 4.20022 22 G = - <
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 23 1.98545 0.65296 1.80241 1.73005 23 C ] - <
+ 1.38629 1.38629 1.38629 1.38629
+ 3.89386 0.02162 6.88959 3.98542 0.01876 1.09861 0.40547
+ 24 1.96486 1.53408 0.55010 2.69887 118 G [ - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 25 4.47612 0.34286 1.77423 2.21391 119 C L - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 26 3.71435 3.19641 2.84131 0.13197 120 U p - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 27 3.18123 2.23054 1.18098 0.60877 121 U r - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 28 0.12234 4.14596 3.30449 2.77083 122 A i - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 29 0.95560 2.00635 1.26122 1.62135 123 a m - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 30 2.43472 0.49870 1.89972 1.86145 124 C ] - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 31 2.36885 1.91431 2.24466 0.42617 125 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 32 1.99009 0.61165 1.59584 2.13601 126 C = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 33 1.12677 1.78023 0.92633 2.19536 127 g = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 34 1.00976 2.60221 0.63685 3.42260 128 G = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03382 6.88959 3.43454 1.46634 0.26236 1.09861 0.40547
+ 35 1.59086 0.80252 1.35196 2.41555 129 c = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.44710 6.85787 1.02314 1.46634 0.26236 3.51631 0.03016
+ 36 3.12832 0.30189 2.27881 2.16819 130 C = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 2.11131 6.41406 0.13093 1.46634 0.26236 5.92595 0.00267
+ 37 0.57651 1.86795 1.86012 2.05532 131 A = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.27640 4.32946 1.47704 1.46634 0.26236 6.81245 0.00110
+ 38 2.96395 2.86913 3.49326 0.14939 132 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03415 4.08721 4.08721 1.46634 0.26236 6.83026 0.00108
+ 39 2.96395 2.86913 3.49326 0.14939 133 U = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03415 4.08721 4.08721 1.46634 0.26236 6.83026 0.00108
+ 40 3.29366 0.12992 3.86188 2.75374 134 C = - -
+ 1.38629 1.38629 1.38629 1.38629
+ 0.03415 4.08721 4.08721 1.46634 0.26236 0.00967 4.64385
+ 41 5.61227 6.76634 0.00620 6.58877 135 G [ - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00205 6.88254 6.88254 1.46634 0.26236 0.22559 1.59970
+ 42 7.50523 6.97196 6.53815 0.00294 136 U R - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 43 7.47647 6.84256 6.54333 0.00308 137 U p - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 44 0.12946 3.82317 2.57597 3.75121 138 A r - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 45 1.95767 3.97633 0.44327 1.61886 139 G i - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 46 1.46810 1.73501 0.72259 2.22795 140 g m - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00204 6.88959 6.88959 1.46634 0.26236 1.09861 0.40547
+ 47 2.71772 0.47057 2.52869 1.47157 141 C ] - >
+ 1.38629 1.38629 1.38629 1.38629
+ 0.00102 6.88857 * 1.46634 0.26236 0.00000 *
+//
diff -r 000000000000 -r 1ae00120dd24 test-data/input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,340 @@
+>ACBA.007.P01_13 08-JUN-2013 20301 bp Acinetobacter baumannii MDR-ZJ06 plasmid pMDR-ZJ06, complete
+TGCTGCTTGGATGCCCGAGGCATAGACTGTACAAAAAAACAGTCATAACAAGCCATGAAA
+ACCGCCACTGCGCCGTTACCACCGCTGCGTTCGGTCAAGGTTCTGGACCAGTTGCGTGAG
+CGCATACGCTACTTGCATTACAGTTTACGAACCGAACAGGCTTATGTCAACTGGGTTCGT
+GCCTTCATCCGTTTCCACGGTGTGCGTCACCCGGCAACCTTGGGCAGCAGCGAAGTCGAG
+GCATTTCTGTCCTGGCTGGCGAACGAGCGCAAGGTTTCGGTCTCCACGCATCGTCAGGCA
+TTGGCGGCCTTGCTGTTCTTCTACGGCAAGGTGCTGTGCACGGATCTGCCCTGGCTTCAG
+GAGATCGGAAGACCTCGGCCGTCGCGGCGCTTGCCGGTGGTGCTGACCCCGGATGAAGTG
+GTTCGCATCCTCGGTTTTCTGGAAGGCGAGCATCGTTTGTTCGCCCAGCTTCTGTATGGA
+ACGGGCATGCGGATCAGTGAGGGTTTGCAACTGCGGGTCAAGGATCTGGATTTCGATCAC
+GGCACGATCATCGTGCGGGAGGGCAAGGGCTCCAAGGATCGGGCCTTGATGTTACCCGAG
+AGCTTGGCACCCAGCCTGCGCGAGCAGCTGTCGCGTGCACGGGCATGGTGGCTGAAGGAC
+CAGGCCGAGGGCCGCAGCGGCGTTGCGCTTCCCGACGCCCTTGAGCGGAAGTATCCGCGC
+GCCGGGCATTCCTGGCCGTGGTTCTGGGTTTTTGCGCAGCACACGCATTCGACCGATCCA
+CGGAGCGGTGTCGTGCGTCGCCATCACATGTATGACCAGACCTTTCAGCGCGCCTTCAAA
+CGTGCCGTAGAAGGCACTGTTGCAAAGTTAGCGATGAGGCAGCCTTTTGTCTTATTCAAA
+GGCCTTACATTTCAAAAACTCTGCTTACCAGGCGCATTTCGCCCAGGGGATCACCATAAT
+AAAATGCTGAGGCCTGGCCTTTGCGTAGTGCACGCATCACCTCAATACCTTTGATGGTGG
