Repository 'integron_finder'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/integron_finder

Changeset 0:1ae00120dd24 (2022-09-22)
Next changeset 1:4768f7f8e93f (2023-02-17)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
added:
integron_finder.xml
macro.xml
test-data/covar.txt
test-data/input.fasta
test-data/integron_log
test-data/integrons_table.tsv
test-data/summary.tsv
test-data/test10_integrons_table.tsv
test-data/test1_integron_log
test-data/test1_integrons_table.tsv
test-data/test1_summary.tsv
test-data/test2_integron_log
test-data/test2_integrons_table.tsv
test-data/test2_summary.tsv
test-data/test3_integron_log
test-data/test3_integrons_table.tsv
test-data/test4_integrons_table.tsv
test-data/test5_integrons_table.tsv
test-data/test5_summary.tsv
test-data/test6_integrons_table.tsv
test-data/test7_integrons_table.tsv
test-data/test8_integrons_table.tsv
test-data/test9_integrons_table.tsv
test-data/test9_summary.tsv
test-data/topology.txt
b
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
[
b'@@ -0,0 +1,228 @@\n+<tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+    <description> is a program that detects integrons in DNA sequences</description>\n+    <macros>\n+       <import>macro.xml</import>\n+    </macros>\n+    <expand macro="edam_info"/>\n+    <expand macro="xrefs"/>\n+    <expand macro="requirements"/>\n+    <command detect_errors="aggressive"><![CDATA[\n+        integron_finder\n+        \'$sequence\'\n+        --cpu @THREADS@\n+        --keep-tmp\n+        $local_max\n+        #if $type_replicon\n+          $type_replicon\n+        #end if\n+        #if $topology_file\n+            --topology-file \'$topology_file\'\n+        #end if\n+        $promoter_attI\n+        -dt $settings.attc_settings.dist_thresh\n+        --calin-threshold $settings.attc_settings.calin_threshold\n+        --max-attc-size $settings.attc_settings.max_attc_size\n+        --min-attc-size $settings.attc_settings.min_attc_size\n+        $settings.attc_settings.keep_palindromes\n+        #if $settings.attc_settings.covar_matrix\n+            --attc-model \'$settings.attc_settings.covar_matrix\'\n+        #end if\n+        $settings.protein_settings.no_proteins\n+        $settings.protein_settings.union_integrases\n+        $settings.protein_settings.func_annot\n+        $gbk\n+        $pdf\n+        && mv Results_Integron_Finder_* Results_Integron_Finder\n+    ]]></command>\n+    <inputs>\n+        <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments..." />\n+        <param name="local_max" argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." />\n+\t      <param name="type_replicon" type="select" optional="true" label="Default replicons topology" help="Set the default topology for replicons, linear, circular (deault: no topology)">\n+\t          <option value="--linear">linear (--linear)</option>\n+\t          <option value="--circ">circular (--circ)</option>\n+\t      </param>\n+        <param name="topology_file" argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/>\n+        <param name="promoter_attI" argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" />\n+        <param argument="--gbk" type="boolean" checked="false" truevalue="--gbk" falsevalue="" label="Genbank output?" help="Generate a GenBank file with the sequence annotated with the same annotations than .integrons file."