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

Changeset 0:bae2bc0f1b66 (2024-08-28)
Next changeset 1:d8e95a03321a (2025-04-23)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm commit cc4c7a0c31ae4bed0c1f0955f3aa72ccdec3b132
added:
argnorm.xml
test-data/blastout.filtered.argnorm.tsv
test-data/blastout.filtered.txt
test-data/deeparg_hamronize.tsv
test-data/deeparg_hamronize_argnorm_results.tsv
test-data/groot-resfinder-results.tsv
test-data/resfinder_PSM7J199_R2.report
b
diff -r 000000000000 -r bae2bc0f1b66 argnorm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/argnorm.xml Wed Aug 28 20:27:17 2024 +0000
[
@@ -0,0 +1,83 @@
+<tool id="argnorm" name="argNorm" version="@VERSION@+galaxy0" profile="22.05">
+    <description>a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)</description>
+    <macros>
+        <token name="@VERSION@">0.6.0</token>
+    </macros>
+    <xrefs>
+       <xref type="bio.tools">argnorm</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@VERSION@">argnorm</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    argnorm
+        '$tool'
+        --db '$db'
+        -i '$input' 
+        -o '$output'
+        $hamronized
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="tsv,txt" label="Specify input file" help="-i" />
+        <param type="select" name="tool" label="The tool you used to do ARG annotation" help="[tool]" >
+            <option value="deeparg" selected="true">DeepARG</option>
+            <option value="argsoap">ARGs_OAP</option>
+            <option value="abricate">ABRicate</option>
+            <option value="resfinder">ResFinder</option>
+            <option value="amrfinderplus">AMRFinderPlus</option>
+            <option value="groot">Groot</option>
+        </param>
+        <param type="select" argument="--db" label="The database you used to do ARG annotation">
+            <option value="sarg" selected="true">SARG</option>
+            <option value="ncbi">NCBI</option>
+            <option value="resfinder">ResFinder</option>
+            <option value="deeparg" selected="true">DeepARG</option>
+            <option value="amrfinderplus">AMRFinderPlus</option>
+            <option value="megares">MEGARes</option>
+            <option value="argannot">ARG-ANNOT</option>
+            <option value="groot-resfinder">Groot ResFinder database </option>
+            <option value="groot-argannot">Groot ARG-ANNOT database </option>
+            <option value="groot-card">Groot CARD database </option>
+            <option value="groot-db">Groot DB (combining all sequences in ResFinder, ARG-annot and CARD)</option>
+            <option value="groot-core-db">Groot Core DB (combining sequences that are present in each of ResFinder, ARG-annot and CARD databases)</option>
+        </param> 
+        <param name="hamronized" type="boolean" label="If the input is hamronized" truevalue="--hamronized" falsevalue="" optional="true" help="Use this if the input is hamronized (processed using the hAMRonization tool)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tsv" label="${tool.name} on ${on_string} : ARG normalized table" />
+    </outputs>
+    <tests>
+        <!-- Test 1 : input : tsv, output : tsv, tool : groot -->
+        <test>
+            <param name="input" value="resfinder_PSM7J199_R2.report"/>
+            <param name="tool" value="groot"/>
+            <param name="db" value="groot-resfinder"/>
+            <output name="output" file="groot-resfinder-results.tsv"/>
+        </test>
+        <!-- Test 2 : input : txt, output : tsv, tool : argsoap -->
+        <test>
+            <param name="input" value="blastout.filtered.txt"/>
+            <param name="tool" value="argsoap"/>
+            <param name="db" value="sarg"/>
+            <output name="output" file="blastout.filtered.argnorm.tsv"/>
+        </test>
+        <!-- Test 3 : input : tsv, output : tsv, tool : deeparg, hamronize : true -->
+        <test>
+            <param name="input" value="deeparg_hamronize.tsv"/>
+            <param name="tool" value="deeparg"/>
+            <param name="db" value="deeparg"/>
+            <param name="hamronized" value="true"/>
+            <output name="output" file="deeparg_hamronize_argnorm_results.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.
