Repository 'cmsearch_deoverlap'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap

Changeset 1:3fd3be28a04c (2024-03-18)
Previous changeset 0:54b16c794341 (2023-08-19) Next changeset 2:874ad23526a0 (2024-03-18)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap commit a9df96eec1bfb4e4d61926b02e8847babd1187ad-dirty
modified:
cmsearch-deoverlap.xml
test-data/1.cmsearch.tblout
test-data/1.cmsearch.tblout.deoverlapped
test-data/1.cmsearch.tblout.sort
b
diff -r 54b16c794341 -r 3fd3be28a04c cmsearch-deoverlap.xml
--- a/cmsearch-deoverlap.xml Sat Aug 19 05:37:02 2023 +0000
+++ b/cmsearch-deoverlap.xml Mon Mar 18 09:34:56 2024 +0000
[
@@ -1,4 +1,4 @@
-<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy0" profile="21.05">
+<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy1" profile="21.05">
     <description>removes lower scoring overlaps from cmsearch results</description>
     <requirements>
         <requirement type="package" version="5.26">perl</requirement>
@@ -13,10 +13,12 @@
         #end if
         #if $dirty:
             $dirty &&
-            mv *.sort '$matches_sort'
+            sed 's/[:blank:]+/,/g' cmsearch_matches.sort > cmsearch_matches.sort.tabular &&
+            mv cmsearch_matches.sort.tabular '$matches_sort'
         #end if
         &&
-        mv *.deoverlapped '$deoverlapped_matches'
+        sed 's/[:blank:]+/,/g' cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular &&
+        mv cmsearch_matches.deoverlapped.tabular '$deoverlapped_matches'
 
     ]]></command>
     <inputs>
b
diff -r 54b16c794341 -r 3fd3be28a04c test-data/1.cmsearch.tblout
--- a/test-data/1.cmsearch.tblout Sat Aug 19 05:37:02 2023 +0000
+++ b/test-data/1.cmsearch.tblout Mon Mar 18 09:34:56 2024 +0000
[
b'@@ -1,983 +1,983 @@\n-#target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target\n-#------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------\n-contig--95399        -         5S_rRNA              RF00001   hmm        3      116      465      575      +     -    6 0.55   0.0   53.3     5e-12 !   -\n-contig--3320537      -         5S_rRNA              RF00001   hmm        4      115      219      329      +     -    6 0.55   0.0   50.4   4.2e-11 !   -\n-contig--2298625      -         5S_rRNA              RF00001   hmm        6      113      132       24      -     -    6 0.57   0.0   47.0   4.6e-10 !   -\n-contig--397992       -         5S_rRNA              RF00001   hmm        4      116     3051     3160      +     -    6 0.63   0.0   43.6   5.4e-09 !   -\n-contig--3348019      -         5_8S_rRNA            RF00002   hmm        1      153      559      711      +     -    6 0.48   0.0  116.0     2e-31 !   -\n-contig--3980131      -         5_8S_rRNA            RF00002   hmm        1      153      257      408      +     -    6 0.49   0.0  101.2   8.4e-27 !   -\n-contig--2250940      -         5_8S_rRNA            RF00002   hmm        1      153      239      390      +     -    6 0.50   0.0   98.9   4.2e-26 !   -\n-contig--364625       -         SSU_rRNA_bacteria    RF00177   hmm       18      957      954        2      -     -    6 0.52   5.2  654.3  1.7e-194 !   -\n-contig--2249925      -         SSU_rRNA_bacteria    RF00177   hmm       19      914        2      898      +     -    6 0.50   5.7  638.4  1.1e-189 !   -\n-contig--2255364      -         SSU_rRNA_bacteria    RF00177   hmm      325     1084      765        1      -     -    6 0.52   3.9  624.0  2.5e-185 !   -\n-contig--2369838      -         SSU_rRNA_bacteria    RF00177   hmm       90      938       20      855      +     -    6 0.52   7.0  609.3  6.6e-181 !   -\n-contig--2271497      -         SSU_rRNA_bacteria    RF00177   hmm        4      812      835        2      -     -    6 0.51   5.0  597.5  2.5e-177 !   -\n-contig--3568828      -         SSU_rRNA_bacteria    RF00177   hmm      311      991      670        5      -     -    6 0.55   4.2  575.6    1e-170 !   -\n-contig--1568447      -         SSU_rRNA_bacteria    RF00177   hmm      291      968        2      684      +     -    6 0.52   5.6  574.2  2.6e-170 !   -\n-contig--2506583      -         SSU_rRNA_bacteria    RF00177   hmm      483     1531        4     1047      +     -    6 0.54   3.6  551.4  2.1e-163 !   -\n-contig--2914153      -         SSU_rRNA_bacteria    RF00177   hmm      139      936      799        1      -     -    6 0.50   4.5  551.2  2.4e-163 !   -\n-contig--3474644      -         SSU_rRNA_bacteria    RF00177   hmm        5      760       51      832      +     -    6 0.51   4.6  526.5  6.8e-156 !   -\n-contig--2972876      -         SSU_rRNA_bacteria    RF00177   hmm      320      925      614        1      -     -    6 0.52   4.1  481.4  2.9e-142 !   -\n-contig--365127       -         SSU_rRNA_bacteria    RF00177   hmm      343      925      567        1      -     -    6 0.56   4.3  478.1    3e-141 !   -\n-contig--363722       -         SSU_rRNA_bacteria    RF00177   hmm      347      918      579        1      -     -    6 0.51   2.5  462.7  1.4e-136 !   -\n-contig--498568       -         SSU_rRNA_bacteria    RF00177   hmm      895     1410      516        2      -     -    6 0.53   0.0  453.1    1e-133 !   -\n-contig--401056       -         SSU_rRNA_bacteria    RF00177   hmm     1024     1532       17      525      +     -    6 0.53   0.1  435.4  2.3e-128 !   -\n-contig--2491978      -         SSU_rRNA_bacteria    RF00177   hmm       11     1084     1024        1      -     -    6 0.54   4.9  434.2  5.3e-128 !   -\n-contig--1720439      -         SSU_rRNA_bacteria    RF00177   h'..b'ontig--3146147\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t345\t663\t421\t1\t-\t-\t6\t0.49\t0.0\t67.7\t3.5e-18\t!\t-\n+contig--1502032\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t3093\t3399\t308\t30\t-\t-\t6\t0.45\t0.0\t67.4\t4.3e-18\t!\t-\n+contig--1111206\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t11\t323\t289\t1\t-\t-\t6\t0.42\t3.2\t66.7\t7e-18\t!\t-\n+contig--365471\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2252\t2503\t1\t279\t+\t-\t6\t0.47\t0.1\t66.6\t7.5e-18\t!\t-\n+contig--2879574\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t340\t458\t1\t117\t+\t-\t6\t0.43\t0.0\t66.0\t1.1e-17\t!\t-\n+contig--332136\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2827\t2983\t487\t331\t-\t-\t6\t0.58\t0.0\t66.0\t1.2e-17\t!\t-\n+contig--3748912\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t799\t1072\t275\t10\t-\t-\t6\t0.47\t0.3\t65.8\t1.3e-17\t!\t-\n+contig--147097\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2942\t3187\t4\t244\t+\t-\t6\t0.52\t0.0\t65.2\t1.9e-17\t!\t-\n+contig--2874819\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2281\t2665\t359\t3\t-\t-\t6\t0.57\t0.0\t65.1\t2.2e-17\t!\t-\n+contig--95399\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2947\t3198\t5\t259\t+\t-\t6\t0.55\t0.1\t64.1\t4.3e-17\t!\t-\n+contig--2918607\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t306\t439\t415\t283\t-\t-\t6\t0.44\t0.6\t63.3\t7.2e-17\t!\t-\n+contig--1796896\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2948\t3185\t2\t241\t+\t-\t6\t0.51\t0.0\t63.2\t8e-17\t!\t-\n+contig--942031\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2919\t3151\t306\t69\t-\t-\t6\t0.55\t0.0\t62.6\t1.2e-16\t!\t-\n+contig--2254163\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t16\t335\t304\t2\t-\t-\t6\t0.38\t5.7\t62.5\t1.3e-16\t!\t-\n+contig--2835645\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2943\t3167\t303\t77\t-\t-\t6\t0.55\t0.0\t62.3\t1.5e-16\t!