/>\n+        <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="pdf output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/>\n+        <section name="settings" title="Advanced Parameters" expanded="False">\n+            <section name="attc_settings" title="Attc options" expanded="False">\n+               <param name="dist_thresh" argument="--distance-thresh" type="integer" value="4000" label="Threshold for clustering (in base)" min="0" help="By default, to cluster an array of attC sites and an integron integrase, they must be less than 4 kb apart. You can here change this value." />\n+               <param name="calin_threshold" type="integer" value="2" label="Threshold to filter CALIN" min="0" help="Keep \'CALIN\' only if attC sites number >= calin-threshold" />\n+               <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/>\n+               <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" />\n+               <param name="keep_palindromes'..b' expect_num_outputs="2">\n+            <param name="sequence" value="input.fasta"/>\n+            <param name="no_logfile" value="true"/>\n+            <section name="settings">\n+                <section name="attc_settings">\n+                    <param name="dist_thresh" value="2000"/>\n+                    <param name="calin_threshold" value="3"/>\n+                    <param name="max_attc_size" value="188"/>\n+                    <param name="min_attc_size" value="30"/>\n+                    <param name="keep_palindromes" value=""/>\n+                </section>\n+            </section>\n+            <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />\n+            <output name="summary" value="summary.tsv" lines_diff="3" />\n+        </test>\n+        <test expect_num_outputs="2">\n+            <param name="sequence" value="input.fasta"/>\n+            <param name="no_logfile" value="true"/>\n+            <section name="settings">\n+                <section name="attc_settings">\n+                    <param name="covar_matrix" value="covar.txt"/>\n+                </section>\n+            </section>\n+            <output name="integrons_table" value="test8_integrons_table.tsv" lines_diff="10" />\n+            <output name="summary" value="summary.tsv" lines_diff="3" />\n+        </test>\n+        <test expect_num_outputs="2">\n+            <param name="sequence" value="input.fasta"/>\n+            <param name="no_logfile" value="true"/>\n+            <section name="settings">\n+                <section name="protein_settings">\n+                    <param name="no_proteins" value="true"/>\n+                </section>\n+            </section>\n+            <output name="integrons_table" value="test9_integrons_table.tsv" lines_diff="3" />\n+            <output name="summary" value="test9_summary.tsv" lines_diff="3" />\n+        </test>\n+        <test expect_num_outputs="2">\n+            <param name="sequence" value="input.fasta"/>\n+            <param name="no_logfile" value="true"/>\n+            <section name="settings">\n+                <section name="protein_settings">\n+                    <param name="union_integrases" value="true" />\n+                    <param name="func_annot" value="true"/>\n+                </section>\n+            </section>\n+            <output name="integrons_table" value="test10_integrons_table.tsv" lines_diff="3" />\n+            <output name="summary" value="summary.tsv" lines_diff="3" />\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+\n+How does it work ?