+
+argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">https://github.com/BigDataBiology/argNorm</citation>
+    </citations>
+</tool>
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/blastout.filtered.argnorm.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastout.filtered.argnorm.tsv Wed Aug 28 20:27:17 2024 +0000
b
b'@@ -0,0 +1,101 @@\n+0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\t15\t16\t17\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n+qseqid\tsseqid\tpident\tlength\tqlen\tslen\tevalue\tbitscore\tqcov\tsample\tscov\tgene\tsubtype\ttype\tcount\tcopy\trpk\trpksum\t\t\t\n+HSM7J4M8@HSM7J4M8_R1@10007@CAVL1ANXX170419:8:1312:3147:65962/1\tgi|751930065|ref|WP_041144773.1|\t84.848\t33\t101\t648\t6.19e-12\t55.5\t0.32673267326732675\tHSM7J4M8\t0.05092592592592592\tgi|751930065|ref|WP_041144773.1|\tmacrolide-lincosamide-streptogramin__macB\tmacrolide-lincosamide-streptogramin\t0.3333333333333333\t0.016975308641975308\t0.51440329218107\t28361.83513176316\tARO:3000535\t\t\n+HSM7J4M8@HSM7J4M8_R1@10017@CAVL1ANXX170419:8:1312:6960:13504/1\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\t100.0\t33\t101\t1107\t9.96e-19\t74.7\t0.32673267326732675\tHSM7J4M8\t0.02981029810298103\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\tmupirocin__Bifidobacteria intrinsic ileS conferring resistance to mupirocin\tmupirocin\t1.0\t0.02981029810298103\t0.903342366757001\t28361.83513176316\tARO:3003730\tARO:3000554\tARO:3007151\n+HSM7J4M8@HSM7J4M8_R1@10018@CAVL1ANXX170419:8:1312:7015:67833/1\tgi|490355791|ref|WP_004235564.1|\t87.5\t32\t101\t510\t4.28e-13\t58.9\t0.31683168316831684\tHSM7J4M8\t0.06274509803921569\tgi|490355791|ref|WP_004235564.1|\tmultidrug__emrB\tmultidrug\t0.3333333333333333\t0.02091503267973856\t0.65359477124183\t28361.83513176316\tARO:3004597\tARO:0000032\tARO:3000007\n+HSM7J4M8@HSM7J4M8_R1@10019@CAVL1ANXX170419:8:1312:7329:85173/1\tgb|AAF74725.1|ARO:3004659|Mef(En2)\t100.0\t33\t101\t401\t1.8e-16\t68.2\t0.32673267326732675\tHSM7J4M8\t0.08229426433915212\tgb|AAF74725.1|ARO:3004659|Mef(En2)\tmacrolide-lincosamide-streptogramin__mef(En2)\tmacrolide-lincosamide-streptogramin\t1.0\t0.08229426433915212\t2.4937655860349124\t28361.83513176316\tARO:3004659\tARO:0000046\tARO:0000017\n+HSM7J4M8@HSM7J4M8_R1@10023@CAVL1ANXX170419:8:1312:8170:40475/1\tZP_04557016\t100.0\t33\t101\t657\t2.5e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10028@CAVL1ANXX170419:8:1312:8966:29123/1\tZP_04557016\t96.97\t33\t101\t657\t1.36e-17\t71.6\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@1002@CAVL1ANXX170419:7:1115:3411:87969/1\tgb|AEY83581|ARO:3000510|mupB\t84.848\t33\t101\t1033\t6.34e-16\t66.6\t0.32673267326732675\tHSM7J4M8\t0.031945788964181994\tgb|AEY83581|ARO:3000510|mupB\tmupirocin__mupB\tmupirocin\t1.0\t0.031945788964181994\t0.9680542110358181\t28361.83513176316\tARO:3000510\tARO:3000554\tARO:3007151\n+HSM7J4M8@HSM7J4M8_R1@10033@CAVL1ANXX170419:8:1312:9879:14531/1\tgi|511019447|ref|WP_016273783.1|\t100.0\t33\t101\t296\t2.91e-18\t72.8\t0.32673267326732675\tHSM7J4M8\t0.11148648648648649\tgi|511019447|ref|WP_016273783.1|\tbeta_lactam__CblA-1\tbeta_lactam\t1.0\t0.11148648648648649\t3.3783783783783785\t28361.83513176316\tARO:3002999\tARO:0000032,ARO:3004129\tARO:3000007,ARO:3000007\n+HSM7J4M8@HSM7J4M8_R1@10034@CAVL1ANXX170419:8:1312:9988:52653/1\tACI02041\t100.0\t33\t101\t639\t3.53e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.051643192488262914\tACI02041\ttetracycline__tet(W)\ttetracycline\t1.0\t0.051643192488262914\t1.5649452269170578\t28361.83513176316\tARO:3000194\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10036@CAVL1ANXX170419:8:1313:10501:70436/1\tP70882\t100.0\t28\t85\t641\t5.38e-12\t55.5\t0.32941176470588235\tHSM7J4M8\t0.0436817472698908\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0436817472698908\t1.5600624024960998\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,'..b'148148148149\tgi|983204316|ref|WP_060470352.1|\tmacrolide-lincosamide-streptogramin__mel\tmacrolide-lincosamide-streptogramin\t1.0\t0.08148148148148149\t2.4691358024691357\t28361.83513176316\tARO:3000616\tARO:0000006,ARO:0000057\tARO:0000000,ARO:0000000\n+HSM7J4M8@HSM7J4M8_R1@10535@CAVL1ANXX170419:8:2103:19290:67725/1\tBAD46890\t100.0\t33\t101\t657\t5.41e-15\t64.3\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tBAD46890\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10538@CAVL1ANXX170419:8:2103:20166:76320/1\tZP_04055725\t84.848\t33\t101\t283\t6.62e-14\t60.8\t