+CGTAAGCCGTCTTCATGGATTTAAATCCCAGCGTGGCGTTGATTATCCGTTTCAGTTTGC
+CATGATCGCATTCAATCACGTTGTTCCGGTACTTAATCTGTCGGTGTTCAACGTCAGACG
+GGCACCGGCCTTCGCGTTTGAGCAGAGCAAGCGCGCGACCATAGGCGGGCGCTTTATCCG
+TGTTGATGAATCGCGGGATCTGCCACTTCTTCACGTTGTTGAGGATTTTACCCAGAAACC
+GGTATGCAGCTTTGCTGTTACGACGGGAGGAGAGATAAAAATCGACAGTGCGGCCCCGGC
+TGTCGACGGCCCGGTACAGATACGCCCAGCGGCCATTGACCTTCACGTAGGTTTCATCCA
+TGTGCCACGGGCAAAGATCGGAAGGGTTACGCCAGTACCAGCGCAGCCGTTTTTCCATTT
+CAGGCGCATAACGCTGAACCCAGCGGTAAATCGTGGAGTGATCGACATTCACTCCGCGTT
+CAGCCAGCATCTCCTGCAGCTCACGGTAACTGATGCCGTATTTGCAGTACCAGCGTACGG
+CCCACAGAATGATGTCACGCTGAAAATGCCGGCCTTTGAATGGGTTCATGTGCAGCTCCA
+TCAGCAAAAGGGGATGATAAGTTTATCACCACCGACTATTTGCAACAGTGCCAAGCGCGG
+TGTCCGGAATTTCAGGTTTGTGTCTCTACAAAGACTAACTATCAGAAAAACTCATCGAGC
+ATCAAATGAAACTGCAATTTATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGC
+CGTTTCTGTAATGAAGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGG
+TATCGGTCTGCGATTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTCA
+AAAATAAGGTTATCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGAGAATGGC
+AAAAGCTTATGCATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACGCTCGTCATCA
+AAATCACTAGCATCAACCAAACCGTTATTCATTCGTGATTGCGCCTGAGCGAGACGAAAT
+ACGCGATCGCTGTTAAAAGGACAATTACAAACAGGAATCGAATGCAACCGGCGCAGGAAC
+ACTGCCAGCGCATCAACAATATTTTCACCTGAATCAGGATATTCTTCTAATACCTGGAAT
+GCTGTTTTCCCGGGGATCGCAGTGGTGAGTAACCATGCATCATCAGGAGTACGGATAAAA
+TGCTTGATAGTCGGAAGAGGCATAAATGCCGTCAGCCAGTTTAGTCTGACCATCTCATCT
+GTAACATCATTGGCAACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATTGGGC
+TTCCCATACAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATCTA
+TACCCATATAAATCAGCATCCAGGTTGGAATTTAATCGCGGCCTCGAGCAAGACGTTTCC
+CGTTGAATATGGCTCATAACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATT
+GTTCATGATGATATATTTTTATCGGCACTGTTGCAAATAGTCGGTGGTGATAAACTTATC
+ATCCCCTTTTGCTGATGGAGCTGCACATGAACCCATTCAAAGGCCGGCATTTTCAGCGTG
+ACATCATTCTGTGGGCCGTACGCTGGTACTGCAAATACGGCACTGTTGCAAAGTTAGCGA
+TGAGGCAGCCTTTTGTCTTATTCAAAGGCCTTACATTTCAAAAACTCTGCTTACCAGGCG
+CATTTCGCCCAGGGGATCACCATAATAAAATGCTGAGGCCTGGCCTTTGCGTAGTGCACG
+CATCACCTCAATACCTTTGATGGTGGCGTAAGCCGTCTTCATGGATTTAAATCCCAGCGT
+GGCGTTGATTATCCGTTTCAGTTTGCCATGATCGCATTCAATCACGTTGTTCCGGTACTT
+AATCTGTCGGTGTTCAACGTCAGACGGGCACCGGCCTTCGCGTTTGAGCAGAGCAAGCGC
+GCGACCATAGGCGGGCGCTTTATCCGTGTTGATGAATCGCGGGATCTGCCACTTCTTCAC
+GTTGTTGAGGATTTTACCCAGAAACCGGTATGCAGCTTTGCTGTTACGACGGGAGGAGAG
+ATAAAAATCGACAGTGCGGCCCCGGCTGTCGACGGCCCGGTACAGATACGCCCAGCGGCC
+ATTGACCTTCACGTAGGTTTCATCCATGTGCCACGGGCAAAGATCGGAAGGGTTACGCCA
+GTACCAGCGCAGCCGTTTTTCCATTTCAGGCGCATAACGCTGAACCCAGCGGTAAATCGT
+GGAGTGATCGACATTCACTCCGCGTTCAGCCAGCATCTCCTGCAGCTCACGGTAACTGAT
+GCCGTATTTGCAGTACCAGCGTACGGCCCACAGAATGATGTCACGCTGAAAATGCCGGCC
+TTTGAATGGGTTCATGTGCAGCTCCATCAGCAAAAGGGGATGATAAGTTTATCACCACCG
+ACTATTTGCAACAGTGCCGTGTACATCGAAATACGGCTTATCAGGCGTTAAAAGATGCTT
+GCGATGACTTGTTTGCAAGACAATTCAGTTATCAGAGTCTTAGTGAAAAAGGTAACACTA
+TTAATCACAAATCAAGATGGGTGAGCGAGGTGGCTTATATTGATAATGAAGCTGTCGTTA
+GACTTATTTTTGCCCCTGCTATTGTGCCTTTAATTACTAGGTTAGAAGAACAATTTACAA
+AGTATGAAATACAACAAATAAGTAATTTAACAAGTGCTTATGCTGTTCGTTTATATGAAA
+TATTGATTGCATGGCGTAGTACTGGAAAAACGCCTCTCATAACTATGTATGATTTTAGAC
+AAAAAATAGGTGTACTCGAGACTGAATACAAACGAATGTATGATTTTAAAAAATATGTTT
+TAGACATTGCATTAAAACAAGTAAATGAACATACCGATATTATTGTCAAAGTTGAACAGC
+ATAAAACAGGTAGATCTATTACTGGTTTTTCATTTAGCTTTAAACAGAAAAAATCAGCCA
+CGCATTCAGTCGAATCTAAAAGAGATCCGAATACATTAGACCTCTTTTCAAAAATAACAG
+ATAAACAACGCCATCTATTCGCCAACAAGCTCTCAGAGCTTCCTGAGATGAGTAAATATT
+CACAAGGCACAGAAAGCTATCAGCAGTTTGCTGTACGTATAGCTGCCATGCTGCAAGATG
+CAGAGAAATTTAAGGAATTACTTCCTTTACTCAGAAAATTAGGATTTCAATGACATTGTT
+AATTGAAATTGTTAAGTTAACAGTCAGGTATTAACACAAGTTGAAAACTGGTTTACATAA
+TGAAAAAACTGTCAGTTTCAGAGTTAGCTAAGCTTTATGGATATTCAAGACAAGCCATAT
+ATGCACATATAAACAAAGGAAATTTATCTAAAGGATCTGATGGATTAATTGACTTTTCAG
+AGGCCCTAAGAGTTTTTGGGGAACCACAAAAAAAAGAGGATACAGTCAATCAAAGTCAAT
+CAATTAACAGTCAAAACTTGACAGAAGTTGACTTACTAAAACGTCAAGTTGACATACTGG
+AAAAACAATTAAATCAGGCAATACAGAGAGAAAATCAATCTTTAGAACGTGAATCGTTTT
+ATCAAGGTAAGCGTAACGCCAACCACACATTCCAATCCTAACTGATCAACTTTACCCTGT
+CTGCCATTATCAACTGCCAGGGTAATCATCATGCACCGCACCAAAGAACAATGGTTCGCT
+TTATTCGCCGAGCAAGCCCAAAGTGGCCTCACCCAAACTGAATTTGCAAAACGTCAGGGC
+ATCATTCCTACATATTTTAGTTATCGCAAGAGACAATTGTTGGCGTTTCAGGATGATGAC
+GGTGGCTTTATTGAGCTGACGCCACAGGGCTTGCAGCTGAATAAATCCATTTTACTACGT
+AAGCGTGATGTGGAATTGCAGTTTCCAGCCGGCACTGATGTGCTGTGGTTAGCGGCCTTG