\n+==================\n+\n+- First, IntegronFinder annotates the DNA sequence\'s CDS with Prodigal.\n+\n+- Second, IntegronFinder detects independently integron integrase and *attC*\n+  recombination sites. The Integron integrase is detected by using the intersection\n+  of two HMM profiles:\n+\n+  - one specific of tyrosine-recombinase (PF00589)\n+  - one specific of the integron integrase, near the patch III domain of tyrosine recombinases.\n+\n+The *attC* recombination site is detected with a covariance model (CM), which\n+models the secondary structure in addition to the few conserved sequence\n+positions.\n+\n+\n+- Third, the results are integrated, and IntegronFinder distinguishes 3 types of\n+  elements:\n+\n+  - complete integron\n+      Integron with integron integrase nearby *attC* site(s)\n+  - In0 element\n+      Integron integrase only, without any *attC* site nearby\n+  - CALIN element\n+      Cluster of *attC* sites Lacking INtegrase nearby.\n+      A rule of thumb to avoid false positive is to filter out singleton of\n+      *attC* site.\n+\n+IntegronFinder can also annotate gene cassettes (CDS nearby *attC* sites) using\n+Resfams, a database of HMM profiles aiming at annotating antibiotic resistance\n+genes. This database is provided but the user can add any other HMM profiles\n+database of its own interest.\n+\n+When available, IntegronFinder annotates the promoters and attI sites by pattern\n+matching.\n+    ]]></help>\n+    <expand macro="citations"/>\n+</tool>\n'
b
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
b
@@ -0,0 +1,40 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.0.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <token name="@THREADS@">\${GALAXY_SLOTS:-2}</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.3.2">hmmer</requirement>
+            <requirement type="package" version="1.1.4">infernal</requirement>
+            <requirement type="package" version="2.6.3">prodigal</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">integron_finder</requirement>
+        </requirements>
+    </xml>
+    <xml name="edam_info">
+        <edam_topics>
+            <edam_topic>topic_0085</edam_topic>
+            <edam_topic>topic_0798</edam_topic>
+            <edam_topic>topic_3047</edam_topic>
+            <edam_topic>topic_0091</edam_topic>
+            <edam_topic>topic_0080</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0239</edam_operation>
+            <edam_operation>operation_3430</edam_operation>
+            <edam_operation>operation_3087</edam_operation>
+            <edam_operation>operation_0362</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+        <xref type='bio.tools'>integron_finder</xref>
