Mercurial > repos > iuc > integron_finder
changeset 0:1ae00120dd24 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bakta/integron_finder commit 6e0d10965c02c249844f1eddd1c7442990695a6a
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--- /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 @@ +<tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> is a program that detects integrons in DNA sequences</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="edam_info"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + integron_finder + '$sequence' + --cpu @THREADS@ + --keep-tmp + $local_max + #if $type_replicon + $type_replicon + #end if + #if $topology_file + --topology-file '$topology_file' + #end if + $promoter_attI + -dt $settings.attc_settings.dist_thresh + --calin-threshold $settings.attc_settings.calin_threshold + --max-attc-size $settings.attc_settings.max_attc_size + --min-attc-size $settings.attc_settings.min_attc_size + $settings.attc_settings.keep_palindromes + #if $settings.attc_settings.covar_matrix + --attc-model '$settings.attc_settings.covar_matrix' + #end if + $settings.protein_settings.no_proteins + $settings.protein_settings.union_integrases + $settings.protein_settings.func_annot + $gbk + $pdf + && mv Results_Integron_Finder_* Results_Integron_Finder + ]]></command> + <inputs> + <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments..." /> + <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." /> + <param name="type_replicon" type="select" optional="true" label="Default replicons topology" help="Set the default topology for replicons, linear, circular (deault: no topology)"> + <option value="--linear">linear (--linear)</option> + <option value="--circ">circular (--circ)</option> + </param> + <param name="topology_file" argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/> + <param name="promoter_attI" argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" /> + <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."/> + <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)"/> + <section name="settings" title="Advanced Parameters" expanded="False"> + <section name="attc_settings" title="Attc options" expanded="False"> + <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." /> + <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" /> + <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/> + <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" /> + <param name="keep_palindromes" argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/> + <param name="covar_matrix" argument="--attc-model" type="data" optional="true" format="txt" label="Covariance Matrix" /> + </section> + <section name="protein_settings" title="Protein options" expanded="False"> + <param name="no_proteins" argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/> + <param name="union_integrases" argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" /> + <param name="func_annot" argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" /> + </section> + </section> + <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/> + </inputs> + <outputs> + <collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out"> + <discover_datasets pattern="(?P<designation>.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" /> + <filter>gbk</filter> + </collection> + <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]"> + <filter> no_logfile == False</filter> + </data> + <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/> + <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/> + <collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out"> + <discover_datasets pattern="(?P<designation>.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" /> + <filter>pdf</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="sequence" value="input.fasta"/> + <output name="integron_log" value="integron_log" lines_diff="3" /> + <output name="integrons_table" value="test1_integrons_table.tsv" lines_diff="3"/> + <output name="summary" value="summary.tsv" lines_diff="3"/> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="local_max" value="true"/> + <param name="type_replicon" value="--linear"/> + <param name="no_logfile" value="true"/> + <output name="integrons_table" value="test2_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="4" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="type_replicon" value="--circ"/> + <param name="no_logfile" value="true"/> + <output name="integrons_table" value="test3_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="topology_file" value="topology.txt"/> + <param name="no_logfile" value="true"/> + <output name="integrons_table" value="test4_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="5" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="promoter_attI" value="true"/> + <param name="no_logfile" value="true"/> + <output name="integrons_table" value="test5_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="4"> + <param name="sequence" value="input.fasta"/> + <param name="gbk" value="true"/> + <param name="pdf" value="true"/> + <param name="no_logfile" value="true"/> + <output_collection name="genbank_out" type="list"> + <element name="ACBA.007.P01_13"> + <assert_contents> + <has_text text="MKTATAPLPPLRSVKVLDQLRERIRYLHYSLRTEQAYVNWVRAFI"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="pdf_out" type="list"> + <element name="ACBA.007.P01_13_1"> + <assert_contents> + <has_text text=">"/> + </assert_contents> + </element> + </output_collection> + <output name="integrons_table" value="test6_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="no_logfile" value="true"/> + <section name="settings"> + <section name="attc_settings"> + <param name="dist_thresh" value="2000"/> + <param name="calin_threshold" value="3"/> + <param name="max_attc_size" value="188"/> + <param name="min_attc_size" value="30"/> + <param name="keep_palindromes" value=""/> + </section> + </section> + <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="no_logfile" value="true"/> + <section name="settings"> + <section name="attc_settings"> + <param name="covar_matrix" value="covar.txt"/> + </section> + </section> + <output name="integrons_table" value="test8_integrons_table.tsv" lines_diff="10" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="no_logfile" value="true"/> + <section name="settings"> + <section name="protein_settings"> + <param name="no_proteins" value="true"/> + </section> + </section> + <output name="integrons_table" value="test9_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="test9_summary.tsv" lines_diff="3" /> + </test> + <test expect_num_outputs="2"> + <param name="sequence" value="input.fasta"/> + <param name="no_logfile" value="true"/> + <section name="settings"> + <section name="protein_settings"> + <param name="union_integrases" value="true" /> + <param name="func_annot" value="true"/> + </section> + </section> + <output name="integrons_table" value="test10_integrons_table.tsv" lines_diff="3" /> + <output name="summary" value="summary.tsv" lines_diff="3" /> + </test> + </tests> + <help><![CDATA[ + +How does it work ? +================== + +- First, IntegronFinder annotates the DNA sequence's CDS with Prodigal. + +- Second, IntegronFinder detects independently integron integrase and *attC* + recombination sites. The Integron integrase is detected by using the intersection + of two HMM profiles: + + - one specific of tyrosine-recombinase (PF00589) + - one specific of the integron integrase, near the patch III domain of tyrosine recombinases. + +The *attC* recombination site is detected with a covariance model (CM), which +models the secondary structure in addition to the few conserved sequence +positions. + + +- Third, the results are integrated, and IntegronFinder distinguishes 3 types of + elements: + + - complete integron + Integron with integron integrase nearby *attC* site(s) + - In0 element + Integron integrase only, without any *attC* site nearby + - CALIN element + Cluster of *attC* sites Lacking INtegrase nearby. + A rule of thumb to avoid false positive is to filter out singleton of + *attC* site. + +IntegronFinder can also annotate gene cassettes (CDS nearby *attC* sites) using +Resfams, a database of HMM profiles aiming at annotating antibiotic resistance +genes. This database is provided but the user can add any other HMM profiles +database of its own interest. + +When available, IntegronFinder annotates the promoters and attI sites by pattern +matching. + ]]></help> + <expand macro="citations"/> +</tool>
--- /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 @@ +<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>
--- /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 * +//
--- /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
--- /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 + + ======================= + +[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. +
--- /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
--- /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
--- /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
--- /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 + + ======================= + +[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. +
--- /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
--- /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
--- /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 + + ======================= + +[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. +
--- /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
--- /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
--- /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 + + ======================= + +[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. +
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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