\t-\n+contig--2252929\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2129\t2312\t194\t5\t-\t-\t6\t0.49\t0.0\t60.4\t5.7e-16\t!\t-\n+contig--747483\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2911\t3160\t332\t79\t-\t-\t6\t0.54\t0.0\t58.6\t2e-15\t!\t-\n+contig--2255132\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t16\t236\t118\t325\t+\t-\t6\t0.37\t2.9\t58.4\t2.2e-15\t!\t-\n+contig--2254117\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t305\t437\t19\t152\t+\t-\t6\t0.48\t0.1\t58.3\t2.4e-15\t!\t-\n+contig--2634789\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1405\t1960\t1086\t580\t-\t-\t6\t0.49\t1.3\t58.2\t2.6e-15\t!\t-\n+contig--3925448\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t175\t460\t23\t294\t+\t-\t6\t0.38\t7.7\t56.8\t6.8e-15\t!\t-\n+contig--236053\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t17\t269\t248\t45\t-\t-\t6\t0.44\t1.0\t56.0\t1.2e-14\t!\t-\n+contig--2918607\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t806\t969\t177\t15\t-\t-\t6\t0.47\t0.1\t55.5\t1.7e-14\t!\t-\n+contig--2251329\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2950\t3195\t3\t252\t+\t-\t6\t0.49\t0.1\t53.8\t5.5e-14\t!\t-\n+contig--2713352\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1419\t1947\t507\t19\t-\t-\t6\t0.51\t0.3\t53.4\t7.2e-14\t!\t-\n+contig--2220335\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2133\t2312\t200\t5\t-\t-\t6\t0.48\t0.0\t53.3\t7.9e-14\t!\t-\n+contig--3433834\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1508\t1962\t2\t414\t+\t-\t6\t0.47\t0.1\t53.1\t9e-14\t!\t-\n+contig--1326571\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t792\t1036\t35\t270\t+\t-\t6\t0.50\t0.0\t52.9\t1e-13\t!\t-\n+contig--2646754\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1272\t1930\t1\t591\t+\t-\t6\t0.51\t0.8\t52.6\t1.3e-13\t!\t-\n+contig--473422\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t18\t224\t198\t2\t-\t-\t6\t0.54\t0.0\t52.0\t1.9e-13\t!\t-\n+contig--2564558\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t317\t455\t1\t140\t+\t-\t6\t0.44\t0.1\t52.0\t1.9e-13\t!\t-\n+contig--3694746\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t791\t966\t184\t10\t-\t-\t6\t0.50\t0.1\t51.0\t3.9e-13\t!\t-\n+contig--3652175\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t792\t967\t185\t11\t-\t-\t6\t0.49\t0.1\t50.8\t4.5e-13\t!\t-\n #\n-# Program:         cmsearch\n-# Version:         1.1.2 (July 2016)\n-# Pipeline mode:   SEARCH\n-# Query file:      ribo.cm\n-# Target file:     50000.1.fa\n-# Option settings: cmsearch -Z 1000 --tblout 1.cmsearch.tblout --noali --cut_ga --hmmonly --cpu 4 ribo.cm 50000.1.fa\n-# Current dir:     /nfs/production/xfam/users/nawrocki/notebook/17_0508_inf_ebi_cmsearch_deoverlap\n-# Date:            Wed May 10 21:28:09 2017\n-# [ok]\n\\ No newline at end of file\n+#\tProgram:\tcmsearch\n+#\tVersion:\t1.1.2\t(July\t2016)\n+#\tPipeline\tmode:\tSEARCH\n+#\tQuery\tfile:\tribo.cm\n+#\tTarget\tfile:\t50000.1.fa\n+#\tOption\tsettings:\tcmsearch\t-Z\t1000\t--tblout\t1.cmsearch.tblout\t--noali\t--cut_ga\t--hmmonly\t--cpu\t4\tribo.cm\t50000.1.fa\n+#\tCurrent\tdir:\t/nfs/production/xfam/users/nawrocki/notebook/17_0508_inf_ebi_cmsearch_deoverlap\n+#\tDate:\tWed\tMay\t10\t21:28:09\t2017\n+#\t[ok]\n\\ No newline at end of file\n'
b
diff -r 54b16c794341 -r 3fd3be28a04c test-data/1.cmsearch.tblout.deoverlapped
--- a/test-data/1.cmsearch.tblout.deoverlapped Sat Aug 19 05:37:02 2023 +0000
+++ b/test-data/1.cmsearch.tblout.deoverlapped Mon Mar 18 09:34:56 2024 +0000
b