+      </xrefs>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2022.02.28.482270 </citation>
+        </citations>
+    </xml>
+</macros>
b
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
[
b'@@ -0,0 +1,377 @@\n+INFERNAL1/a [1.1 | October 2013]\n+NAME     attC_4\n+STATES   145\n+NODES    35\n+CLEN     47\n+W        895\n+ALPH     RNA\n+RF       yes\n+CONS     yes\n+MAP      yes\n+DATE     Mon Jan 19 20:03:31 2015\n+COM      [1] cmbuild --hand attc_4.cm attc_train_set_4.sto\n+COM      [2] cmcalibrate attc_4.cm\n+PBEGIN   0.05\n+PEND     0.05\n+WBETA    1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA  1.52588e-05\n+N3OMEGA  1.52588e-05\n+ELSELF   -0.08926734\n+NSEQ     96\n+EFFN     96.000000\n+CKSUM    3931512547\n+NULL     0.000  0.000  0.000  0.000\n+EFP7GF   -9.9186 0.72993\n+ECMLC    0.63005    -4.33175     4.20996     1600000      260875  0.004600\n+ECMGC    0.41832   -12.02668     0.81138     1600000       85985  0.004652\n+ECMLI    0.58141    -4.10957     4.92170     1600000      228880  0.005243\n+ECMGI    0.42824   -10.63745     1.38026     1600000       68728  0.005820\n+CM\n+                                             [ ROOT    0 ]      -      - - - - -\n+     S     0    -1 0     1     6     1     2   895  1874 -12.592 -12.531  -0.002 -11.308 -11.588 -11.983\n+    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\n+    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\n+                                             [ MATP    1 ]      1    141 G C [ ]\n+    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\n+    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\n+    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\n+     D     6     2 3     7     6     0     0   887  1865  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319\n+    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\n+    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\n+                                             [ MATP    2 ]      2    140 c g R m\n+    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\n+    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\n+    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\n+     D    12     8 6    13     6     0     0   885  1864  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319\n+    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\n+    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\n+                                             [ MATP    3 ]      3    139 C G s i\n+    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\n+    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\n+    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\n+     D    18    14 6    19     6     0     0   884  1862  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319\n+    IL    19    19 5    19     6     1     5   891  1869  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934 '..b'1.46634  0.26236  1.09861  0.40547\n+     26   3.71435  3.19641  2.84131  0.13197    120 U p - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     27   3.18123  2.23054  1.18098  0.60877    121 U r - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     28   0.12234  4.14596  3.30449  2.77083    122 