0.32673267326732675\tHSM7J4M8\t0.1166077738515901\tZP_04055725\tbacitracin__bacA\tbacitracin\t1.0\t0.1166077738515901\t3.53356890459364\t28361.83513176316\tARO:3002986\tARO:3000629,ARO:3000630,ARO:3000631\tARO:3000053,ARO:3000053,ARO:3000053\n+HSM7J4M8@HSM7J4M8_R1@10544@CAVL1ANXX170419:8:2103:2552:10242/1\tAF472622.2.gene1.p01\t96.97\t33\t101\t321\t7.35e-17\t68.9\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAF472622.2.gene1.p01\tbeta_lactam__CfxA3\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\tARO:3003003\tARO:0000044\tARO:3000007\n+HSM7J4M8@HSM7J4M8_R1@10551@CAVL1ANXX170419:8:2103:4570:86818/1\tM14730.gene.p01\t100.0\t33\t101\t266\t5.17e-18\t71.6\t0.32673267326732675\tHSM7J4M8\t0.12406015037593984\tM14730.gene.p01\tmacrolide-lincosamide-streptogramin__erm(F)\tmacrolide-lincosamide-streptogramin\t1.0\t0.12406015037593984\t3.7593984962406015\t28361.83513176316\tARO:3000498\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+HSM7J4M8@HSM7J4M8_R1@10552@CAVL1ANXX170419:8:2103:4941:41693/1\tP70882\t100.0\t33\t101\t641\t2.21e-18\t73.9\t0.32673267326732675\tHSM7J4M8\t0.0514820592823713\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0514820592823713\t1.5600624024960998\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10556@CAVL1ANXX170419:8:2103:6322:54059/1\tAAM48125\t100.0\t33\t101\t321\t5.77e-17\t69.3\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48125\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\tARO:3003002\tARO:0000044\tARO:3000007\n+HSM7J4M8@HSM7J4M8_R1@10568@CAVL1ANXX170419:8:2103:9384:19852/1\tBAD46890\t100.0\t33\t101\t657\t2.63e-17\t70.9\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tBAD46890\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10569@CAVL1ANXX170419:8:2103:9417:90711/1\tAAZ79478\t100.0\t33\t101\t657\t2.68e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tAAZ79478\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8@HSM7J4M8_R1@10570@CAVL1ANXX170419:8:2103:9525:62852/1\tAAM48116\t100.0\t33\t101\t321\t2.25e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48116\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\tARO:3003002\tARO:0000044\tARO:3000007\n'
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/blastout.filtered.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastout.filtered.txt Wed Aug 28 20:27:17 2024 +0000
b
b"@@ -0,0 +1,100 @@\n+qseqid\tsseqid\tpident\tlength\tqlen\tslen\tevalue\tbitscore\tqcov\tsample\tscov\tgene\tsubtype\ttype\tcount\tcopy\trpk\trpksum\n+HSM7J4M8@HSM7J4M8_R1@10007@CAVL1ANXX170419:8:1312:3147:65962/1\tgi|751930065|ref|WP_041144773.1|\t84.848\t33\t101\t648\t6.19e-12\t55.5\t0.32673267326732675\tHSM7J4M8\t0.05092592592592592\tgi|751930065|ref|WP_041144773.1|\tmacrolide-lincosamide-streptogramin__macB\tmacrolide-lincosamide-streptogramin\t0.3333333333333333\t0.016975308641975308\t0.51440329218107\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10017@CAVL1ANXX170419:8:1312:6960:13504/1\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\t100.0\t33\t101\t1107\t9.96e-19\t74.7\t0.32673267326732675\tHSM7J4M8\t0.02981029810298103\tgb|ADP36409.1|ARO:3003730|Bifidobacteria\tmupirocin__Bifidobacteria intrinsic ileS conferring resistance to mupirocin\tmupirocin\t1.0\t0.02981029810298103\t0.903342366757001\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10018@CAVL1ANXX170419:8:1312:7015:67833/1\tgi|490355791|ref|WP_004235564.1|\t87.5\t32\t101\t510\t4.28e-13\t58.9\t0.31683168316831684\tHSM7J4M8\t0.06274509803921569\tgi|490355791|ref|WP_004235564.1|\tmultidrug__emrB\tmultidrug\t0.3333333333333333\t0.02091503267973856\t0.65359477124183\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10019@CAVL1ANXX170419:8:1312:7329:85173/1\tgb|AAF74725.1|ARO:3004659|Mef(En2)\t100.0\t33\t101\t401\t1.8e-16\t68.2\t0.32673267326732675\tHSM7J4M8\t0.08229426433915212\tgb|AAF74725.1|ARO:3004659|Mef(En2)\tmacrolide-lincosamide-streptogramin__mef(En2)\tmacrolide-lincosamide-streptogramin\t1.0\t0.08229426433915212\t2.4937655860349124\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10023@CAVL1ANXX170419:8:1312:8170:40475/1\tZP_04557016\t100.0\t33\t101\t657\t2.5e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10028@CAVL1ANXX170419:8:1312:8966:29123/1\tZP_04557016\t96.97\t33\t101\t657\t1.36e-17\t71.6\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tZP_04557016\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@1002@CAVL1ANXX170419:7:1115:3411:87969/1\tgb|AEY83581|ARO:3000510|mupB\t84.848\t