+CTCAGAGCGCTCTGACCATGAAAATGTTTCTTGATGTGCCCCAGGTCTATTTGCATAAAC
+AGCCGGTCGACTTTCGTAAATCTATTAATGGTTTATCGTTGCTAGTTGAGCAAGAGATGC
+AGCTCTCGCCTTTTAGTGGCGCACTGTTTGTATTTTGCAATCAGCAGCGTACCCGGTTAA
+AAGTACTGTACTGGGATAGCACAGGCTTTTGCTTGTGGTACAAGCGGCTTGAAAAAGACA
+AGTTCCGCTGGCCAAGGCAGATGCCTGGCAAAATCCTGTCTATTAGCGAACAACAGTGGC
+ATTGGCTGTTGCAAGGTGTCGATATTCAAAAAATCACCGCCCATCAGCCACTGCATTACC
+AGAGTGTGGGCTGATATGACGATCGGCTATAAATCCTTGTGATCGCATCCAAAACAATCT
+AAATCTTACCAAGCACTTAGTCCAATTGGCCGTTACAATAGCGGCCATGAAAAAGACACC
+TCAATCCTTACCTGATGATGTTGAACTGCTCAAGAAAATGCTGCTTGAGCAGACGCAAAA
+GCTTGAGCGGAAACTGGCGCAAAAAGATAAACGCATCGCCAAATTAGAGCGGGTTAACCA
+GCAACTGTCGGACAAGCTGCAGCAATTGCTGGAGCGTTACAACCTGAAGAAGTACCAGAA
+ATTTAGCCCCAGCAGCGAGACCTACGAAGGTGATGGCGAAGTCTTAAATGAGGCCGAACA
+GCTGATTGAAGACGAGTCAGTAGCGACAGAGCCAGATAATCAGACGACCGAGAGCGCTGA
+GAAAGCCGCTAAGCCACGCCGCCCACGGATTGCCCCTGAGCTGCCGCGCGTTGATGTTAT
+CCATGATATTGACGATAAAACCTGTACCTGCTGCGGCCATGCGCTGCATCAAATGGGTGA
+AGAAGTCAGTGAGCAACTCGAGTTCGTCCCAGCACAAATCCGGGTGCTTAGAAACGTGCG
+GCTGAAATACAGCTGCCGGCAGTGTGAGACCAACGGCACCAAGGTCGAGATAAAAATTGC
+CGATGTGCCGCCAGCAGTTATCCCGAAAAGCATGGCCACACCGAGTCTGCTTGCCCAAAT
+CATCAGCAGCAAAATGCACTATGGCTTGCCGCTGTACCGTCAGGAGCAGTTGTTTAATCA
+GGCCGGCATTGAGCTTAGCCGTCAAACGATGAGCCGCTGGCTGATAAGCTGTGCAGAGAA
+ACTGAAACCGTTACTGGCGTTAATGAAAGCTGAGCTTCTGAAACAGCCGGTGCTATGGGC
+AGATGAAACCACGGTTAATGTGCTGGATGTTGAGAAAAGCACCTGCTACATGTGGGTATA
+TGGCTGTGGCTTAGAGCAAAGTACTGGCCCCAAACTGGTGCTGTTTGATTATCAGGATAG
+TCGCAGCAGCATACATCCCACCGACTTCCTGGCGGGGTTTGCCGGCTATCTGCAGGTTGA
+TGGTTATGCCGGATATGAGAAAACCCATGCAACCTTAGTCGGCTGCTGGGCACATGCCAG
+ACGTAAGTTCGTTGAAGCACAAAAAGCGCAGGGTAAAGGCAAAACGGGTAAGGCGGATGT
+GGCCCTTAACCATATCCAGAAACTCTATGCACTGGAGAGTCAATTAAAAACCGTGCCGCC
+TGATAAGAAATATGACGCCAGACAAACGCTAGCCAAGCCACTGTTAGAACAATTCAAAAG
+CTGGCTGGATAAATCAAGCGAGAGTGTCACGAAAGAAAGTTTACTGGGAGCCGCTATTAC
+GTATAGCCTGAACCAGTGGCCCAAGCTGATGCGCTATCTGGATGATGGCAGGTTGAATAT
+CGACAACAATCGCGCTGAGCGCGCCATCAAACCGTTCGTGATTGGTCGCAAGGCATGGCT
+GTTTGCCAATACCAAGTCGGGTGCACAGGCCAGTGCCGCATTGTACAGCTTGGTCGAAAC
+CGCCAAAATCAATGGTCTGGAACCCTATGATTACTTATGCCGGTTGCTGACAGAGTTGCC
+CAAAGCCAATACCCACGAGCAATTGCAACAACTACTGCCTTACTGATCAACAGCCACACC
+GCAAGGTGTGGTTGGTGTTACGCTTACTTATCAAGAACAGATTGAAGCTATGCAGCGCTT
+ACTAGAAGCACCAAAAGCCAATATGACTACCTTTACCGATCAGAGCTTTAAACAGGATAT
+AGCAACGGATCCTCGGTCGGAACTAGCAACGAACTATGACGAATTGACTACTCCTCAGCA
+AGACAATAAGCGTATTCCTATCCCGGAGCATGTTGAACCAGAACAGAAGAAGAGAGGCTT
+CCTAAGCCGCTTTTTCCTTCCATATGGTTAGCCAAGACTCCAGTTTTTTGAAGAGCCAAT
+TTCAGTGCAAGCACTTGAAATAATGACTCCTCAAAAAACCGGATGATGTTTATTAAAACT
+GAATAAAACCGTGGAACATCGCTCAATTAGTGATCGTGGAACATGAATAATCAATAAAAA
+GCCGTTCTGGTGCCCTATACTCCAGAACGGCTTACGTTAATATAATGATATTTAAAGAGA
+AATATCAAGCATTTCGTATAAGAAATTTTATGTTAAATGATTGTTAGAAATGCCCCTTGA
+TCGAGGCATTTTCTATAAAGAATACTAAAAACTAATTAAAGCCAACCAAGTTTCAAAACA
+AGGCAGTTCTCAGCAATCATATTTTTAAATTATATAACTCCCAACTGAGCTTTTGCTCCA
+ACGATAAGGCTTTCATTTTGAGTTTCTAAGGCAAATAAACCATACATCAAAGGAGAGGCC
+GCTGCTCTTTCTAAAGTCTGTTCATATAGTTTATTCCAAACTTTACCCCCTAGTTTTTCA
+TACTCGATGATTAGAGTTTTGAGGCTTTCTTCTCCAAACAAAGTTACATGCCCAGCAAAA
+TCAATCGCTGGGTCATCTATATGGGCTGTTGACCAATCAATAACGCCTGAAACAGCTCCA
+TCCTTTGAAGCTAGTACATGCCCAGCATATAAATCGCCATGTATAAATTGGGTGAAATCT
+GCCCATAGAACATCATTATCCAACCATTTTCTGTAGCGGGTTTCCAATTGCTCACTTATA
+CCAATTTCAGATTTTACTAACTGCAAATTGTTTGCTATTTCAGGTCTTAAATCTGAAGGT
+TTCATAATTTTCAAATCATTTTCCCGAACTTCTTTTTCAGGAATACTATGGATTTCAAAT
+AAGGTTTTTGCCAAAGATGTTATGTATTTCGGGCTATCTTTGTCCATATTCCAAATTATT
+TCATAGGTTTCAGCATCCAAATTTAAAACAGGATTATCTTTAAGTATGGGATAAGCCACT
+AATTCTGTAGATGAAATTCTCCAATCAGGAACCTCTACAGAAAGATGTTTTTTTACCAAT
+TCTAAAATGCGTTTTTCTTTCTTGATTTGTTCCCTCATGCCATCACGACGAGGAATACGC
+AGCAACCATTGTTGCCCCTTTGTATCAAGAGCAAAAACGACCTTAAAATCAATGCCCATT
+TCATTGAAATTCATTTTGTCCGTAAGCAACAAGCCGTGTGCTTCAGCAAGTGATTGAATA
+TCTTGAATTGTCATTTTTAATTTCCTTTAAAGAGTTCAATAATTAATGTTCGGATTAGAT
+TGGCTATCATTAACAATCTCTCTCAAAAGTCTTGATGATTTTGTGGTCTTTGATCTCGTA
+GATAATGTCAGCAATATTATCGACCAATTGCTTGTCATGAGATACGAAGATAATAGTTCC
+TGCATAGGACTTCATCATTGTTTCTAATGCGGCAATACTTTTTAGGTCAAGATAGTTTCC
+TGGTTCATCCATAAGCAAAATATTATATTTTCCTAAAAGCATTTTGGATAAAAGCAGTTT
+GATGATTTCACCTCCCGATAAGTCGGATAAGTTTTTTTGAATATCATTCGCTCCGATCCC
+CATTGAAGCCAATACTGCACGAATTTCCGCAACTGTGTACTCGCACTCTTCCTGCATAAA
+GGAGAGCACAGATTTATGCGTGTTAAATTTATATCCTGTTTGTGTAAAGTAGCCAATTTC
+AGCTTTTGGAGATATGGTTAATCCATCAGCACGTTCTGATATCATTTTTAACAAGGACGT
+TTTCCCTGTTCCATTCGATCCAGTTATAGCGACTTTAGCGCCAAGCGGTATTATAAAGTT
+AGCGTCATCAAAGATAGTACGGCTACCAAATTTTAAGCTCAGACCATCTGCCGTAATCGG