A i - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     29   0.95560  2.00635  1.26122  1.62135    123 a m - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     30   2.43472  0.49870  1.89972  1.86145    124 C ] - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     31   2.36885  1.91431  2.24466  0.42617    125 U = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     32   1.99009  0.61165  1.59584  2.13601    126 C = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     33   1.12677  1.78023  0.92633  2.19536    127 g = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     34   1.00976  2.60221  0.63685  3.42260    128 G = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.03382  6.88959  3.43454  1.46634  0.26236  1.09861  0.40547\n+     35   1.59086  0.80252  1.35196  2.41555    129 c = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.44710  6.85787  1.02314  1.46634  0.26236  3.51631  0.03016\n+     36   3.12832  0.30189  2.27881  2.16819    130 C = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          2.11131  6.41406  0.13093  1.46634  0.26236  5.92595  0.00267\n+     37   0.57651  1.86795  1.86012  2.05532    131 A = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.27640  4.32946  1.47704  1.46634  0.26236  6.81245  0.00110\n+     38   2.96395  2.86913  3.49326  0.14939    132 U = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.03415  4.08721  4.08721  1.46634  0.26236  6.83026  0.00108\n+     39   2.96395  2.86913  3.49326  0.14939    133 U = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.03415  4.08721  4.08721  1.46634  0.26236  6.83026  0.00108\n+     40   3.29366  0.12992  3.86188  2.75374    134 C = - -\n+          1.38629  1.38629  1.38629  1.38629\n+          0.03415  4.08721  4.08721  1.46634  0.26236  0.00967  4.64385\n+     41   5.61227  6.76634  0.00620  6.58877    135 G [ - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00205  6.88254  6.88254  1.46634  0.26236  0.22559  1.59970\n+     42   7.50523  6.97196  6.53815  0.00294    136 U R - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     43   7.47647  6.84256  6.54333  0.00308    137 U p - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     44   0.12946  3.82317  2.57597  3.75121    138 A r - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     45   1.95767  3.97633  0.44327  1.61886    139 G i - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     46   1.46810  1.73501  0.72259  2.22795    140 g m - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00204  6.88959  6.88959  1.46634  0.26236  1.09861  0.40547\n+     47   2.71772  0.47057  2.52869  1.47157    141 C ] - >\n+          1.38629  1.38629  1.38629  1.38629\n+          0.00102  6.88857        *  1.46634  0.26236  0.00000        *\n+//\n'
b
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
b