33\t101\t1033\t6.34e-16\t66.6\t0.32673267326732675\tHSM7J4M8\t0.031945788964181994\tgb|AEY83581|ARO:3000510|mupB\tmupirocin__mupB\tmupirocin\t1.0\t0.031945788964181994\t0.9680542110358181\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10033@CAVL1ANXX170419:8:1312:9879:14531/1\tgi|511019447|ref|WP_016273783.1|\t100.0\t33\t101\t296\t2.91e-18\t72.8\t0.32673267326732675\tHSM7J4M8\t0.11148648648648649\tgi|511019447|ref|WP_016273783.1|\tbeta_lactam__CblA-1\tbeta_lactam\t1.0\t0.11148648648648649\t3.3783783783783785\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10034@CAVL1ANXX170419:8:1312:9988:52653/1\tACI02041\t100.0\t33\t101\t639\t3.53e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.051643192488262914\tACI02041\ttetracycline__tet(W)\ttetracycline\t1.0\t0.051643192488262914\t1.5649452269170578\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10036@CAVL1ANXX170419:8:1313:10501:70436/1\tP70882\t100.0\t28\t85\t641\t5.38e-12\t55.5\t0.32941176470588235\tHSM7J4M8\t0.0436817472698908\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0436817472698908\t1.5600624024960998\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10049@CAVL1ANXX170419:8:1313:13934:25045/1\tAAM48125\t100.0\t33\t101\t321\t6.27e-18\t72.0\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48125\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10055@CAVL1ANXX170419:8:1313:15440:95003/1\tQ02607\t100.0\t33\t101\t266\t1.09e-17\t70.9\t0.32673267326732675\tHSM7J4M8\t0.12406015037593984\tQ02607\tmacrolide-lincosamide-streptogramin__erm(F)\tmacrolide-lincosamide-streptogramin\t1.0\t0.12406015037593984\t3.7593984962406015\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10062@CAVL1ANXX170419:8:1313:16983:59428/1\tCP004067.1.gene46.p01\t100.0\t33\t101\t306\t4.62e-17\t69.7\t0.32673267326732675\tHSM7J4M8\t0.10784313725490197\tCP004067.1.gene46.p01\taminoglycoside__APH(2'')-Ig\taminoglycoside\t1.0\t0.10784313725490197\t3.2679738562091503\t28361.83513176316\n+HSM"..b'\t100.0\t28\t85\t640\t3.74e-13\t58.5\t0.32941176470588235\tHSM7J4M8\t0.04375\tFN594949.1.gene24.p01\ttetracycline__tet(44)\ttetracycline\t1.0\t0.04375\t1.5625\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10514@CAVL1ANXX170419:8:2103:13328:98394/1\tZ21523.gene.p01\t96.552\t29\t87\t657\t1.49e-14\t62.8\t0.3333333333333333\tHSM7J4M8\t0.0441400304414003\tZ21523.gene.p01\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0441400304414003\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10517@CAVL1ANXX170419:8:2103:14435:84844/1\tZP_03989103\t100.0\t29\t90\t639\t1.78e-14\t62.4\t0.32222222222222224\tHSM7J4M8\t0.04538341158059468\tZP_03989103\ttetracycline__tet(32)\ttetracycline\t1.0\t0.04538341158059468\t1.5649452269170578\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@1051@CAVL1ANXX170419:7:1116:16548:53295/1\tgb|AAF74725.1|ARO:3004659|Mef(En2)\t100.0\t33\t101\t401\t8.12e-16\t66.6\t0.32673267326732675\tHSM7J4M8\t0.08229426433915212\tgb|AAF74725.1|ARO:3004659|Mef(En2)\tmacrolide-lincosamide-streptogramin__mef(En2)\tmacrolide-lincosamide-streptogramin\t1.0\t0.08229426433915212\t2.4937655860349124\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10524@CAVL1ANXX170419:8:2103:16740:84348/1\tAAV37206\t100.0\t33\t101\t321\t3.21e-17\t70.1\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAV37206\tbeta_lactam__CfxA5\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10531@CAVL1ANXX170419:8:2103:18518:6060/1\tgi|983204316|ref|WP_060470352.1|\t81.818\t33\t101\t405\t1.53e-11\t54.3\t0.32673267326732675\tHSM7J4M8\t0.08148148148148149\tgi|983204316|ref|WP_060470352.1|\tmacrolide-lincosamide-streptogramin__mel\tmacrolide-lincosamide-streptogramin\t1.0\t0.08148148148148149\t2.4691358024691357\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10535@CAVL1ANXX170419:8:2103:19290:67725/1\tBAD46890\t100.0\t33\t101\t657\t5.41e-15\t64.3\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tBAD46890\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10538@CAVL1ANXX170419:8:2103:20166:76320/1\tZP_04055725\t84.848\t33\t101\t283\t6.62e-14\t60.8\t0.32673267326732675\tHSM7J4M8\t0.1166077738515901\tZP_04055725\tbacitracin__bacA\tbacitracin\t1.0\t0.1166077738515901\t3.53356890459364\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10544@CAVL1ANXX170419:8:2103:2552:10242/1\tAF472622.2.gene1.p01\t96.97\t33\t101\t321\t7.35e-17\t68.9\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAF472622.2.gene1.p01\tbeta_lactam__CfxA3\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