| Previous changeset 0:09b7b0b2e2c2 (2022-06-27) Next changeset 2:824497684a1f (2022-10-31) |
|
Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee |
|
modified:
macro.xml recentrifuge.xml test-data/centrifuge_test/test2_csv.log test-data/centrifuge_test/test2_csv.rcf.data.csv test-data/centrifuge_test/test2_csv.rcf.stat.csv test-data/kraken_test/test1_csv.log test-data/kraken_test/test1_csv.rcf.data.csv test-data/kraken_test/test1_csv.rcf.html test-data/kraken_test/test1_csv.rcf.stat.csv test-data/kraken_test/test3_rcf.data.tsv test-data/kraken_test/test3_rcf.stat.tsv test-data/kraken_test/test3_tsv.log |
|
added:
test-data/centrifuge_test/centrifuge_1.out test-data/centrifuge_test/centrifuge_2.out test-data/centrifuge_test/test4_rcf.data.tsv test-data/centrifuge_test/test4_rcf.stat.tsv test-data/centrifuge_test/test4_tsv.html |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 macro.xml --- a/macro.xml Mon Jun 27 11:03:22 2022 +0000 +++ b/macro.xml Fri Aug 26 10:57:30 2022 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.9.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[rcf -V]]></version_command> @@ -16,6 +16,16 @@ <requirement type="package" version="@TOOL_VERSION@">recentrifuge</requirement> </requirements> </xml> + <xml name="edam"> + <edam_topics> + <edam_topic>topic_3174</edam_topic> + <edam_topic>topic_3697</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2238</edam_operation> + <edam_operation>operation_3460</edam_operation> + </edam_operations> + </xml> <xml name="input_database"> <section name="database" title="Database type" expanded="true"> <param name="cached_db" label="Cached database with clade-specific marker genes" type="select"> |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 recentrifuge.xml --- a/recentrifuge.xml Mon Jun 27 11:03:22 2022 +0000 +++ b/recentrifuge.xml Fri Aug 26 10:57:30 2022 +0000 |
| [ |
| @@ -7,10 +7,28 @@ <macros> <import>macro.xml</import> </macros> + <expand macro='edam'/> <expand macro='xrefs'/> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ + #import re + #*====================================== + Make a dir with all input files + ======================================*# + mkdir input_dir && + #for $input in $input_file + #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) + #if $file_type.filetype == "centrifuge" + ln -s '$input' 'input_dir/${input_identifier}.out' && + #else if $file_type.filetype == "clark" + ln -s '$input' 'input_dir/${input_identifier}.csv' && + #else if $file_type.filetype == "kraken" + ln -s '$input' 'input_dir/${input_identifier}.krk' && + #else + ln -s '$input' 'input_dir/$input_identifier' && + #end if + #end for #*====================================== database input ======================================*# @@ -19,23 +37,25 @@ #*====================================== Recentrifuge input file ======================================*# + #if $file_type.filetype == "centrifuge" - -f '$input_file' + -f input_dir + #set $default_scoring = 'SHEL' + #else if $file_type.filetype == "kraken" + -k input_dir + #set $default_scoring = 'KRAKEN' + #else if $file_type.filetype == "clark" + -r input_dir #set $default_scoring = 'SHEL' #else if $file_type.filetype == "lmat" - -l '$input_file' + -l input_dir #set $default_scoring = 'LMAT' - #else if $file_type.filetype == "clark" - -r '$input_file' - #set $default_scoring = 'SHEL' - #else if $file_type.filetype == "kraken" - -k '$input_file' - #set $default_scoring = 'KRAKEN' #else if $file_type.filetype == "generic" - -g '$input_file' + -g input_dir --format '$file_type.format' #set $default_scoring = 'GENERIC' #end if + #*====================================== Output options ======================================*# @@ -83,12 +103,12 @@ #*====================================== Log file output ======================================*# - &> $logfile + | tee "$logfile" ]]> </command> <inputs> <!-- INPUT FILES --> - <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/> + <param name="input_file" type="data" format="tabular" multiple="true" optional="false" label="Select taxonomy file tabular formated"/> <conditional name="file_type"> <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)"> <option value="centrifuge">Centrifuge</option> @@ -126,6 +146,7 @@ <option value="TSV" >TSV</option> </param> <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/> + <param name="no_logfile" type="boolean" truevalue="True" falsevalue="False" label="Remove the log file"/> </section> <!