b'@@ -1,357 +1,357 @@\n-contig--1001177      -         SSU_rRNA_bacteria    RF00177   hmm      640      954        4      319      +     -    6 0.52   0.8  257.9     1e-74 !   -\n-contig--1003442      -         SSU_rRNA_bacteria    RF00177   hmm       27      355      328        1      -     -    6 0.55   0.7  194.1   1.8e-55 !   -\n-contig--1003814      -         LSU_rRNA_eukarya     RF02543   hmm     1502     1896        1      399      +     -    6 0.51   0.0  227.9   1.7e-66 !   -\n-contig--1007451      -         LSU_rRNA_eukarya     RF02543   hmm     2381     2690        1      308      +     -    6 0.50   0.0  214.7   1.7e-62 !   -\n-contig--10143        -         LSU_rRNA_bacteria    RF02541   hmm      858     1739      800        1      -     -    6 0.49   3.4  446.1  4.8e-132 !   -\n-contig--101864       -         LSU_rRNA_eukarya     RF02543   hmm       33      358      310        2      -     -    6 0.48   0.1  184.9   1.6e-53 !   -\n-contig--1029476      -         SSU_rRNA_bacteria    RF00177   hmm      832     1348      174      700      +     -    6 0.44   0.0  368.0  5.4e-108 !   -\n-contig--1031478      -         LSU_rRNA_bacteria    RF02541   hmm     1347     1717      372        1      -     -    6 0.54   0.5  177.9   3.7e-51 !   -\n-contig--1040384      -         LSU_rRNA_bacteria    RF02541   hmm      832     1566      774       40      -     -    6 0.44   3.4  425.7  6.7e-126 !   -\n-contig--1042219      -         LSU_rRNA_bacteria    RF02541   hmm     2100     2435      339        2      -     -    6 0.55   0.5  215.9   1.3e-62 !   -\n-contig--1082627      -         LSU_rRNA_bacteria    RF02541   hmm     2498     2842        1      334      +     -    6 0.54   0.1  314.4   2.6e-92 !   -\n-contig--1085416      -         SSU_rRNA_bacteria    RF00177   hmm      124      547      392        1      -     -    6 0.49   0.1  263.5   2.1e-76 !   -\n-contig--108732       -         LSU_rRNA_eukarya     RF02543   hmm     1486     1885        1      403      +     -    6 0.57   0.0  216.5   4.7e-63 !   -\n-contig--1089773      -         LSU_rRNA_eukarya     RF02543   hmm     2963     3385      403        6      -     -    6 0.49   0.0  152.2   1.2e-43 !   -\n-contig--1098909      -         SSU_rRNA_eukarya     RF01960   hmm      596      928      314        1      -     -    6 0.45   0.2  115.9   4.3e-32 !   -\n-contig--110110       -         LSU_rRNA_eukarya     RF02543   hmm       13      341        2      321      +     -    6 0.42   2.9  181.4   1.9e-52 !   -\n-contig--1111206      -         LSU_rRNA_bacteria    RF02541   hmm       84      472      360        2      -     -    6 0.42   1.9  190.5   5.9e-55 !   -\n-contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      844      966        1      122      +     -    6 0.52   0.0  110.0   6.1e-31 !   -\n-contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      914     1051      183      321      +     -    6 0.47   0.0  105.8   1.1e-29 !   -\n-contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      922     1052      342      469      +     -    6 0.50   0.0   92.7     1e-25 !   -\n-contig--1133023      -         LSU_rRNA_eukarya     RF02543   hmm     1590     2115        9      557      +     -    6 0.56   0.0  261.0   1.9e-76 !   -\n-contig--1149779      -         SSU_rRNA_bacteria    RF00177   hmm     1224     1526      303        2      -     -    6 0.51   0.0  219.3   4.4e-63 !   -\n-contig--1159799      -         LSU_rRNA_eukarya     RF02543   hmm     2940     3340      375        2      -     -    6 0.47   0.0  192.7   7.1e-56 !   -\n-contig--1171145      -         SSU_rRNA_eukarya     RF01960   hmm       23      410        2      365      +     -    6 0.41   0.8  211.7   5.2e-61 !   -\n-contig--1176662      -         LSU_rRNA_bacteria    RF02541   hmm     2436     2727        2      293      +     -    6 0.49   0.0  222.3   1.5e-64 !   -\n-contig--1187407      -         LSU_rRNA_eukarya     RF02543   hmm      930     1237      305        1  '..b'-\t6\t0.57\t30.5\t2226.7\t0\t!\t-\n+contig--397992\t-\t5S_rRNA\tRF00001\thmm\t4\t116\t3051\t3160\t+\t-\t6\t0.63\t0.0\t43.6\t5.4e-09\t!\t-\n+contig--3980131\t-\t5_8S_rRNA\tRF00002\thmm\t1\t153\t257\t408\t+\t-\t6\t0.49\t0.0\t101.2\t8.4e-27\t!\t-\n+contig--3980131\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t1783\t1850\t2\t69\t+\t-\t6\t0.44\t0.0\t51.2\t1.4e-12\t!\t-\n+contig--401056\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t3\t1408\t882\t2330\t+\t-\t6\t0.49\t12.7\t974.7\t1.9e-291\t!\t-\n+contig--401056\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t1024\t1532\t17\t525\t+\t-\t6\t0.53\t0.1\t435.4\t2.3e-128\t!\t-\n+contig--4068604\t-\tLSU_rRNA_archaea\tRF02540\thmm\t1162\t1771\t2\t562\t+\t-\t6\t0.53\t2.7\t300.4\t3.5e-88\t!\t-\n+contig--423976\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t85\t1697\t400\t2002\t+\t-\t6\t0.46\t18.0\t884.8\t2.3e-264\t!\t-\n+contig--473422\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t31\t377\t326\t1\t-\t-\t6\t0.56\t2.1\t173.0\t1.1e-49\t!\t-\n+contig--486161\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t930\t1120\t10\t197\t+\t-\t6\t0.32\t0.0\t62.8\t8.9e-16\t!\t-\n+contig--496748\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t36\t332\t1\t303\t+\t-\t6\t0.55\t0.0\t162.3\t1e-46\t!\t-\n+contig--498568\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t895\t1410\t516\t2\t-\t-\t6\t0.53\t0.0\t453.1\t1e-133\t!\t-\n+contig--515926\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1316\t1799\t494\t3\t-\t-\t6\t0.47\t1.0\t277.9\t1.5e-81\t!\t-\n+contig--518767\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t246\t552\t24\t320\t+\t-\t6\t0.45\t3.3\t153.5\t4.9e-44\t!\t-\n+contig--540576\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t48\t383\t341\t2\t-\t-\t6\t0.46\t0.0\t179.2\t6.1e-51\t!\t-\n+contig--547077\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t835\t1141\t307\t1\t-\t-\t6\t0.50\t0.1\t218.3\t2.4e-63\t!\t-\n+contig--577902\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2963\t3198\t1\t235\t+\t-\t6\t0.44\t0.1\t121.1\t2.8e-34\t!\t-\n+contig--579351\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t1147\t1689\t1\t450\t+\t-\t6\t0.38\t0.1\t131.8\t2.9e-37\t!\t-\n+contig--585322\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t1365\t1677\t1\t310\t+\t-\t6\t0.52\t0.1\t116.2\t1.5e-32\t!\t-\n+contig--594041\t-\tSSU_rRNA_archaea\tRF01959\thmm\t34\t358\t2\t320\t+\t-\t6\t0.54\t0.1\t209.1\t3.9e-60\t!\t-\n+contig--64232\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2937\t3375\t1\t398\t+\t-\t6\t0.42\t1.0\t172.8\t7e-50\t!\t-\n+contig--664339\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t597\t990\t380\t1\t-\t-\t6\t0.45\t0.4\t148.1\t8.4e-42\t!\t-\n+contig--664472\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t30\t388\t2\t331\t+\t-\t6\t0.56\t0.4\t213.3\t2.9e-61\t!\t-\n+contig--669436\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t1390\t1751\t368\t2\t-\t-\t6\t0.47\t0.2\t158.7\t2.3e-45\t!\t-\n+contig--68307\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t73\t381\t2\t310\t+\t-\t6\t0.41\t1.2\t138.5\t1.6e-39\t!\t-\n+contig--696001\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t5\t571\t69\t625\t+\t-\t6\t0.49\t0.1\t384.7\t5e-113\t!\t-\n+contig--724357\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t989\t1339\t3\t348\t+\t-\t6\t0.49\t0.8\t236.5\t8e-69\t!\t-\n+contig--747483\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2559\t2899\t332\t2\t-\t-\t6\t0.51\t0.0\t258.7\t1.6e-75\t!\t-\n+contig--759897\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2581\t2910\t1\t318\t+\t-\t6\t0.53\t0.1\t263.6\t5.3e-77\t!