+GAACTTATTGTGCAGTTCTAGGGCTGAACTTTGACGAAAACGAATAGAACGCAAATGCTC
+TGGTGCTTGAATATCTTCTAATGCAGCCAAACGCTTTTCCATACTCTTAGCTGCCTGATA
+CAGTTTTCTTTGCTTGGTGCCAGTCATTTTTGCATGCCCAAGTCGTCCAGCACTTTCGGT
+AGAGTTTTTGGATTTTTCTCCTTTTTTCTTATTGTCTAATCGATTAGCTTGCTGGCGTTT
+TTCTTGCACAGCAGATTCTAATCGCTCCCGTTCCTTCATCATCAGCTCATATTCTACGGC
+TTGGTGTTGTCGCTCTTCTTCTTTTTGACGCAAGTAATCCGAGTAACCACCCCAATATTC
+CGTAATTTTACCGTCTTTTAACTCCCATATCTTGTCTACAACCATATCAAGAAAATATCG
+GTCATGACTGATAACAAGTAATGCTCCATCAAATGCTTTAAGTTGACCAATAAGTAGATC
+TATTCCATTGAGATCAAGGTGGCTGGTTGGTTCATCCGCTAGAATGCCATGTACTTGTTG
+GGAAAATGCGGCAGCAATTTTTGCACGAGTTTCCTCTCCGCCACTCATTGTGTCGTTTTG
+TACATTGGAAACACCAAGGCGAGATAACATTGCCCGGTCTTCGACCGTTTCTATTTCGAT
+TCCGCCCAGTTGGCTGATATGTGCAAAATCACCAAAACGCTGTAATGTCGCTTCGGCTAA
+AACAATTTCGCCATTAAGTACTTTGAGTAAACTACTCTTTCCTGCTCCGTTATCACCCAC
+AAGACCAATACGGTCATAAGAGTGAATTTCCAATTCATCAATATCCAAAACATCACGCCC
+AGCATAATCCAAGCGTATGTTTCTCGCTTTAATAATTAAACTCATTTTTATTTACTCCTG
+TTTAGCTCTTGAAATTTTTTATGCAGCAAACAGGATTTAGGTGAAAACAAAAGCTAGCAT
+CACAGTGTCCTCCCAAAAAAAAAGCTATTCATCCACAGGGTGGACAAATAGCTAGTCAAT
+TAAGTTATAACTGGAAACTATGCACTAAAAGCATACTTATAAATTAAGCATACTTTTACT
+TTATATATCCGCATATATTCTTAAAGACACAACAAAAGCCCACCATTATAAAATAGTGTC
+ACTATGCAAATAGTTGTGTCTTAACGAATGCGGATAGAATGCATAAACTTACCTAAAAAA
+TAAAATTCAGTTTTATGATAACTTTACTGTTAAAAGAAGTCTAGACAACCTGAGGGATCC
+CCACAAAATTTCCATTCATACAATCAGCTATCAGCCTGTTTGATTACTGCCCAGTCCCAC
+TGAACCACCCACTGTAGTATTTGTTTAAGTCCCTGCTGATAATATTGCCTGCGTATTCGC
+TGTTTGGGTTCTTTGCAAAGTAATATCCCAAGGAAATTCAGGGCCAATACCCGCCTATTT
+TTAACGGTGTTAGCTTGATAACGCAGGTGCAAACCCGCTTTCTCCGCTGCGCTACCTAGC
+AGGTAATGAAACCAATTAACCAATGCGGCCAGTAGTAGCAGTATCTCTAAGCGAGATTTC
+TTCTTGGTACCATGCAAATCGCTACCCAGGCCATAGCGGTGACTTTTCTGATCACGGAAG
+CTTTCTTCAATTTGCATTCGGCTACTGTAGCACTTAGCAATTTTATCCGCATACCCATGG
+CAGTCAGCTAAGGATGACACCAACAACCATGGTTCCTTATACGTCTTATTTTTATCGCGT
+TTCAATAGCTTATAACCTTTGCCAACCAGGACGGCCTGCGTTTCATAGTGTTGTGTTTGG
+GCAAGCATGATTTTTCCTACACTTTTTGGATCCTTCTTCGCTTGCCGATAAAGCTGATTA
+ACACTGATAAACTTGTCCTGCTCTGCCAATTTAAGCTTCACATTGCCTCGAACTCTAGCT
+ACATAATGCCATCCCAGCTTACGCACTTGTTTCAGCCATGGAACTTTAAACCCCGCGTCA
+GTGACAATTACGGGCTTACAGTCCTTGGGTAGCATGGCTTTAAGCTGCTTTAAAAACGCC
+CCGTGTAGGTGTGGGCAGGTATAATCTTCTGCGGCGGCAATCTTCTGTAGCAGAGTCAAC
+GCTCTACCGTCAGCGGCAATGCTGGCACGCAGGATAAAGTGTCGCTTGGCAGTATCGGCA
+TTGCTCCAGTCAACCAAAATCATCGGCTTAGTTTTATGGCCAACAATAGAAGCCGTCAGC
+GCAGCATAAATCAATGGCAGCTCTCGTTGCAGGTTAGGATTATTGAGTAGACGATCTGCC
+CGTTTGATACTGACCTTATCTGAAGAGCCAGGCATCGCCCGGCCAATCGCAGTAACGGTG
+CAACACGCATCCTTTGCCAGGGCGGTTACCGCATCTAGCAAAACCGAAAATCGGGCTTTA
+TGCATTGATTTTGGCGTGACAAAGGTGAGGAAATCAGCGAGCATAGCTTTTACATTCATG
+GTGAGCATCCGCGGTGTGGGAGTTTTGGCGAATGATCAGATCAGGAACCGCCATGAATGT
+TCCCCAATCAACTAACATTTTATTTTAACTACAGAATTTCTGGGGATACCTCAGGTGGTT
+TGCAACTCTTTGGTTTAATTGGTTTGATTTATGGGCCAATTATTTTTGCGTTAACCATGG
+TGCTGTTACGGCTTTATACTATTGAGTTTAAAGATTTTCTGGAACGCCAAGACAATAGCT
+AACAATAAGATTGTTGTACTTTAGCGCTTCGCCCTGCCCATATCGGTATACAGTGCATTT
+ACGGGAGAAAAAACGGCTCAAACAGGAAAAAATGAAATGACTGAGTCAGCCGAGAAGAAT
+TTCCCCGCTTATTCGCACCTTCCCTAGATTGCTTTTGAGCCATGCATGCATTTGTTTTTA
+ACCTTCTAAACTGTAGTTGAAACCTATCTTTTCCTCAAAATATCCTCTATGTTGTCCAAG
+GAAAAGATAATCCAAAACTTTGGAAAAACATAGTAAGTGTTTCAGAATTGCACTTGATAA
+ACGAAACTTCATTACTTAATAATAACTATACAGCATCTATCCGTTATAGAAGTCAGGATA
+CACCAGTAAAAGTAACCCAGAATGAAAATGGATATATATTTGAATTTTCTGCACCACAAT
+GGGCTCCAGCCGTTGGACAGAGTTTAGTACTTTTCCAAGAAAATGAGTGCCTTGGAGGCG
+GAGTTATTTCTGAAATCCACTAGTAATATATACTAACTCATTCCCTATAACCTTCGAATC
+AAGGATTTTTATCCAACCTTTTGTAAAAGATTCAAACCATAGCTGGTAATTCTCTTCCAT
+TCCCTTCTCCTTTCCAGATAAAGACTTTATTGGAAAAGATATTACAAAGTTTTGAGTATG
+AAAAAGCTGTAGGAAATCCAAGATATTTACATCTTGCTGTTTTAGCACAGGAAGCATCTT
+TAAAAGGAATACTACATCATAAGTACCTTTGTAGACATCACTCTCTTTATTCAAAAACCT
+ATACTTTATCGTCGTCTTTAACTTCCCAATAATGCTACTCAAAAAAGCTATCTCAGCTCT
+ATCAATATCGTATGCATGATATATTATTTTTTCATTTTCATTCCATTGGTATAAAGCTAA
+TGGATTGAAGCCACAACCAAAATCTAAAATAGATGAGACATGTTTGATATTTCCAAATAC
+ATAAGTGTAAAAGTCATTTAATGTTGCGACTCTTTCATTCGTCGAAGAATGAATCTTTAG
+TAAATCTTCTATTGATAACTGCCCCTGATTGTACTTTTTTAATAATTTATCCCAATTAGG
+ATAGGCAGAATAGTAAGACCCCCATATTTGATGCAATTTCTTTTTAGAATAATTCTCAAC
+TTCCTTTAATTTATATTTCTTCTCAGAAATGGAAACAACCTTTTCAACAATATCTGAATC
+AAGGTTTTCGTACTTTTTTGATTCAAGTATCTTCTTAACAACATCATTCTTATCCATTTG
+AAAGAACCTACAAGTTAAGTATTTGATAGGAACTGTCATTTCGGGTTTTTTGCGGTTTCG
+GGTCAAAATTCGGTTTTTCCCCCGAACTACGACTGTTTTCGCACCCCGAACAACTAATCC
+AATCAGAATTTTCCGGCAACGCCGACTCTAAGAAGTGTAATTCCAGTCCATTTCTGCCGT
+CAACCCCTGATTCGCGTTAATGCGACAAAGCTCAAACACATAACTCCCCCACGAAGCCAT