-- ADVANCED OPTIONS --> <section name="advanced_option" title="Coarse tuning of algorithm parameters"> @@ -184,7 +205,9 @@ <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report"> <filter> output_option['nohtml'] == False</filter> </data> - <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> + <filter> output_option['no_logfile'] == False </filter> + </data> <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv"> <filter> output_option['extra'] == 'CSV' </filter> </data> @@ -270,6 +293,29 @@ <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/> <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/> </test> + <test expect_num_outputs="3"> <!-- Test sumarized output TEST_4 --> + <section name="database"> + <param name="database_name" value="test-db-2022"/> + </section> + <param name="input_file" value="centrifuge_test/centrifuge.out,centrifuge_test/centrifuge_1.out,centrifuge_test/centrifuge_2.out"/> + <conditional name="file_type"> + <param name="filetype" value="centrifuge"/> + </conditional> + <section name="output_option" > + <param name="extra" value="TSV"/> + <param name="no_logfile" value="True"/> + </section> + <section name="advanced_option"> + <param name="scoring" value="LENGTH"/> + </section> + <section name="more_advanced_option"> + <param name="summary" value="ADD"/> + <param name="strain" value="true"/> + </section> + <output name="data_tsv" file="centrifuge_test/test4_rcf.data.tsv" lines_diff="2"/> + <output name="stat_tsv" file="centrifuge_test/test4_rcf.stat.tsv" lines_diff="2"/> + <output name="html_report" file="centrifuge_test/test4_tsv.html" lines_diff="12"/> + </test> </tests> <help><![CDATA[ **What it does** |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/centrifuge_1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_test/centrifuge_1.out Fri Aug 26 10:57:30 2022 +0000 |
| b |
| b'@@ -0,0 +1,11000 @@\n+readID\tseqID\ttaxID\tscore\t2ndBestScore\thitLength\tqueryLength\tnumMatches\n+M03963:301:000000000-CT5Y5:1:1101:10606:1000\tunclassified\t0\t0\t0\t0\t486\t1\n+M03963:301:000000000-CT5Y5:1:1101:17509:1002\tNZ_KI973153.1\t208224\t38416\t38416\t211\t513\t2\n+M03963:301:000000000-CT5Y5:1:1101:17509:1002\tNZ_AP022126.1\t208224\t38416\t38416\t211\t513\t2\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_AP022126.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_CP082147.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_KI973153.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:20657:1003\tNZ_CP082147.1\t208224\t60516\t0\t261\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:11961:1003\tunclassified\t0\t0\t0\t0\t192\t1\n+M03963:301:000000000-CT5Y5:1:1101:17530:1006\tNZ_CP082147.1\t208224\t31329\t0\t192\t494\t1\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_KI973153.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_CP082147.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_AP022126.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:16099:1007\tNZ_AP022126.1\t208224\t55585\t55585\t299\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:16099:1007\tNZ_KI973153.1\t208224\t55585\t55585\t299\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14350:1007\tNZ_KI973153.1\t208224\t28132\t28132\t220\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14350:1007\tNZ_AP022126.1\t208224\t28132\t28132\t220\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tspecies\t208224\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP050966.1\t158484\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_LR134485.1\t133448\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP044098.1\t1639133\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP073048.1\t1639133\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:16190:1013\tNZ_AP022126.1\t208224\t15665\t0\t207\t208\t1\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_KI973153.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_AP022126.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_CP082147.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:17080:1007\tgenus\t547\t56169\t0\t252\t554\t1\n+M03963:301:000000000-CT5Y5:1:1101:12530:1014\tNZ_KI973153.1\t208224\t15440\t15440\t202\t505\t2\n+M03963:301:000000000-CT5Y5:1:1101:12530:1014\tNZ_AP022126.1\t208224\t15440\t15440\t202\t505\t2\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_KI973153.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_CP082147.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_AP022126.