\t-\n+contig--808802\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1647\t2125\t2\t466\t+\t-\t6\t0.49\t0.0\t201.0\t2.3e-58\t!\t-\n+contig--813107\t-\tSSU_rRNA_archaea\tRF01959\thmm\t437\t924\t1\t487\t+\t-\t6\t0.55\t3.2\t375.6\t1.9e-110\t!\t-\n+contig--828224\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t202\t735\t7\t519\t+\t-\t6\t0.58\t6.6\t405.3\t3e-119\t!\t-\n+contig--862423\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t929\t1352\t1\t423\t+\t-\t6\t0.52\t0.0\t341.6\t4.9e-100\t!\t-\n+contig--866163\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t21\t324\t310\t1\t-\t-\t6\t0.45\t0.0\t170.6\t2.4e-48\t!\t-\n+contig--912998\t-\tSSU_rRNA_archaea\tRF01959\thmm\t701\t1366\t1\t666\t+\t-\t6\t0.55\t1.3\t526.9\t3.5e-156\t!\t-\n+contig--924893\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t642\t950\t303\t1\t-\t-\t6\t0.51\t0.1\t197.5\t2.6e-57\t!\t-\n+contig--942031\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2566\t2881\t307\t3\t-\t-\t6\t0.54\t0.1\t240.5\t4.8e-70\t!\t-\n+contig--94612\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t24\t518\t79\t500\t+\t-\t6\t0.28\t0.3\t87.3\t8.1e-24\t!\t-\n+contig--95399\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2591\t2923\t1\t336\t+\t-\t6\t0.53\t0.3\t253.9\t4.4e-74\t!\t-\n+contig--95399\t-\t5S_rRNA\tRF00001\thmm\t3\t116\t465\t575\t+\t-\t6\t0.55\t0.0\t53.3\t5e-12\t!\t-\n+contig--97491\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2434\t2863\t2\t424\t+\t-\t6\t0.46\t0.2\t317.7\t1.5e-93\t!\t-\n+contig--978828\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t1151\t1521\t341\t2\t-\t-\t6\t0.45\t0.0\t301.7\t3.4e-88\t!\t-\n+contig--984009\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t3\t285\t284\t1\t-\t-\t6\t0.45\t0.0\t152.1\t9.3e-43\t!\t-\n'
b
diff -r 54b16c794341 -r 3fd3be28a04c test-data/1.cmsearch.tblout.sort
--- a/test-data/1.cmsearch.tblout.sort Sat Aug 19 05:37:02 2023 +0000
+++ b/test-data/1.cmsearch.tblout.sort Mon Mar 18 09:34:56 2024 +0000
b
b'@@ -1,971 +1,971 @@\n-contig--1001177      -         SSU_rRNA_bacteria    RF00177   hmm      640      954        4      319      +     -    6 0.52   0.8  257.9     1e-74 !   -\n-contig--1001177      -         SSU_rRNA_archaea     RF01959   hmm      591      909        4      318      +     -    6 0.52   0.8  177.2   1.7e-50 !   -\n-contig--1001177      -         SSU_rRNA_microsporidia RF02542   hmm      531      832       12      319      +     -    6 0.52   0.8  121.6   1.8e-33 !   -\n-contig--1001177      -         SSU_rRNA_eukarya     RF01960   hmm      892     1209       15      319      +     -    6 0.52   0.4  113.2   2.9e-31 !   -\n-contig--1003442      -         SSU_rRNA_bacteria    RF00177   hmm       27      355      328        1      -     -    6 0.55   0.7  194.1   1.8e-55 !   -\n-contig--1003442      -         SSU_rRNA_archaea     RF01959   hmm       37      338      314        2      -     -    6 0.56   0.6   83.8   2.9e-22 !   -\n-contig--1003814      -         LSU_rRNA_eukarya     RF02543   hmm     1502     1896        1      399      +     -    6 0.51   0.0  227.9   1.7e-66 !   -\n-contig--1007451      -         LSU_rRNA_eukarya     RF02543   hmm     2381     2690        1      308      +     -    6 0.50   0.0  214.7   1.7e-62 !   -\n-contig--1007451      -         LSU_rRNA_archaea     RF02540   hmm     2152     2407       15      307      +     -    6 0.51   0.0   67.8     5e-18 !   -\n-contig--1007451      -         LSU_rRNA_bacteria    RF02541   hmm     2078     2337       21      307      +     -    6 0.50   0.0   55.5   3.1e-14 !   -\n-contig--10143        -         LSU_rRNA_bacteria    RF02541   hmm      858     1739      800        1      -     -    6 0.49   3.4  446.1  4.8e-132 !   -\n-contig--10143        -         LSU_rRNA_archaea     RF02540   hmm      937     1546      798      202      -     -    6 0.49   0.9  234.0   3.5e-68 !   -\n-contig--10143        -         LSU_rRNA_eukarya     RF02543   hmm     1139     1634      655      203      -     -    6 0.49   1.2   92.5   1.2e-25 !   -\n-contig--101864       -         LSU_rRNA_eukarya     RF02543   hmm       33      358      310        2      -     -    6 0.48   0.1  184.9   1.6e-53 !   -\n-contig--101864       -         LSU_rRNA_archaea     RF02540   hmm      177      500      307        2      -     -    6 0.48   0.1  100.9   4.9e-28 !   -\n-contig--101864       -         LSU_rRNA_bacteria    RF02541   hmm      196      509      307        1      -     -    6 0.48   0.1   82.5   2.2e-22 !   -\n-contig--1029476      -         SSU_rRNA_bacteria    RF00177   hmm      832     1348      174      700      +     -    6 0.44   0.0  368.0  5.4e-108 !   -\n-contig--1029476      -         SSU_rRNA_archaea     RF01959   hmm      790     1300      177      697      +     -    6 0.44   0.0  249.5   2.3e-72 !   -\n-contig--1029476      -         SSU_rRNA_eukarya     RF01960   hmm     1129     1645      217      698      +     -    6 0.44   0.4  178.8   4.4e-51 !   -\n-contig--1029476      -         SSU_rRNA_microsporidia RF02542   hmm      752     1149      217      698      +     -    6 0.44   0.1  130.8     3e-36 !   -\n-contig--1031478      -         LSU_rRNA_bacteria    RF02541   hmm     1347     1717      372        1      -     -    6 0.54   0.5  177.9   3.7e-51 !   -\n-contig--1031478      -         LSU_rRNA_archaea     RF02540   hmm     1435     1814      372        2      -     -    6 0.54   0.3   88.8   2.3e-24 !   -\n-contig--1040384      -         LSU_rRNA_bacteria    RF02541   hmm      832     1566      774       40      -     -    6 0.44   3.4  425.7  6.7e-126 !   -\n-contig--1040384      -         LSU_rRNA_archaea     RF02540   hmm      909     1596      774      115      -     -    6 0.45   0.3  240.5     4e-70 !   -\n-contig--1040384      -         LSU_rRNA_eukarya     RF02543   hmm      935     1648      772      140      -     -    6 0.44   6.7   78.7   1.7e-21 !   -\n-contig--1042219      -         LSU_rRNA_bacteria    RF02541   hmm     2100     2435      339       '..b'g--759897\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2581\t2910\t1\t318\t+\t-\t6\t0.53\t0.1\t263.6\t5.3e-77\t!\t-\n+contig--759897\t-\tLSU_rRNA_archaea\tRF02540\thmm\t2652\t2975\t1\t317\t+\t-\t6\t0.53\t0.1\t150.8\t4.6e-43\t!\t-\n+contig--759897\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2934\t3159\t2\t230\t+\t-\t6\t0.54\t0.0\t70.5\t4.9e-19\t!\t-\n+contig--808802\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t1647\t2125\t2\t466\t+\t-\t6\t0.49\t0.0\t201.0\t2.3e-58\t!\t-\n+contig--813107\t-\tSSU_rRNA_archaea\tRF01959\thmm\t437\t924\t1\t487\t+\t-\t6\t0.55\t3.2\t375.6\t1.9e-110\t!\t-\n+contig--813107\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t499\t967\t13\t486\t+\t-\t6\t0.55\t2.4\t249.9\t2.6e-72\t!\t-\n+contig--813107\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t379\t846\t8\t487\t+\t-\t6\t0.55\t0.6\t198.7\t8.9e-57\t!\t-\n+contig--813107\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t886\t1224\t159\t488\t+\t-\t6\t0.56\t0.2\t142.6\t3.8e-40\t!\t-\n+contig--828224\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t202\t735\t7\t519\t+\t-\t6\t0.58\t6.6\t405.3\t3e-119\t!\t-\n+contig--828224\t-\tSSU_rRNA_archaea\tRF01959\thmm\t187\t685\t6\t518\t+\t-\t6\t0.58\t7.3\t197.8\t9.8e-57\t!\t-\n+contig--828224\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t153\t618\t20\t519\t+\t-\t6\t0.59\t2.1\t101.9\t1.6e-27\t!