b'@@ -0,0 +1,340 @@\n+>ACBA.007.P01_13 08-JUN-2013 20301 bp Acinetobacter baumannii MDR-ZJ06 plasmid pMDR-ZJ06, complete\n+TGCTGCTTGGATGCCCGAGGCATAGACTGTACAAAAAAACAGTCATAACAAGCCATGAAA\n+ACCGCCACTGCGCCGTTACCACCGCTGCGTTCGGTCAAGGTTCTGGACCAGTTGCGTGAG\n+CGCATACGCTACTTGCATTACAGTTTACGAACCGAACAGGCTTATGTCAACTGGGTTCGT\n+GCCTTCATCCGTTTCCACGGTGTGCGTCACCCGGCAACCTTGGGCAGCAGCGAAGTCGAG\n+GCATTTCTGTCCTGGCTGGCGAACGAGCGCAAGGTTTCGGTCTCCACGCATCGTCAGGCA\n+TTGGCGGCCTTGCTGTTCTTCTACGGCAAGGTGCTGTGCACGGATCTGCCCTGGCTTCAG\n+GAGATCGGAAGACCTCGGCCGTCGCGGCGCTTGCCGGTGGTGCTGACCCCGGATGAAGTG\n+GTTCGCATCCTCGGTTTTCTGGAAGGCGAGCATCGTTTGTTCGCCCAGCTTCTGTATGGA\n+ACGGGCATGCGGATCAGTGAGGGTTTGCAACTGCGGGTCAAGGATCTGGATTTCGATCAC\n+GGCACGATCATCGTGCGGGAGGGCAAGGGCTCCAAGGATCGGGCCTTGATGTTACCCGAG\n+AGCTTGGCACCCAGCCTGCGCGAGCAGCTGTCGCGTGCACGGGCATGGTGGCTGAAGGAC\n+CAGGCCGAGGGCCGCAGCGGCGTTGCGCTTCCCGACGCCCTTGAGCGGAAGTATCCGCGC\n+GCCGGGCATTCCTGGCCGTGGTTCTGGGTTTTTGCGCAGCACACGCATTCGACCGATCCA\n+CGGAGCGGTGTCGTGCGTCGCCATCACATGTATGACCAGACCTTTCAGCGCGCCTTCAAA\n+CGTGCCGTAGAAGGCACTGTTGCAAAGTTAGCGATGAGGCAGCCTTTTGTCTTATTCAAA\n+GGCCTTACATTTCAAAAACTCTGCTTACCAGGCGCATTTCGCCCAGGGGATCACCATAAT\n+AAAATGCTGAGGCCTGGCCTTTGCGTAGTGCACGCATCACCTCAATACCTTTGATGGTGG\n+CGTAAGCCGTCTTCATGGATTTAAATCCCAGCGTGGCGTTGATTATCCGTTTCAGTTTGC\n+CATGATCGCATTCAATCACGTTGTTCCGGTACTTAATCTGTCGGTGTTCAACGTCAGACG\n+GGCACCGGCCTTCGCGTTTGAGCAGAGCAAGCGCGCGACCATAGGCGGGCGCTTTATCCG\n+TGTTGATGAATCGCGGGATCTGCCACTTCTTCACGTTGTTGAGGATTTTACCCAGAAACC\n+GGTATGCAGCTTTGCTGTTACGACGGGAGGAGAGATAAAAATCGACAGTGCGGCCCCGGC\n+TGTCGACGGCCCGGTACAGATACGCCCAGCGGCCATTGACCTTCACGTAGGTTTCATCCA\n+TGTGCCACGGGCAAAGATCGGAAGGGTTACGCCAGTACCAGCGCAGCCGTTTTTCCATTT\n+CAGGCGCATAACGCTGAACCCAGCGGTAAATCGTGGAGTGATCGACATTCACTCCGCGTT\n+CAGCCAGCATCTCCTGCAGCTCACGGTAACTGATGCCGTATTTGCAGTACCAGCGTACGG\n+CCCACAGAATGATGTCACGCTGAAAATGCCGGCCTTTGAATGGGTTCATGTGCAGCTCCA\n+TCAGCAAAAGGGGATGATAAGTTTATCACCACCGACTATTTGCAACAGTGCCAAGCGCGG\n+TGTCCGGAATTTCAGGTTTGTGTCTCTACAAAGACTAACTATCAGAAAAACTCATCGAGC\n+ATCAAATGAAACTGCAATTTATTCATATCAGGATTATCAATACCATATTTTTGAAAAAGC\n+CGTTTCTGTAATGAAGGAGAAAACTCACCGAGGCAGTTCCATAGGATGGCAAGATCCTGG\n+TATCGGTCTGCGATTCCGACTCGTCCAACATCAATACAACCTATTAATTTCCCCTCGTCA\n+AAAATAAGGTTATCAAGTGAGAAATCACCATGAGTGACGACTGAATCCGGTGAGAATGGC\n+AAAAGCTTATGCATTTCTTTCCAGACTTGTTCAACAGGCCAGCCATTACGCTCGTCATCA\n+AAATCACTAGCATCAACCAAACCGTTATTCATTCGTGATTGCGCCTGAGCGAGACGAAAT\n+ACGCGATCGCTGTTAAAAGGACAATTACAAACAGGAATCGAATGCAACCGGCGCAGGAAC\n+ACTGCCAGCGCATCAACAATATTTTCACCTGAATCAGGATATTCTTCTAATACCTGGAAT\n+GCTGTTTTCCCGGGGATCGCAGTGGTGAGTAACCATGCATCATCAGGAGTACGGATAAAA\n+TGCTTGATAGTCGGAAGAGGCATAAATGCCGTCAGCCAGTTTAGTCTGACCATCTCATCT\n+GTAACATCATTGGCAACGCTACCTTTGCCATGTTTCAGAAACAACTCTGGCGCATTGGGC\n+TTCCCATACAATCGATAGATTGTCGCACCTGATTGCCCGACATTATCGCGAGCCCATCTA\n+TACCCATATAAATCAGCATCCAGGTTGGAATTTAATCGCGGCCTCGAGCAAGACGTTTCC\n+CGTTGAATATGGCTCATAACACCCCTTGTATTACTGTTTATGTAAGCAGACAGTTTTATT\n+GTTCATGATGATATATTTTTATCGGCACTGTTGCAAATAGTCGGTGGTGATAAACTTATC\n+ATCCCCTTTTGCTGATGGAGCTGCACATGAACCCATTCAAAGGCCGGCATTTTCAGCGTG\n+ACATCATTCTGTGGGCCGTACGCTGGTACTGCAAATACGGCACTGTTGCAAAGTTAGCGA\n+TGAGGCAGCCTTTTGTCTTATTCAAAGGCCTTACATTTCAAAAACTCTGCTTACCAGGCG\n+CATTTCGCCCAGGGGATCACCATAATAAAATGCTGAGGCCTGGCCTTTGCGTAGTGCACG\n+CATCACCTCAATACCTTTGATGGTGGCGTAAGCCGTCTTCATGGATTTAAATCCCAGCGT\n+GGCGTTGATTATCCGTTTCAGTTTGCCATGATCGCATTCAATCACGTTGTTCCGGTACTT\n+AATCTGTCGGTGTTCAACGTCAGACGGGCACCGGCCTTCGCGTTTGAGCAGAGCAAGCGC\n+GCGACCATAGGCGGGCGCTTTATCCGTGTTGATGAATCGCGGGATCTGCCACTTCTTCAC\n+GTTGTTGAGGATTTTACCCAGAAACCGGTATGCAGCTTTGCTGTTACGACGGGAGGAGAG\n+ATAAAAATCGACAGTGCGGCCCCGGCTGTCGACGGCCCGGTACAGATACGCCCAGCGGCC\n+ATTGACCTTCACGTAGGTTTCATCCATGTGCCACGGGCAAAGATCGGAAGGGTTACGCCA