+ATAAACTCCGATTTCGAGGTGTTATCGGCGTTGTTGACCAAATCCGTCGCTGGATGGCCG
+TTCCCCAACCCGTTGATACCACTCAATTCACTGGCTGGCGAACAGGCATACCAAGCCCTA
+TCAGCTTGTTCATCACCTTCACGCCAGCCAGGATTTCGCCCACCTGGGCGTTGTAGTTCC
+GCAGGCTCAGCGTTGGCCCGATGAGTTGCTTGAACCGGTACATGGCGGTCTCGGCTATCG
+AGCGCTGGTGATAGCCGGAGTCTTTCTTCCATTGCTTCAGTTCACCGGCCTTGAGCGCCG
+TCACCGCCTCGTTGCGGGGATGGCCTTCCTCCCACGGTGCCGCATTTTTTCTCGGCGGTA
+TGGTGGCTTTCGCCCCCTTTTTCTTCAGTAGCGCATGACAGGCCTTGGTGTCATACGCAC
+CATCGGCGCTGACCTGTTTTATCTTGCGTCGTAAGGGGTTGAGCAACGTCGGTAACACCT
+CGTTATCCGCCACCGTCTCCAGGCTGACTTCGGCAGCGATGACCGCATGGGTTGTGGCAT
+CCACCGCCAAGTGGAGCTTGCGCCACACTCGTCGCTTCTCCTTGCCGTGTTTGCGAATTT
+TCCATTCGCCTTCGCCATAGACCTTGAGGCCGGTGGCATCAATGACCAAGTGAGCCACCG
+GGCCTTGGCTGGGGAGGCGGTACTTGATGTCGACGGTCTTGGCGCGCTTGCTGATACAGC
+TATAGTCCGGCGACTGCAAAGGCACCGCCATCAGTTGGAACAACGAGTTAATGAAGCCTT
+CTAGCGCCCGCAGCGGCAACTTGAACAAGCCTTTTAGCATCAGGGCCGTCTCAATGGCGG
+TGTCACTGTAGTGGAAACCTCTCCCTCGGCGGCCATGGTGGACCAGGCAATGCCACTGCT
+TAATGGCTTGTTCGTCCATCCAGGGGTATAGGAAGTATAAACCACCTTTTTGCTCCTCAT
+CCGAAGTATCTTACCTGAAATTCCCTCACTCGTTTACCGCTCAAGCCCCAATTTTAACTG
+CCGGTCCAGCCTAAACCGCTCTAATAAGGTTCGATTTGGCGGTAAAATCTCTAGCCTGAT
+AGCTCGAGAGATACAAACTGCCCCACCGCCCCGTTTAAAAGTTGGCAGTGTTGAGCAGTG
+TTGGATTTGGGGTCGTCAGTCAAAGAGACGACTCTGTGATGGATCGAACAGGCTGGGAGT
+CAGTGGCGGCGCTCGTTCTGGTGGCAGCTCACGCTGCTTGGCGGCATTCGCCTTGGCTGT
+TTTCTGTTTCAGATGCTTGAGAATCTGCTCAATGACCTTCGGATCTTCGATGCTGGCAAT
+CACTTTGACGTGACCGCCGCAGTGTTCGCAGACTTCAATATCAATATTGAAGACTCGCTT
+GAGGCGTTGCATCCAGGTCATGGCGCGGTGGCGCTCTGCAGGACTCTTGTCACGCCAGTT
+AGTATCGAGACCTTCCGATTTGTCGGGCTTCTTGCCCCGCTTGGCGGGTGTTACTTGAAC
+TCGGTGTTTGCTGTTCGGTGCAAAGACGCCGTGGAAGCGTGTGAGGTTGACTCGCGGCTT
+AGGTACCAACGCAGCGAGTTTGGCGATGAAGTCCAGCGGCTCGAAGATCACATGGGTGGT
+GCCATTGCGGTACGGAGTTTTGAGCTCGTAACGCACCTGCCCATTGGCGGTTAATGCCAG
+ACGTTTTTCTGAAACCGCTGGCCGACTAATGTAGCGACACAAGCGCTCAAGCTTATCCCG
+CTGATGCGCTTCGGCCATCACACCGGCGTGTAGCGAGAAACCAGCATGGTTGGCTACTCG
+ACTGCTTGAGTCGGCTTTATCCTCACGCCCTGGCAAGGTTTGCAGGGTGAAGACTTTGCG
+CCCTTGCTGGGGGCCGACGGCAATGCGATACGTAACCGAAGCACCATGTAATTGAGTCAG
+CGTATCGTCTTCGCCCTCTTCCAGTGTCAACCACGTATTCTCGGCATCACGCTCCAAAAT
+CCCACGCTTTTCCATGCAGCGAGCGATGCGATGGCTGAGGGTGTGAGCGAGCGTATTCAG
+CTCATCGTAAGTGGGTGCCTTGACACGATGGAAGCGTTGCTTGCCATAGTCATCTTCGGC
+ATAGACACCATCGAGAAACAGCATGTGGTAGTGGACATTGAGATTTAGCGCGGAGCCAAA
+GCGTTGGATAAGAGTCACTGAGCCAGTTTGTGCAGAGGCTTTGGTGTAACCGGCTTTTTT
+GATCAGATGAGTTGAGAGTGTACGATAGACGATACTCAAGACCTGGCCCATCAGCTGGGG
+ATGGCGAGCCAGCAAAAAGCGTAGCTGGAAAGGAAAGCTGAGCACCCACTGGCGAATGGG
+CTCCTTGGGGAAGACTTCGTCTATCAGCAGCGCCGCACTCTCGGCCATCCGGCGGGCACC
+GCAGCTAGGGCAAAAGCCGCGTCGTTTACAGCTGAAGGCGACCAGACGCTCGTGATGACA
+ATCCTCGCAGCGAACCCGCATGAAACCATACTCCAGACGGCCACATTGGAGGAGGTCGTT
+GAATTCTTGTTGGATGTAGCGAGGCAGGTGTTGACCTTGGGCTTCGAGTGAGGCTTTGAA
+GGCTGGGTAGTGCTGCTCAACCAGCTGGTAGAGCAGCGTCTGGTCGGGTTGGTGGCGTTC
+GTAACCGTTTGTTTGAGTGGGCGATTGACTCGCCGTGGCGTTCCTTGCCAGCGACATGGG
+TATCCTCCGCTGATACTGTGGTTATGTACAGTATCAGCGGCTTGCGTTCAGACGTCCAGT
+CTGGCCCTAGACATCGCTAAATGCTTAACCCGCAATAGCCCTCACGAGTTGTTATCAGCC
+ACTACCGGTTGAGCGAGAAGGTTTTGGGTTCAGGGTGCTATTGCTCCACCAATCACAATA
+CTGAAGCCCCAACTGTTATCAGTTGGGGCTTTTTCTTGTCTGTTTGCGGCGGTTGCGTTT
+TATCGGTAGTCGTCGAGCTCTGCACCATCCCACATAAGAGCTTAACGGTGCGATCTTCAA
+CGCCATCACACAAAACTTTCTTTTTCACGCACAGTCAACTTATTGGATGTTTTATTAACA
+ACCCAAAAGGAGATATTTAGCGGGCGGCCGGAAGGTGAATGCTAGGCATGATCTAACCCT
+CGGTCTCTGGCGTCGCGACTGCGAAATTTCGCGAGGGTTTCCGAGAAGGTGATTGCGCTT
+CGCAGATCTCCAGGCGCGTGGGTGCGGACGTAGTCAGCGCCATTGCCGATCGCGTGAAGT
+TCCGCCGCAAGGCTCGCTGGACCCAGATCCTTTACAGGAAGGCCAACGGTGGCGCCCAAG
+AAGGATTTCCGCGACACCGAGACCAATAGCGGAAGCCCCAACGCCGACTTCAGCTTTTGA
+AGGTTCGACAGCACGTGCAGCGATGTTTCCGGTGCGGGGCTCAAGAAAAATCCCATCCCC
+GGATCGAGGATGAGCCGGTCGGCAGCGACCCCGCTCCGTCGCAAGGCGGAAACCCGCGCC
+TCGAAGAACCGCACAATCTCGTCGAGCGCGTCTTCGGGTCGAAGGTGACCGGTGCGGGTG
+GCGATGCCATCCCGCTGCGCTGAGTGCATAACCACCAGCCTGCAGTCCGCCTCAGCAATA
+TCGGGATAGAGCGCAGGGTCAGGAAATCCTTGGATATCGTTCAGGTAGCCCACGCCGCGC
+TTGAGCGCATAGCGCTGGGTTTCCGGTTGGAAGCTGTCGATTGAAACACGGTGCATCTGA
+TCGGACAGGGCGTCTAAGAGCGGCGCAATACGTCTGATCTCATCGGCCGGCGATACAGGC
+CTCGCGTCCGGATGGCTGGCGGCCGGTCCGACATCCACGACGTCTGATCCGACTCGCAGC
+ATTTCGATCGCCGCGGTGACAGCGCCGGCGGGGTCTAGCCGCCGGCTCTCATCGAAGAAG
+GAGTCCTCGGTGAGATTCAGAATGCCGAACACCGTCACCATGGCGTCGGCCTCCGCAGCG
+ACTTCCACGATGGGGATCGGGCGAGCAAAAAGGCAGCAATTATGAGCCCCATACCTACAA
+AGCCCCACGCATCAAGCTTTTGCCCATGAAGCAACCAGGCAATGGCTGTAATTATGACGA
+CGCCGAGTCCCGACCAGACTGCATAAGCAACACCGACAGGGATGGATTTCAGAACCAGAG