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:10572:1018\tNZ_CP082147.1\t208224\t23741\t3136\t298\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:21652:1019\tNZ_AP022126.1\t208224\t50625\t50625\t240\t548\t2\n+M03963:301:000000000-CT5Y5:1:1101:21652:1019\tNZ_KI973153.1\t208224\t50625\t50625\t240\t548\t2\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_CP082147.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_AP022126.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_KI973153.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_AP022126.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_CP082147.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_KI973153.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:22318:1029\tunclassified\t0\t0\t0\t0\t601\t1\n+M03963:301:000000000-CT5Y5:1:1101:14070:1030\tNZ_CP082147.1\t208224\t36389\t0\t237\t540\t1\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_AP022126.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_CP082147.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_KI973153.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000'..b'00000000-CT5Y5:1:1101:24054:5307\tNZ_CP022525.1\t2908851\t123412\t0\t520\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tfamily\t543\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tgenus\t2100764\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tgenus\t613\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:9413:5315\tNZ_KI973153.1\t208224\t100990\t100990\t546\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:9413:5315\tNZ_AP022126.1\t208224\t100990\t100990\t546\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tfamily\t543\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tgenus\t613\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tgenus\t2100764\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:21823:5318\tNZ_CP082147.1\t208224\t70688\t0\t406\t406\t1\n+M03963:301:000000000-CT5Y5:1:1101:24209:5321\tNZ_CP011863.1\t61645\t13070\t4045\t219\t220\t1\n+M03963:301:000000000-CT5Y5:1:1101:15800:5318\tNZ_AP022126.1\t208224\t49834\t49834\t454\t456\t2\n+M03963:301:000000000-CT5Y5:1:1101:15800:5318\tNZ_KI973153.1\t208224\t49834\t49834\t454\t456\t2\n+M03963:301:000000000-CT5Y5:1:1101:5824:5316\tNZ_AP022126.1\t208224\t56455\t0\t469\t601\t1\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_KI973153.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_AP022126.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_CP082147.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_AP022126.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_KI973153.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_CP082147.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:10058:5318\tNZ_AP022126.1\t208224\t37421\t29988\t442\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:4834:5320\tNZ_CP082147.1\t208224\t65536\t3349\t271\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_AP022126.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_CP082147.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_KI973153.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:24457:5327\tunclassified\t0\t0\t0\t0\t362\t1\n+M03963:301:000000000-CT5Y5:1:1101:23515:5334\tNZ_AP022126.1\t208224\t7938\t7938\t156\t156\t2\n+M03963:301:000000000-CT5Y5:1:1101:23515:5334\tNZ_KI973153.1\t208224\t7938\t7938\t156\t156\t2\n+M03963:301:000000000-CT5Y5:1:1101:8587:5327\tNZ_AP022126.1\t208224\t59226\t59226\t505\t566\t2\n+M03963:301:000000000-CT5Y5:1:1101:8587:5327\tNZ_KI973153.1\t208224\t59226\t59226\t505\t566\t2\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_KI973153.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_AP022126.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_CP082147.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:19382:5328\tNZ_AP022126.1\t208224\t146312\t146312\t570\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:19382:5328\tNZ_CP082147.1\t208224\t146312\t146312\t570\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:18774:5334\tNZ_KI973153.1\t208224\t119538\t119538\t575\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:18774:5334\tNZ_AP022126.1\t208224\t119538\t119538\t575\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:7082:5336\tNZ_CP082147.1\t208224\t9090\t7586\t156\t300\t1\n+M03963:301:000000000-CT5Y5:1:1101:18565:5334\tunclassified\t0\t0\t0\t0\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:5483:5337\tunclassified\t0\t0\t0\t0\t238\t1\n+M03963:301:000000000-CT5Y5:1:1101:20275:5333\tNZ_CP082147.1\t208224\t47075\t0\t492\t600\t1\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t642\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t2100764\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t613\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tfamily\t543\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19048:5331\tNZ_KI973153.1\t208224\t81796\t81796\t301\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:19048:5331\tNZ_AP022126.1\t208224\t81796\t81796\t301\t602\t3\n' |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/centrifuge_2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_test/centrifuge_2.out Fri Aug 26 10:57:30 2022 +0000 |