10551@CAVL1ANXX170419:8:2103:4570:86818/1\tM14730.gene.p01\t100.0\t33\t101\t266\t5.17e-18\t71.6\t0.32673267326732675\tHSM7J4M8\t0.12406015037593984\tM14730.gene.p01\tmacrolide-lincosamide-streptogramin__erm(F)\tmacrolide-lincosamide-streptogramin\t1.0\t0.12406015037593984\t3.7593984962406015\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10552@CAVL1ANXX170419:8:2103:4941:41693/1\tP70882\t100.0\t33\t101\t641\t2.21e-18\t73.9\t0.32673267326732675\tHSM7J4M8\t0.0514820592823713\tP70882\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0514820592823713\t1.5600624024960998\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10556@CAVL1ANXX170419:8:2103:6322:54059/1\tAAM48125\t100.0\t33\t101\t321\t5.77e-17\t69.3\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48125\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10568@CAVL1ANXX170419:8:2103:9384:19852/1\tBAD46890\t100.0\t33\t101\t657\t2.63e-17\t70.9\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tBAD46890\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10569@CAVL1ANXX170419:8:2103:9417:90711/1\tAAZ79478\t100.0\t33\t101\t657\t2.68e-16\t67.8\t0.32673267326732675\tHSM7J4M8\t0.0502283105022831\tAAZ79478\ttetracycline__tet(Q)\ttetracycline\t1.0\t0.0502283105022831\t1.5220700152207\t28361.83513176316\n+HSM7J4M8@HSM7J4M8_R1@10570@CAVL1ANXX170419:8:2103:9525:62852/1\tAAM48116\t100.0\t33\t101\t321\t2.25e-17\t70.5\t0.32673267326732675\tHSM7J4M8\t0.102803738317757\tAAM48116\tbeta_lactam__CfxA2\tbeta_lactam\t1.0\t0.102803738317757\t3.115264797507788\t28361.83513176316\n'
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/deeparg_hamronize.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deeparg_hamronize.tsv Wed Aug 28 20:27:17 2024 +0000
b
b'@@ -0,0 +1,100 @@\n+input_file_name\tgene_symbol\tgene_name\treference_database_name\treference_database_version\treference_accession\tanalysis_software_name\tanalysis_software_version\tgenetic_variation_type\tantimicrobial_agent\tcoverage_percentage\tcoverage_depth\tcoverage_ratio\tdrug_class\tinput_gene_length\tinput_gene_start\tinput_gene_stop\tinput_protein_length\tinput_protein_start\tinput_protein_stop\tinput_sequence_id\tnucleotide_mutation\tnucleotide_mutation_interpretation\tpredicted_phenotype\tpredicted_phenotype_confidence_level\tamino_acid_mutation\tamino_acid_mutation_interpretation\treference_gene_length\treference_gene_start\treference_gene_stop\treference_protein_length\treference_protein_start\treference_protein_stop\tresistance_mechanism\tstrand_orientation\tsequence_identity\n+HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t191\t223\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t274\t306\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tUGD\tAAC75089.1|FEATURES|ugd|peptide|ugd\tdeeparg_db\t1\tAAC75089.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tpeptide\t\t242\t274\t\t\t\tCAW05ANXX170413:3:1311:9080:27889/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t452\t484\t\t\t\tCAVL1ANXX170419:7:1112:17911:9537/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t428\t471\t\t\t\tCAW05ANXX170413:3:2313:9964:68847/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t81.8\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t277\t\t\t\tCAW05ANXX170413:4:2211:15535:39005/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t125\t156\t\t\t\tCAW05ANXX170413:3:1315:16625:39188/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tCLASS_A\tP30898|FEATURES|class_A|beta-lactam|class_A\tdeeparg_db\t1\tP30898\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t168\t214\t\t\t\tCAW05ANXX170413:4:2110:17870:97415/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1034\t1066\t\t\t\tCAVL1ANXX170419:7:2114:1131:86489/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t84.8\n+HSM7J4M8\tTETW\tCAO78565|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tCAO78565\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t395\t435\t\t\t\tCAW05ANXX170413:2:2115:3176:4503/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETW\tAAL09826|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tAAL09826\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t265\t324\t\t\t\tCAVL1ANXX170419:8:1111:1611:100037/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t91.7\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t448\t480\t\t\t\tCAVL1ANXX170419:7:1301:9203:5016/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1036\t1094\t\t\t\tCAW05ANXX170