\n+GTACCAGCGCAGCCGTTTTTCCATTTCAGGCGCATAACGCTGAACCCAGCGGTAAATCGT\n+GGAGTGATCGACATTCACTCCGCGTTCAGCCAGCATCTCCTGCAGCTCACGGTAACTGAT\n+GCCGTATTTGCAGTACCAGCGTACGGCCCACAGAATGATGTCACGCTGAAAATGCCGGCC\n+TTTGAATGGGTTCATGTGCAGCTCCATCAGCAAAAGGGGATGATAAGTTTATCACCACCG\n+ACTATTTGCAACAGTGCCGTGTACATCGAAATACGGCTTATCAGGCGTTAAAAGATGCTT\n+GCGATGACTTGTTTGCAAGACAATTCAGTTATCAGAGTCTTAGTGAAAAAGGTAACACTA\n+TTAATCACAAATCAAGATGGGTGAGCGAGGTGGCTTATATTGATAATGAAGCTGTCGTTA\n+GACTTATTTTTGCCCCTGCTATTGTGCCTTTAATTA'..b'TCTTCAA\n+CGCCATCACACAAAACTTTCTTTTTCACGCACAGTCAACTTATTGGATGTTTTATTAACA\n+ACCCAAAAGGAGATATTTAGCGGGCGGCCGGAAGGTGAATGCTAGGCATGATCTAACCCT\n+CGGTCTCTGGCGTCGCGACTGCGAAATTTCGCGAGGGTTTCCGAGAAGGTGATTGCGCTT\n+CGCAGATCTCCAGGCGCGTGGGTGCGGACGTAGTCAGCGCCATTGCCGATCGCGTGAAGT\n+TCCGCCGCAAGGCTCGCTGGACCCAGATCCTTTACAGGAAGGCCAACGGTGGCGCCCAAG\n+AAGGATTTCCGCGACACCGAGACCAATAGCGGAAGCCCCAACGCCGACTTCAGCTTTTGA\n+AGGTTCGACAGCACGTGCAGCGATGTTTCCGGTGCGGGGCTCAAGAAAAATCCCATCCCC\n+GGATCGAGGATGAGCCGGTCGGCAGCGACCCCGCTCCGTCGCAAGGCGGAAACCCGCGCC\n+TCGAAGAACCGCACAATCTCGTCGAGCGCGTCTTCGGGTCGAAGGTGACCGGTGCGGGTG\n+GCGATGCCATCCCGCTGCGCTGAGTGCATAACCACCAGCCTGCAGTCCGCCTCAGCAATA\n+TCGGGATAGAGCGCAGGGTCAGGAAATCCTTGGATATCGTTCAGGTAGCCCACGCCGCGC\n+TTGAGCGCATAGCGCTGGGTTTCCGGTTGGAAGCTGTCGATTGAAACACGGTGCATCTGA\n+TCGGACAGGGCGTCTAAGAGCGGCGCAATACGTCTGATCTCATCGGCCGGCGATACAGGC\n+CTCGCGTCCGGATGGCTGGCGGCCGGTCCGACATCCACGACGTCTGATCCGACTCGCAGC\n+ATTTCGATCGCCGCGGTGACAGCGCCGGCGGGGTCTAGCCGCCGGCTCTCATCGAAGAAG\n+GAGTCCTCGGTGAGATTCAGAATGCCGAACACCGTCACCATGGCGTCGGCCTCCGCAGCG\n+ACTTCCACGATGGGGATCGGGCGAGCAAAAAGGCAGCAATTATGAGCCCCATACCTACAA\n+AGCCCCACGCATCAAGCTTTTGCCCATGAAGCAACCAGGCAATGGCTGTAATTATGACGA\n+CGCCGAGTCCCGACCAGACTGCATAAGCAACACCGACAGGGATGGATTTCAGAACCAGAG\n+AAAGAAAATAAAATGCGATGCCATAACCGATTATGACAACGGCGGAAGGGGCAAGCTTAG\n+TAAAGCCCTCGCTAGATTTTAATGCGGATGTTGCGATTACTTCGCCAACTATTGCGATAA\n+CAAGAAAAAGCCAGCCTTTCATGATATATCTCCCAATTTGTGTAGGGCTTATTATGCACG\n+CTTAAAAATAATAAAAGCAGACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTA\n+GTGCATCTAACGCTTGAGTTAAGCCGCGCCGCGAAGCGGCGTCGGCTTGAACGAATTGTT\n+AGACATTATTTGCCGACTACCTTGGTGATCTCGCCTTTCACGTAGTGGACAAATTCTTCC\n+AACTGATCTGCGCGCGAGGCCAAGCGATCTTCTTCTTGTCCAAGATAAGCCTGTCTAGCT\n+TCAAGTATGACGGGCTGATACTGGGCCGGCAGGCGCTCCATTGCCCAGTCGGCAGCGACA\n+TCCTTCGGCGCGATTTTGCCGGTTACTGCGCTGTACCAAATGCGGGACAACGTAAGCACT\n+ACATTTCGCTCATCGCCAGCCCAGTCGGGCGGCGAGTTCCATAGCGTTAAGGTTTCATTT\n+AGCGCCTCAAATAGATCCTGTTCAGGAACCGGATCAAAGAGTTCCTCCGCCGCTGGACCT\n+ACCAAGGCAACGCTATGTTCTCTTGCTTTTGTCAGCAAGATAGCCAGATCAATGTCGATC\n+GTGGCTGGCTCGAAGATACCTGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGT\n+TCGCGCTTAGCTGGATAACGCCACGGAATGATGTCGTCGTGCACAACAATGGTGACTTCT\n+ACAGCGCGGAGAATCTCGCTCTCTCCAGGGGAAGCCGAAGTTTCCAAAAGGTCGTTGATC\n+AAAGCTCGCCGCGTTGTTTCATCAAGCCTTACGGTCACCGTAACCAGCAAATCAATATCA\n+CTGTGTGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGTACGGCCAGCAACGTC\n+GGTTCGAGATGGCGCTCGATGACGCCAACTACCTCTGATAGTTGAGTCGATACTTCGGCG\n+ATCACCGCTTCCCTCATGATGTTTAACGCCCAGCTTCAGACGCGCGGAGGCCGTAAGGCC\n+GTAGCGTCGGCTGGAAGCATTGGTTAGAGCATGAGCGATTTACTGTATTCATGGCTTTCG\n+AAAAATTGTATCTGCACAGGTTGCTAGTACGACGTACACAATAGGCCCGAGCAGTATGAG\n+CGCCGCCCAGCCCTGAGGAGAACTTGGCGCTTTACCCGCGTAGGTGACGATCTCCACCAC\n+CAGTAGCGCCCAGGCCGCAAGGAATATGGCGATGTTTCGCGGCCTTAACCAAGTGCGCTT\n+CTGAGCCTTGTCTAGAAGATTCACCACGTCACTACCGTCAAAGAAGTGGTGGCCGCAGTG\n+AGCGCAACGATGTGCATCTACGAAATTCTGGCGGCCACAGCGTGCGCAGTTCATTTTTGC\n+TCTAACGCCCTAGCTAAGCCGACGGACAGCCCGCAGGGCTGGCCGGTCGGCTTGAGCGCC\n+ATGTTGGGCGACAACTGCCTTGCGCATTGCATACCTACGGAACATGACGCCTCCACGGGA\n+GACATTTTGCTCCTCAACTACACTGAAACCATGCCGCAGGAAAAAGGGCTTGGCGACCAG\n+ACTGGCTTCTGTGAAGAGCGAAACACCTGGGAGGGCTTTCTCAACCTCACGGTACAGAAC\n+AGACGCGACGCCCCGACGCTCGGAACCCGGTGCGGTGTAAAGAAACTCGATGTGGCCGCT\n+AAGCTCGTAAGAGATGAACCCGATAACCGCATCTCCCTCAATTGCTAGAAGAGTCTGTAG\n+GCCAGATAAGCGAGCTGACCAAGCCTCTATATCTGCGGGACGCGGTGCCCACGCATTCCT\n+TTGCGAAGCGTCATAGTGAGACGCTCCAAGTACATGAATAGACTCAGTAAATACGACTGC\n+GATAGAGGCGACGTCAGATTCAGTGCAAGTGCGTACGTTCATATCGGTTTTCTTGTTGCC\n+CAACGCCTGAGTTAAGCCGGAGCGCTTTGCGGCCGCGGCGTTGTGACAATTTTTCCGAAC\n+AACTCCGCGGCCGCGAAGCGATCTCGGCTTGAACGAATTGTTAGGTGGCGGTACTTGGGT\n+CGATATCAAAGTGCATCACTTCTTCCCGTATGCCCAACTTTGTATAGAGAGCCACTGCGG\n+GATCGTCACCGTAATCTGCTTGCACGTAGATCACATAAGCACCAAGCGCGTTGGCCTCAT\n+GCTTGAGGAGATTGATGAGCGCGGTGGCAATGCCTTGCCTCCGGTGCTCGCCGGAGACTG\n+CGAGATCATAGATATAGATCTCACTACGCGCCTGCTCAAACTTTGGCAGAACGTAAGCCG\n+CGAGAGCGCCAACAACCGCTTCTTGGTCGAAGGCAGCAAGCGCGATGAATGTCTTACTAC\n+GGAGCAAGTTCCCGAGGTAATCGGAGTCCGGCTGATGTTGGGAGTAGGTGGCTACGTCTC\n+CGAACTCACGACCGAAAAGATCAAGAGCAGCCCTCATGGATTTGACTTGGTCAGGGCCGA\n+GCCTACATGTGCGAATGATGCCCATACTTGAGCCACCTAACTTTGTTTTAGGGCGACTGC\n+CCTGCTGCGTAACATCGTTGCTGCTGCGTAACATCGTTGCTGCTCCATAACATCAAACAT\n+CGACCCACGGCGTAACGCGCT\n'
b
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 <http://www.gnu.org/licenses/>.
+
+                     =======================
+
+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
+
+                     =======================
+
+
+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.
+
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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 <http://www.gnu.org/licenses/>.
+
+                     =======================
+
+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
+
+                     =======================
+
+
+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.
+
b
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
b
@@ -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
b
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
b
@@ -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
b
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 <http://www.gnu.org/licenses/>.
+
+                     =======================
+
+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
+
+                     =======================
+
+
+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.
+
b
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
b
@@ -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
b
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
b
@@ -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
b
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 <http://www.gnu.org/licenses/>.
+
+                     =======================
+
+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
+
+                     =======================
+
+
+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.
+
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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