+AAAGAAAATAAAATGCGATGCCATAACCGATTATGACAACGGCGGAAGGGGCAAGCTTAG
+TAAAGCCCTCGCTAGATTTTAATGCGGATGTTGCGATTACTTCGCCAACTATTGCGATAA
+CAAGAAAAAGCCAGCCTTTCATGATATATCTCCCAATTTGTGTAGGGCTTATTATGCACG
+CTTAAAAATAATAAAAGCAGACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTA
+GTGCATCTAACGCTTGAGTTAAGCCGCGCCGCGAAGCGGCGTCGGCTTGAACGAATTGTT
+AGACATTATTTGCCGACTACCTTGGTGATCTCGCCTTTCACGTAGTGGACAAATTCTTCC
+AACTGATCTGCGCGCGAGGCCAAGCGATCTTCTTCTTGTCCAAGATAAGCCTGTCTAGCT
+TCAAGTATGACGGGCTGATACTGGGCCGGCAGGCGCTCCATTGCCCAGTCGGCAGCGACA
+TCCTTCGGCGCGATTTTGCCGGTTACTGCGCTGTACCAAATGCGGGACAACGTAAGCACT
+ACATTTCGCTCATCGCCAGCCCAGTCGGGCGGCGAGTTCCATAGCGTTAAGGTTTCATTT
+AGCGCCTCAAATAGATCCTGTTCAGGAACCGGATCAAAGAGTTCCTCCGCCGCTGGACCT
+ACCAAGGCAACGCTATGTTCTCTTGCTTTTGTCAGCAAGATAGCCAGATCAATGTCGATC
+GTGGCTGGCTCGAAGATACCTGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGT
+TCGCGCTTAGCTGGATAACGCCACGGAATGATGTCGTCGTGCACAACAATGGTGACTTCT
+ACAGCGCGGAGAATCTCGCTCTCTCCAGGGGAAGCCGAAGTTTCCAAAAGGTCGTTGATC
+AAAGCTCGCCGCGTTGTTTCATCAAGCCTTACGGTCACCGTAACCAGCAAATCAATATCA
+CTGTGTGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGTACGGCCAGCAACGTC
+GGTTCGAGATGGCGCTCGATGACGCCAACTACCTCTGATAGTTGAGTCGATACTTCGGCG
+ATCACCGCTTCCCTCATGATGTTTAACGCCCAGCTTCAGACGCGCGGAGGCCGTAAGGCC
+GTAGCGTCGGCTGGAAGCATTGGTTAGAGCATGAGCGATTTACTGTATTCATGGCTTTCG
+AAAAATTGTATCTGCACAGGTTGCTAGTACGACGTACACAATAGGCCCGAGCAGTATGAG
+CGCCGCCCAGCCCTGAGGAGAACTTGGCGCTTTACCCGCGTAGGTGACGATCTCCACCAC
+CAGTAGCGCCCAGGCCGCAAGGAATATGGCGATGTTTCGCGGCCTTAACCAAGTGCGCTT
+CTGAGCCTTGTCTAGAAGATTCACCACGTCACTACCGTCAAAGAAGTGGTGGCCGCAGTG
+AGCGCAACGATGTGCATCTACGAAATTCTGGCGGCCACAGCGTGCGCAGTTCATTTTTGC
+TCTAACGCCCTAGCTAAGCCGACGGACAGCCCGCAGGGCTGGCCGGTCGGCTTGAGCGCC
+ATGTTGGGCGACAACTGCCTTGCGCATTGCATACCTACGGAACATGACGCCTCCACGGGA
+GACATTTTGCTCCTCAACTACACTGAAACCATGCCGCAGGAAAAAGGGCTTGGCGACCAG
+ACTGGCTTCTGTGAAGAGCGAAACACCTGGGAGGGCTTTCTCAACCTCACGGTACAGAAC
+AGACGCGACGCCCCGACGCTCGGAACCCGGTGCGGTGTAAAGAAACTCGATGTGGCCGCT
+AAGCTCGTAAGAGATGAACCCGATAACCGCATCTCCCTCAATTGCTAGAAGAGTCTGTAG
+GCCAGATAAGCGAGCTGACCAAGCCTCTATATCTGCGGGACGCGGTGCCCACGCATTCCT
+TTGCGAAGCGTCATAGTGAGACGCTCCAAGTACATGAATAGACTCAGTAAATACGACTGC
+GATAGAGGCGACGTCAGATTCAGTGCAAGTGCGTACGTTCATATCGGTTTTCTTGTTGCC
+CAACGCCTGAGTTAAGCCGGAGCGCTTTGCGGCCGCGGCGTTGTGACAATTTTTCCGAAC
+AACTCCGCGGCCGCGAAGCGATCTCGGCTTGAACGAATTGTTAGGTGGCGGTACTTGGGT
+CGATATCAAAGTGCATCACTTCTTCCCGTATGCCCAACTTTGTATAGAGAGCCACTGCGG
+GATCGTCACCGTAATCTGCTTGCACGTAGATCACATAAGCACCAAGCGCGTTGGCCTCAT
+GCTTGAGGAGATTGATGAGCGCGGTGGCAATGCCTTGCCTCCGGTGCTCGCCGGAGACTG
+CGAGATCATAGATATAGATCTCACTACGCGCCTGCTCAAACTTTGGCAGAACGTAAGCCG
+CGAGAGCGCCAACAACCGCTTCTTGGTCGAAGGCAGCAAGCGCGATGAATGTCTTACTAC
+GGAGCAAGTTCCCGAGGTAATCGGAGTCCGGCTGATGTTGGGAGTAGGTGGCTACGTCTC
+CGAACTCACGACCGAAAAGATCAAGAGCAGCCCTCATGGATTTGACTTGGTCAGGGCCGA
+GCCTACATGTGCGAATGATGCCCATACTTGAGCCACCTAACTTTGTTTTAGGGCGACTGC
+CCTGCTGCGTAACATCGTTGCTGCTGCGTAACATCGTTGCTGCTCCATAACATCAAACAT
+CGACCCACGGCGTAACGCGCT
diff -r 000000000000 -r 1ae00120dd24 test-data/integron_log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/integron_log Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,73 @@
+
+**************************************************************************
+ ___ _ _____ _ _
+|_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
+ | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
+ | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
+|___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
+ |___/
+
+**************************************************************************
+
+integron_finder version 2.0.2
+Using:
+ - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+ - numpy 1.19.4
+ - pandas 1.1.5
+ - matplolib 3.3.3
+ - biopython 1.78
+
+ - Prodigal V2.6.3: February, 2016
+ - INFERNAL 1.1.4 (Dec 2020)
+ - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+
+Authors:
+ - Jean Cury, Bertrand Neron, Eduardo Rocha,
+
+Citation:
+
+ Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
+ IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
+ Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
+
+ If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
+
+ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
+ PMID: 29112715
+
+
+ =======================
+
+integron_finder is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+integron_finder is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (COPYING file).