413:4:2308:19209:54439/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t83.1\n+HSM7J4M8\tTETW\tgi:168258996:gb:ACA23181.1:|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tgi:168258996:gb:ACA23181.1:\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t528\t560\t\t\t\tCAW05ANXX170413:2:2204:11751:81368/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETW\tgi:168258996:gb:ACA23181.1:|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tgi:168258996:gb:ACA23181.1:\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t558\t590\t\t\t\tCAW05ANXX170413:2:2204:11751:81368/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tDFRF\tAAD01868.1|FEATURES|dfrF|diaminopyrimidine|dfrF\tdeeparg_db\t1\tAAD01868.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tdiaminopyrimidin'..b'gb:ACA23181.1:\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t315\t347\t\t\t\tCAW05ANXX170413:3:1314:11295:28913/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t150\t189\t\t\t\tCAW05ANXX170413:3:2205:5211:23750/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t97.5\n+HSM7J4M8\tTET32\tABV82118|FEATURES|tet32|tetracycline|tet32\tdeeparg_db\t1\tABV82118\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t133\t165\t\t\t\tCAVL1ANXX170419:7:1215:13452:55459/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t109\t150\t\t\t\tCAW05ANXX170413:1:1207:3793:26741/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tUGD\tAAC75089.1|FEATURES|ugd|peptide|ugd\tdeeparg_db\t1\tAAC75089.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tpeptide\t\t230\t262\t\t\t\tCAW05ANXX170413:4:2307:19282:72087/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t90.9\n+HSM7J4M8\tERMF\tQ02607|FEATURES|ermF|MLS|ermF\tdeeparg_db\t1\tQ02607\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tMLS\t\t179\t235\t\t\t\tCAW05ANXX170413:4:2209:12378:13125/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tCFXA2\tAY769933.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2\tdeeparg_db\t1\tAY769933.1.gene1.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t145\t174\t\t\t\tCAW05ANXX170413:4:1109:11895:18811/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t432\t463\t\t\t\tCAVL1ANXX170419:7:1104:3594:54825/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.5\n+HSM7J4M8\tCFXA2\tAF118110.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2\tdeeparg_db\t1\tAF118110.1.gene1.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t154\t202\t\t\t\tCAW05ANXX170413:4:2307:3068:73276/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t98.0\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t143\t175\t\t\t\tCAW05ANXX170413:4:1214:2819:98466/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t84.8\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1066\t1101\t\t\t\tCAW05ANXX170413:1:1102:10487:59991/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t80.6\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t578\t610\t\t\t\tCAVL1ANXX170419:8:1106:3865:26466/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t578\t610\t\t\t\tCAVL1ANXX170419:8:1106:3865:26466/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t97\t129\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t21\t53\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1017\t1049\t\t\t\tCAW05ANXX170413:4:2210:5154:42720/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t93.9\n+HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t275\t\t\t\tCAW05ANXX170413:4:2109:16067:23574/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.8\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t547\t579\t\t\t\tCAVL1ANXX170419:8:1310:19520:23144/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t786\t817\t\t\t\tCAW05ANXX170413:2:2307:7561:79956/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.9\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t489\t521\t\t\t\tCAW05ANXX170413:3:2104:12736:98854/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\n'
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/deeparg_hamronize_argnorm_results.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deeparg_hamronize_argnorm_results.tsv Wed Aug 28 20:27:17 2024 +0000
b