| b |
| b'@@ -0,0 +1,11000 @@\n+readID\tseqID\ttaxID\tscore\t2ndBestScore\thitLength\tqueryLength\tnumMatches\n+M03963:301:000000000-CT5Y5:1:1101:10606:1000\tunclassified\t0\t0\t0\t0\t486\t1\n+M03963:301:000000000-CT5Y5:1:1101:17509:1002\tNZ_KI973153.1\t208224\t38416\t38416\t211\t513\t2\n+M03963:301:000000000-CT5Y5:1:1101:17509:1002\tNZ_AP022126.1\t208224\t38416\t38416\t211\t513\t2\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_AP022126.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_CP082147.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:16741:1003\tNZ_KI973153.1\t208224\t10513\t10513\t175\t176\t3\n+M03963:301:000000000-CT5Y5:1:1101:20657:1003\tNZ_CP082147.1\t208224\t60516\t0\t261\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:11961:1003\tunclassified\t0\t0\t0\t0\t192\t1\n+M03963:301:000000000-CT5Y5:1:1101:17530:1006\tNZ_CP082147.1\t208224\t31329\t0\t192\t494\t1\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_KI973153.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_CP082147.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:11134:1006\tNZ_AP022126.1\t208224\t81225\t81225\t300\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:16099:1007\tNZ_AP022126.1\t208224\t55585\t55585\t299\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:16099:1007\tNZ_KI973153.1\t208224\t55585\t55585\t299\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14350:1007\tNZ_KI973153.1\t208224\t28132\t28132\t220\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14350:1007\tNZ_AP022126.1\t208224\t28132\t28132\t220\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tspecies\t208224\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP050966.1\t158484\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_LR134485.1\t133448\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP044098.1\t1639133\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:14857:1012\tNZ_CP073048.1\t1639133\t1741\t1741\t89\t90\t5\n+M03963:301:000000000-CT5Y5:1:1101:16190:1013\tNZ_AP022126.1\t208224\t15665\t0\t207\t208\t1\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_KI973153.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_AP022126.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:9353:1014\tNZ_CP082147.1\t208224\t10225\t10225\t173\t174\t3\n+M03963:301:000000000-CT5Y5:1:1101:17080:1007\tgenus\t547\t56169\t0\t252\t554\t1\n+M03963:301:000000000-CT5Y5:1:1101:12530:1014\tNZ_KI973153.1\t208224\t15440\t15440\t202\t505\t2\n+M03963:301:000000000-CT5Y5:1:1101:12530:1014\tNZ_AP022126.1\t208224\t15440\t15440\t202\t505\t2\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_KI973153.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_CP082147.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:14081:1015\tNZ_AP022126.1\t208224\t21013\t21013\t235\t236\t3\n+M03963:301:000000000-CT5Y5:1:1101:10572:1018\tNZ_CP082147.1\t208224\t23741\t3136\t298\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:21652:1019\tNZ_AP022126.1\t208224\t50625\t50625\t240\t548\t2\n+M03963:301:000000000-CT5Y5:1:1101:21652:1019\tNZ_KI973153.1\t208224\t50625\t50625\t240\t548\t2\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_CP082147.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_AP022126.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:15156:1022\tNZ_KI973153.1\t208224\t11552\t11552\t182\t485\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_AP022126.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_CP082147.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:19202:1023\tNZ_KI973153.1\t208224\t24336\t24336\t171\t473\t3\n+M03963:301:000000000-CT5Y5:1:1101:22318:1029\tunclassified\t0\t0\t0\t0\t601\t1\n+M03963:301:000000000-CT5Y5:1:1101:14070:1030\tNZ_CP082147.1\t208224\t36389\t0\t237\t540\t1\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_AP022126.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_CP082147.