+If not, see .
+
+ =======================
+
+command used: integron_finder /tmp/tmp3_ir6t5a/files/7/8/a/dataset_78ad162b-8ddf-4d54-a7e8-be6ee3804d0a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+
+ =======================
+
+[0m
+INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
+
+INFO : Starting Default search ... :
+INFO : Default search done... :
+INFO : In replicon ACBA.007.P01_13, there are:
+INFO : - 1 complete integron(s) found with a total 3 attC site(s)
+INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
+INFO : - 0 In0 element(s) found with a total of 0 attC site
+INFO : Adding proteins ... :
+INFO : Writing out results for replicon ACBA.007.P01_13
+INFO : Merging integrons results.
+
diff -r 000000000000 -r 1ae00120dd24 test-data/integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmpkclck5y7/files/3/6/4/dataset_3649b3c6-dc10-47e0-9968-13ce47e5dce0.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 9.799999999999998e-65 protein SMR_qac_E-NCBIFAM NF000276.2 complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 2.7999999999999994e-183 protein ANT_3pp_AadA1-NCBIFAM NF033126.1 complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 7.899999999999999e-69 protein AAC_3_I-NCBIFAM NF033083.0 complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,3 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/c/d/d/dataset_cdd097ee-d7c0-4424-9c3c-3ddd5d20887a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot
+ID_replicon CALIN complete In0 topology size
+ACBA.007.P01_13 0 1 0 circ 20301
diff -r 000000000000 -r 1ae00120dd24 test-data/test10_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test10_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/c/d/d/dataset_cdd097ee-d7c0-4424-9c3c-3ddd5d20887a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --union-integrases --func-annot
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 9.799999999999998e-65 protein SMR_qac_E-NCBIFAM NF000276.2 complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 2.7999999999999994e-183 protein ANT_3pp_AadA1-NCBIFAM NF033126.1 complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 7.899999999999999e-69 protein AAC_3_I-NCBIFAM NF033083.0 complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test1_integron_log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_integron_log Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,73 @@
+
+**************************************************************************
+ ___ _ _____ _ _
+|_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
+ | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
+ | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
+|___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
+ |___/
+
+**************************************************************************
+
+integron_finder version 2.0.2
+Using:
+ - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+ - numpy 1.19.4
+ - pandas 1.1.5
+ - matplolib 3.3.3
+ - biopython 1.78
+
+ - Prodigal V2.6.3: February, 2016
+ - INFERNAL 1.1.4 (Dec 2020)
+ - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+
+Authors:
+ - Jean Cury, Bertrand Neron, Eduardo Rocha,
+
+Citation:
+
+ Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
+ IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
+ Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
+
+ If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
+
+ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
+ PMID: 29112715
+
+
+ =======================
+
+integron_finder is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+integron_finder is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (COPYING file).
+If not, see .
+
+ =======================
+
+command used: integron_finder /tmp/tmpz_euzvww/files/1/d/e/dataset_1dee618f-a951-40e4-8697-ae8f535f1e8b.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+
+ =======================
+
+[0m
+INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
+
+INFO : Starting Default search ... :
+INFO : Default search done... :
+INFO : In replicon ACBA.007.P01_13, there are:
+INFO : - 1 complete integron(s) found with a total 3 attC site(s)
+INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
+INFO : - 0 In0 element(s) found with a total of 0 attC site
+INFO : Adding proteins ... :
+INFO : Writing out results for replicon ACBA.007.P01_13
+INFO : Merging integrons results.
+
diff -r 000000000000 -r 1ae00120dd24 test-data/test1_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/7/8/a/dataset_78ad162b-8ddf-4d54-a7e8-be6ee3804d0a.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test1_summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1_summary.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,3 @@
+# cmd: integron_finder /tmp/tmpz_euzvww/files/1/d/e/dataset_1dee618f-a951-40e4-8697-ae8f535f1e8b.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_replicon CALIN complete In0 topology size
+ACBA.007.P01_13 0 1 0 circ 20301
diff -r 000000000000 -r 1ae00120dd24 test-data/test2_integron_log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_integron_log Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,79 @@
+
+**************************************************************************
+ ___ _ _____ _ _
+|_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
+ | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
+ | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
+|___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
+ |___/
+
+**************************************************************************
+
+integron_finder version 2.0.2
+Using:
+ - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+ - numpy 1.19.4
+ - pandas 1.1.5
+ - matplolib 3.3.3
+ - biopython 1.78
+
+ - Prodigal V2.6.3: February, 2016
+ - INFERNAL 1.1.4 (Dec 2020)
+ - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+
+Authors:
+ - Jean Cury, Bertrand Neron, Eduardo Rocha,
+
+Citation:
+
+ Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
+ IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
+ Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
+
+ If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
+
+ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
+ PMID: 29112715
+
+
+ =======================
+
+integron_finder is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+integron_finder is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (COPYING file).
+If not, see .
+
+ =======================
+
+command used: integron_finder /tmp/tmpz_euzvww/files/e/9/9/dataset_e996a731-6537-452b-87d7-09654e6d628a.dat --cpu 1 --keep-tmp --local-max -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+
+ =======================
+
+[0m
+INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
+
+INFO : Starting Default search ... :
+INFO : Default search done... :
+INFO : In replicon ACBA.007.P01_13, there are:
+INFO : - 1 complete integron(s) found with a total 3 attC site(s)
+INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
+INFO : - 0 In0 element(s) found with a total of 0 attC site
+INFO : Starting search with local_max...:
+INFO : Search with local_max done... :
+INFO : In replicon ACBA.007.P01_13, there are:
+INFO : - 1 complete integron(s) found with a total 4 attC site(s)
+INFO : - 0 CALIN element(s) found with a total of 0 attC site(s)
+INFO : - 0 In0 element(s) found with a total of 0 attC site
+INFO : Adding proteins ... :
+INFO : Writing out results for replicon ACBA.007.P01_13
+INFO : Merging integrons results.