b'@@ -0,0 +1,100 @@\n+input_file_name\tgene_symbol\tgene_name\treference_database_name\treference_database_version\treference_accession\tanalysis_software_name\tanalysis_software_version\tgenetic_variation_type\tantimicrobial_agent\tcoverage_percentage\tcoverage_depth\tcoverage_ratio\tdrug_class\tinput_gene_length\tinput_gene_start\tinput_gene_stop\tinput_protein_length\tinput_protein_start\tinput_protein_stop\tinput_sequence_id\tnucleotide_mutation\tnucleotide_mutation_interpretation\tpredicted_phenotype\tpredicted_phenotype_confidence_level\tamino_acid_mutation\tamino_acid_mutation_interpretation\treference_gene_length\treference_gene_start\treference_gene_stop\treference_protein_length\treference_protein_start\treference_protein_stop\tresistance_mechanism\tstrand_orientation\tsequence_identity\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n+HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t191\t223\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t274\t306\t\t\t\tCAVL1ANXX170419:8:1211:20929:16342/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tUGD\tAAC75089.1|FEATURES|ugd|peptide|ugd\tdeeparg_db\t1\tAAC75089.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tpeptide\t\t242\t274\t\t\t\tCAW05ANXX170413:3:1311:9080:27889/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\tARO:3003577\tARO:3000454\tARO:3000053\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t452\t484\t\t\t\tCAVL1ANXX170419:7:1112:17911:9537/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t87.9\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t428\t471\t\t\t\tCAW05ANXX170413:3:2313:9964:68847/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t81.8\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t277\t\t\t\tCAW05ANXX170413:4:2211:15535:39005/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t125\t156\t\t\t\tCAW05ANXX170413:3:1315:16625:39188/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tCLASS_A\tP30898|FEATURES|class_A|beta-lactam|class_A\tdeeparg_db\t1\tP30898\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t168\t214\t\t\t\tCAW05ANXX170413:4:2110:17870:97415/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3002999\tARO:0000032,ARO:3004129\tARO:3000007,ARO:3000007\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1034\t1066\t\t\t\tCAVL1ANXX170419:7:2114:1131:86489/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t84.8\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tTETW\tCAO78565|FEATURES|tetW|tetracycline|tetW\tdeeparg_db\t1\tCAO78565\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t395\t435\t\t\t\tCAW05ANXX170413:2:2115:3176:4503/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000194\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:300'..b'0.1.gene1.p01|FEATURES|CfxA2|beta-lactam|CfxA2\tdeeparg_db\t1\tAF118110.1.gene1.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tbeta-lactam\t\t154\t202\t\t\t\tCAW05ANXX170413:4:2307:3068:73276/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t98.0\tARO:3003002\tARO:0000044\tARO:3000007\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t143\t175\t\t\t\tCAW05ANXX170413:4:1214:2819:98466/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t84.8\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1066\t1101\t\t\t\tCAW05ANXX170413:1:1102:10487:59991/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t80.6\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t578\t610\t\t\t\tCAVL1ANXX170419:8:1106:3865:26466/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t578\t610\t\t\t\tCAVL1ANXX170419:8:1106:3865:26466/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t97\t129\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t21\t53\t\t\t\tCAW05ANXX170413:3:1307:3879:36407/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t1017\t1049\t\t\t\tCAW05ANXX170413:4:2210:5154:42720/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t93.9\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tTETQ\tZP_04557016|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZP_04557016\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t245\t275\t\t\t\tCAW05ANXX170413:4:2109:16067:23574/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.8\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tTETQ\tBAD46890|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tBAD46890\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t547\t579\t\t\t\tCAVL1ANXX170419:8:1310:19520:23144/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+HSM7J4M8\tRPOB2\tBAD59497.1|FEATURES|rpoB2|multidrug|rpoB2\tdeeparg_db\t1\tBAD59497.1\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\tmultidrug\t\t786\t817\t\t\t\tCAW05ANXX170413:2:2307:7561:79956/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t96.9\tARO:3000501\tARO:3000169,ARO:3000517,ARO:3000530,ARO:3000534\tARO:3000157,ARO:3000157,ARO:3000157,ARO:3000157\n+HSM7J4M8\tTETQ\tZ21523.gene.p01|FEATURES|tetQ|tetracycline|tetQ\tdeeparg_db\t1\tZ21523.gene.p01\tdeeparg\t1.0.2\tgene_presence_detected\t\t\t\t\ttetracycline\t\t489\t521\t\t\t\tCAW05ANXX170413:3:2104:12736:98854/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t100.0\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n'