\t-\n+contig--828224\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t301\t642\t27\t365\t+\t-\t6\t0.57\t0.0\t53.7\t2.6e-13\t!\t-\n+contig--862423\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t929\t1352\t1\t423\t+\t-\t6\t0.52\t0.0\t341.6\t4.9e-100\t!\t-\n+contig--862423\t-\tSSU_rRNA_archaea\tRF01959\thmm\t887\t1306\t3\t422\t+\t-\t6\t0.52\t0.0\t203.9\t1.4e-58\t!\t-\n+contig--862423\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t1186\t1650\t3\t422\t+\t-\t6\t0.52\t0.0\t131.4\t9.1e-37\t!\t-\n+contig--862423\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t809\t1154\t3\t422\t+\t-\t6\t0.52\t0.0\t91.9\t1.7e-24\t!\t-\n+contig--866163\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t21\t324\t310\t1\t-\t-\t6\t0.45\t0.0\t170.6\t2.4e-48\t!\t-\n+contig--866163\t-\tSSU_rRNA_archaea\tRF01959\thmm\t30\t308\t295\t1\t-\t-\t6\t0.44\t0.0\t79.1\t7.5e-21\t!\t-\n+contig--912998\t-\tSSU_rRNA_archaea\tRF01959\thmm\t701\t1366\t1\t666\t+\t-\t6\t0.55\t1.3\t526.9\t3.5e-156\t!\t-\n+contig--912998\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t752\t1411\t3\t666\t+\t-\t6\t0.55\t0.5\t377.0\t1e-110\t!\t-\n+contig--912998\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t992\t1701\t2\t657\t+\t-\t6\t0.55\t0.0\t288.0\t4.6e-84\t!\t-\n+contig--912998\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t634\t1210\t2\t664\t+\t-\t6\t0.55\t0.0\t240.1\t2.7e-69\t!\t-\n+contig--924893\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t642\t950\t303\t1\t-\t-\t6\t0.51\t0.1\t197.5\t2.6e-57\t!\t-\n+contig--924893\t-\tLSU_rRNA_archaea\tRF02540\thmm\t647\t917\t296\t10\t-\t-\t6\t0.52\t0.1\t83.8\t7.5e-23\t!\t-\n+contig--942031\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2566\t2881\t307\t3\t-\t-\t6\t0.54\t0.1\t240.5\t4.8e-70\t!\t-\n+contig--942031\t-\tLSU_rRNA_archaea\tRF02540\thmm\t2637\t2934\t307\t8\t-\t-\t6\t0.55\t0.1\t160.7\t4.7e-46\t!\t-\n+contig--942031\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2919\t3151\t306\t69\t-\t-\t6\t0.55\t0.0\t62.6\t1.2e-16\t!\t-\n+contig--94612\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t24\t518\t79\t500\t+\t-\t6\t0.28\t0.3\t87.3\t8.1e-24\t!\t-\n+contig--95399\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2591\t2923\t1\t336\t+\t-\t6\t0.53\t0.3\t253.9\t4.4e-74\t!\t-\n+contig--95399\t-\tLSU_rRNA_archaea\tRF02540\thmm\t2663\t2982\t2\t329\t+\t-\t6\t0.53\t0.3\t141.3\t3.3e-40\t!\t-\n+contig--95399\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2947\t3198\t5\t259\t+\t-\t6\t0.55\t0.1\t64.1\t4.3e-17\t!\t-\n+contig--95399\t-\t5S_rRNA\tRF00001\thmm\t3\t116\t465\t575\t+\t-\t6\t0.55\t0.0\t53.3\t5e-12\t!\t-\n+contig--97491\t-\tLSU_rRNA_eukarya\tRF02543\thmm\t2434\t2863\t2\t424\t+\t-\t6\t0.46\t0.2\t317.7\t1.5e-93\t!\t-\n+contig--97491\t-\tLSU_rRNA_archaea\tRF02540\thmm\t2194\t2580\t5\t422\t+\t-\t6\t0.46\t0.0\t126.2\t1.1e-35\t!\t-\n+contig--97491\t-\tLSU_rRNA_bacteria\tRF02541\thmm\t2116\t2510\t7\t423\t+\t-\t6\t0.46\t0.0\t92.2\t2.6e-25\t!\t-\n+contig--978828\t-\tSSU_rRNA_eukarya\tRF01960\thmm\t1151\t1521\t341\t2\t-\t-\t6\t0.45\t0.0\t301.7\t3.4e-88\t!\t-\n+contig--978828\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t774\t1059\t341\t2\t-\t-\t6\t0.45\t0.0\t157.5\t2.5e-44\t!\t-\n+contig--978828\t-\tSSU_rRNA_archaea\tRF01959\thmm\t852\t1184\t341\t2\t-\t-\t6\t0.45\t0.0\t128.7\t7.6e-36\t!\t-\n+contig--978828\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t897\t1229\t341\t2\t-\t-\t6\t0.45\t0.0\t96.6\t5.4e-26\t!\t-\n+contig--984009\t-\tSSU_rRNA_bacteria\tRF00177\thmm\t3\t285\t284\t1\t-\t-\t6\t0.45\t0.0\t152.1\t9.3e-43\t!\t-\n+contig--984009\t-\tSSU_rRNA_archaea\tRF01959\thmm\t7\t269\t275\t1\t-\t-\t6\t0.46\t0.0\t97.6\t1.9e-26\t!\t-\n+contig--984009\t-\tSSU_rRNA_microsporidia\tRF02542\thmm\t5\t219\t277\t2\t-\t-\t6\t0.46\t0.0\t53.2\t8.5e-13\t!\t-\n'