+
diff -r 000000000000 -r 1ae00120dd24 test-data/test2_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,18 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/d/8/b/dataset_d8bd8cc0-78f5-4a59-b73a-d6819c72d20b.dat --cpu 1 --keep-tmp --local-max --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete No NA lin
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_2 905 1609 -1 NA protein protein NA complete No NA lin
+integron_01 ACBA.007.P01_13 attc_001 1453 1504 1 0.31 attC attC attc_4 complete No NA lin
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_3 1722 2537 -1 NA protein protein NA complete No NA lin
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_4 2667 2900 1 NA protein protein NA complete No NA lin
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_5 2791 3495 -1 NA protein protein NA complete No NA lin
+integron_01 ACBA.007.P01_13 attc_002 3339 3390 1 0.31 attC attC attc_4 complete No 1835.0 lin
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_6 3546 4313 1 NA protein protein NA complete No NA lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA CALIN No NA lin
+integron_02 ACBA.007.P01_13 attc_001 17825 17884 -1 5.1e-10 attC attC attc_4 CALIN No NA lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA CALIN No NA lin
+integron_02 ACBA.007.P01_13 attc_002 18681 18749 -1 0.016 attC attC attc_4 CALIN No 797.0 lin
+integron_02 ACBA.007.P01_13 attc_003 19079 19149 -1 3.3e-05 attC attC attc_4 CALIN No 330.0 lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA CALIN No NA lin
+integron_02 ACBA.007.P01_13 attc_004 19618 19726 -1 5.5e-08 attC attC attc_4 CALIN No 469.0 lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA CALIN No NA lin
diff -r 000000000000 -r 1ae00120dd24 test-data/test2_summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_summary.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,3 @@
+# cmd: integron_finder /tmp/tmpz_euzvww/files/e/9/9/dataset_e996a731-6537-452b-87d7-09654e6d628a.dat --cpu 1 --keep-tmp --local-max -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_replicon CALIN complete In0 topology size
+ACBA.007.P01_13 0 1 0 circ 20301
diff -r 000000000000 -r 1ae00120dd24 test-data/test3_integron_log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3_integron_log Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,73 @@
+
+**************************************************************************
+ ___ _ _____ _ _
+|_ _|_ __ | |_ ___ __ _ _ __ ___ _ __ | ___(_)_ __ __| | ___ _ __
+ | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \ | |_ | | '_ \ / _` |/ _ \ '__|
+ | || | | | || __/ (_| | | | (_) | | | | | _| | | | | | (_| | __/ |
+|___|_| |_|\__\___|\__, |_| \___/|_| |_| |_| |_|_| |_|\__,_|\___|_|
+ |___/
+
+**************************************************************************
+
+integron_finder version 2.0.2
+Using:
+ - Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+ - numpy 1.19.4
+ - pandas 1.1.5
+ - matplolib 3.3.3
+ - biopython 1.78
+
+ - Prodigal V2.6.3: February, 2016
+ - INFERNAL 1.1.4 (Dec 2020)
+ - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+
+Authors:
+ - Jean Cury, Bertrand Neron, Eduardo Rocha,
+
+Citation:
+
+ Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
+ IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.
+ Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
+
+ If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
+
+ Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
+ PMID: 29112715
+
+
+ =======================
+
+integron_finder is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+integron_finder is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program (COPYING file).
+If not, see .
+
+ =======================
+
+command used: integron_finder /tmp/tmpz_euzvww/files/4/3/f/dataset_43f32a10-119c-4fb5-bdaf-498b2d3b61b3.dat --cpu 1 --keep-tmp --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+
+ =======================
+
+[0m
+INFO : ############ Processing replicon ACBA.007.P01_13 (1/1) ############
+
+INFO : Starting Default search ... :
+INFO : Default search done... :
+INFO : In replicon ACBA.007.P01_13, there are:
+INFO : - 0 complete integron(s) found with a total 0 attC site(s)
+INFO : - 1 CALIN element(s) found with a total of 3 attC site(s)
+INFO : - 1 In0 element(s) found with a total of 0 attC site
+INFO : Adding proteins ... :
+INFO : Writing out results for replicon ACBA.007.P01_13
+INFO : Merging integrons results.
+
diff -r 000000000000 -r 1ae00120dd24 test-data/test3_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/2/9/7/dataset_2978faa9-7392-48d8-9759-c12e419d7fe1.dat --cpu 1 --keep-tmp --circ -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test4_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/8/8/3/dataset_883ade04-f62d-4f17-85e7-122e7b43d339.dat --cpu 1 --keep-tmp --topology-file /tmp/tmp3_ir6t5a/files/d/7/c/dataset_d7c8e07c-4b44-480f-9059-a9bff8bf5be6.dat -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI In0 Yes NA lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA CALIN Yes NA lin
+integron_02 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 CALIN Yes NA lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA CALIN Yes NA lin
+integron_02 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 CALIN Yes 1196.0 lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA CALIN Yes NA lin
+integron_02 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 CALIN Yes 469.0 lin
+integron_02 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA CALIN Yes NA lin
diff -r 000000000000 -r 1ae00120dd24 test-data/test5_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,11 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/a/8/c/dataset_a8c83ef3-ab8b-416f-adb8-54a6ba99e378.dat --cpu 1 --keep-tmp --promoter-attI -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 Pc_int1 25 51 -1 NA Promoter Pc_1 NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test5_summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test5_summary.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,3 @@
+# cmd: integron_finder /tmp/tmpz_euzvww/files/4/3/f/dataset_43f32a10-119c-4fb5-bdaf-498b2d3b61b3.dat --cpu 1 --keep-tmp --linear -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40
+ID_replicon CALIN complete In0 topology size
+ACBA.007.P01_13 1 0 1 lin 20301
diff -r 000000000000 -r 1ae00120dd24 test-data/test6_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test6_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/4/3/2/dataset_432b6fe2-79b8-45f0-a295-e5ab18425476.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --gbk --pdf
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test7_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test7_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/7/e/3/dataset_7e32f99d-dba8-4527-9e8f-4ac9ca88d7db.dat --cpu 1 --keep-tmp -dt 2000 --calin-threshold 3 --max-attc-size 188 --min-attc-size 30
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test8_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test8_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,10 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/e/4/5/dataset_e459a473-6554-4525-9ec1-505e63711366.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --attc-model /tmp/tmp3_ir6t5a/files/3/0/3/dataset_303db187-2a98-45e2-8c99-3d5694175a98.dat
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_1 55 1014 1 1.9000000000000001e-25 protein intI intersection_tyr_intI complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_20 17375 17722 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC dataset_303db187-2a98-45e2-8c99-3d5694175a98 complete Yes NA circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_21 17886 18665 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC dataset_303db187-2a98-45e2-8c99-3d5694175a98 complete Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_22 19090 19749 -1 NA protein protein NA complete Yes NA circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC dataset_303db187-2a98-45e2-8c99-3d5694175a98 complete Yes 469.0 circ
+integron_01 ACBA.007.P01_13 ACBA.007.P01_13_23 19721 20254 -1 NA protein protein NA complete Yes NA circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test9_integrons_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test9_integrons_table.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,5 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/5/5/a/dataset_55aed596-7c76-44f2-817c-e12d708ca8b9.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins
+ID_integron ID_replicon element pos_beg pos_end strand evalue type_elt annotation model type default distance_2attC considered_topology
+integron_01 ACBA.007.P01_13 attc_001 17825 17884 -1 1e-09 attC attC attc_4 CALIN Yes NA circ
+integron_01 ACBA.007.P01_13 attc_002 19080 19149 -1 0.0001 attC attC attc_4 CALIN Yes 1196.0 circ
+integron_01 ACBA.007.P01_13 attc_003 19618 19726 -1 1.1e-07 attC attC attc_4 CALIN Yes 469.0 circ
diff -r 000000000000 -r 1ae00120dd24 test-data/test9_summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test9_summary.tsv Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,3 @@
+# cmd: integron_finder /tmp/tmp3_ir6t5a/files/5/5/a/dataset_55aed596-7c76-44f2-817c-e12d708ca8b9.dat --cpu 1 --keep-tmp -dt 4000 --calin-threshold 2 --max-attc-size 200 --min-attc-size 40 --no-proteins
+ID_replicon CALIN complete In0 topology size
+ACBA.007.P01_13 1 0 0 circ 20301
diff -r 000000000000 -r 1ae00120dd24 test-data/topology.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/topology.txt Thu Sep 22 13:51:14 2022 +0000
@@ -0,0 +1,4 @@
+# topology data for testing integron_finder on galaxy server
+ACBA.007.P01_13 lin
+LIAN.001.C02_10 circ
+PSSU.001.C01_13 circ