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/groot-resfinder-results.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groot-resfinder-results.tsv Wed Aug 28 20:27:17 2024 +0000
b
b'@@ -0,0 +1,29 @@\n+0\t1\t2\t3\tARO\tconfers_resistance_to\tresistance_to_drug_classes\n+erm(G)_1_M15332\t70\t735\t240M19D121M99D173M83D\tARO:3000522\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_15_U48430\t107\t753\t11D287M63D196M22D89M85D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_6_AF242872\t155\t747\t11D299M51D312M74D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_21_U35228\t125\t738\t53D163M145D363M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_10_U86375\t143\t738\t11D205M145D363M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_11_M19270\t112\t738\t11D205M2D73M70D127M12D224M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+lnu(C)_1_AY928180\t41\t495\t51D277M14D148M5D\tARO:3002837\tARO:0000046\tARO:0000017\n+erm(B)_2_K00551\t126\t738\t5'..b'ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(B)_7_AF368302\t146\t711\t11D287M63D312M38D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+erm(F)_3_M17808\t38\t801\t11D358M35D103M57D181M56D\tARO:3000498\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+tet(W)_6_FN396364\t68\t1920\t3D634M36D576M22D251M398D\t\t\t\n+tet(O)_1_M18896\t66\t1920\t1D169M43D422M63D171M300D750M1D\tARO:3000190\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+ant(6)-Ia_3_KF864551\t407\t867\t1D854M12D\tARO:3002629\tARO:0000040\tARO:0000016\n+tet(Q)_3_U73497\t293\t2013\t13D495M62D267M274D238M70D117M17D124M336D\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+tet(Q)_4_Z21523\t294\t1974\t13D495M62D267M58D71M145D238M70D117M17D124M297D\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+erm(B)_1_JN899585\t163\t738\t11D287M63D363M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+tet(W)_4_AJ427422\t127\t1920\t3D1900M17D\t\t\t\n+erm(B)_12_U18931\t198\t738\t11D713M14D\tARO:3000375\tARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867\tARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026\n+tet(W)_1_DQ060146\t120\t1920\t3D1018M49D833M17D\tARO:3000194\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n+tet(Q)_1_L33696\t2132\t1926\t1D708M3D334M2D874M4D\tARO:3000191\tARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668\tARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050\n'
b
diff -r 000000000000 -r bae2bc0f1b66 test-data/resfinder_PSM7J199_R2.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/resfinder_PSM7J199_R2.report Wed Aug 28 20:27:17 2024 +0000
b
@@ -0,0 +1,28 @@
+erm(G)_1_M15332 70 735 240M19D121M99D173M83D
+erm(B)_15_U48430 107 753 11D287M63D196M22D89M85D
+erm(B)_6_AF242872 155 747 11D299M51D312M74D
+erm(B)_21_U35228 125 738 53D163M145D363M14D
+erm(B)_10_U86375 143 738 11D205M145D363M14D
+erm(B)_11_M19270 112 738 11D205M2D73M70D127M12D224M14D
+lnu(C)_1_AY928180 41 495 51D277M14D148M5D
+erm(B)_2_K00551 126 738 53D143M28D158M36D306M14D
+tet(O)_2_M20925 73 1920 213D283M62D361M118D109M23D750M1D
+erm(B)_18_X66468 125 762 77D163M145D363M14D
+tet(Q)_2_X58717 218 1926 1D179M21D149M30D461M163D323M44D102M32D124M163D111M23D
+tet(O)_3_Y07780 56 1920 213D193M58D171M66D113M138D194M105D112M59D251M77D169M1D
+erm(F)_2_M17124 36 801 11D358M35D103M137D101M56D
+tet(W)_5_AJ427421 111 1920 3D1682M47D171M17D
+tetO_4_AIOQ01000025 64 1920 1D169M43D656M300D571M44D135M1D
+erm(B)_9_AF299292 164 738 11D205M8D500M14D
+erm(B)_7_AF368302 146 711 11D287M63D312M38D
+erm(F)_3_M17808 38 801 11D358M35D103M57D181M56D
+tet(W)_6_FN396364 68 1920 3D634M36D576M22D251M398D
+tet(O)_1_M18896 66 1920 1D169M43D422M63D171M300D750M1D
+ant(6)-Ia_3_KF864551 407 867 1D854M12D
+tet(Q)_3_U73497 293 2013 13D495M62D267M274D238M70D117M17D124M336D
+tet(Q)_4_Z21523 294 1974 13D495M62D267M58D71M145D238M70D117M17D124M297D
+erm(B)_1_JN899585 163 738 11D287M63D363M14D
+tet(W)_4_AJ427422 127 1920 3D1900M17D
+erm(B)_12_U18931 198 738 11D713M14D
+tet(W)_1_DQ060146 120 1920 3D1018M49D833M17D
+tet(Q)_1_L33696 2132 1926 1D708M3D334M2D874M4D