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000000000-CT5Y5:1:1101:20703:1032\tNZ_KI973153.1\t208224\t4500\t4500\t192\t206\t3\n+M03963:301:000'..b'00000000-CT5Y5:1:1101:24054:5307\tNZ_CP022525.1\t2908851\t123412\t0\t520\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tfamily\t543\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tgenus\t2100764\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:24773:5318\tgenus\t613\t20000\t20000\t230\t230\t3\n+M03963:301:000000000-CT5Y5:1:1101:9413:5315\tNZ_KI973153.1\t208224\t100990\t100990\t546\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:9413:5315\tNZ_AP022126.1\t208224\t100990\t100990\t546\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tfamily\t543\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tgenus\t613\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:6038:5318\tgenus\t2100764\t18818\t18818\t224\t224\t3\n+M03963:301:000000000-CT5Y5:1:1101:21823:5318\tNZ_CP082147.1\t208224\t70688\t0\t406\t406\t1\n+M03963:301:000000000-CT5Y5:1:1101:24209:5321\tNZ_CP011863.1\t61645\t13070\t4045\t219\t220\t1\n+M03963:301:000000000-CT5Y5:1:1101:15800:5318\tNZ_AP022126.1\t208224\t49834\t49834\t454\t456\t2\n+M03963:301:000000000-CT5Y5:1:1101:15800:5318\tNZ_KI973153.1\t208224\t49834\t49834\t454\t456\t2\n+M03963:301:000000000-CT5Y5:1:1101:5824:5316\tNZ_AP022126.1\t208224\t56455\t0\t469\t601\t1\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_KI973153.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_AP022126.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:16336:5322\tNZ_CP082147.1\t208224\t69938\t69938\t404\t404\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_AP022126.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_KI973153.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:18232:5323\tNZ_CP082147.1\t208224\t9522\t9522\t168\t168\t3\n+M03963:301:000000000-CT5Y5:1:1101:10058:5318\tNZ_AP022126.1\t208224\t37421\t29988\t442\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:4834:5320\tNZ_CP082147.1\t208224\t65536\t3349\t271\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_AP022126.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_CP082147.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:10449:5326\tNZ_KI973153.1\t208224\t14600\t14600\t296\t298\t3\n+M03963:301:000000000-CT5Y5:1:1101:24457:5327\tunclassified\t0\t0\t0\t0\t362\t1\n+M03963:301:000000000-CT5Y5:1:1101:23515:5334\tNZ_AP022126.1\t208224\t7938\t7938\t156\t156\t2\n+M03963:301:000000000-CT5Y5:1:1101:23515:5334\tNZ_KI973153.1\t208224\t7938\t7938\t156\t156\t2\n+M03963:301:000000000-CT5Y5:1:1101:8587:5327\tNZ_AP022126.1\t208224\t59226\t59226\t505\t566\t2\n+M03963:301:000000000-CT5Y5:1:1101:8587:5327\tNZ_KI973153.1\t208224\t59226\t59226\t505\t566\t2\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_KI973153.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_AP022126.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:17592:5335\tNZ_CP082147.1\t208224\t38642\t38642\t308\t308\t3\n+M03963:301:000000000-CT5Y5:1:1101:19382:5328\tNZ_AP022126.1\t208224\t146312\t146312\t570\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:19382:5328\tNZ_CP082147.1\t208224\t146312\t146312\t570\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:18774:5334\tNZ_KI973153.1\t208224\t119538\t119538\t575\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:18774:5334\tNZ_AP022126.1\t208224\t119538\t119538\t575\t602\t2\n+M03963:301:000000000-CT5Y5:1:1101:7082:5336\tNZ_CP082147.1\t208224\t9090\t7586\t156\t300\t1\n+M03963:301:000000000-CT5Y5:1:1101:18565:5334\tunclassified\t0\t0\t0\t0\t602\t1\n+M03963:301:000000000-CT5Y5:1:1101:5483:5337\tunclassified\t0\t0\t0\t0\t238\t1\n+M03963:301:000000000-CT5Y5:1:1101:20275:5333\tNZ_CP082147.1\t208224\t47075\t0\t492\t600\t1\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t642\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t2100764\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tgenus\t613\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19208:5335\tfamily\t543\t57122\t57122\t368\t368\t4\n+M03963:301:000000000-CT5Y5:1:1101:19048:5331\tNZ_KI973153.1\t208224\t81796\t81796\t301\t602\t3\n+M03963:301:000000000-CT5Y5:1:1101:19048:5331\tNZ_AP022126.1\t208224\t81796\t81796\t301\t602\t3\n' |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test2_csv.log --- a/test-data/centrifuge_test/test2_csv.log Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/centrifuge_test/test2_csv.log Fri Aug 26 10:57:30 2022 +0000 |
| [ |
| @@ -1,13 +1,14 @@ -=-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +[90mCentrifuge .out files to analyze:[0m ['input_dir/centrifuge_out.out'] [90mLoading NCBI nodes...[0m[92m OK! [0m [90mLoading NCBI names...[0m[92m OK! [0m [90mBuilding dict of parent to children taxa...[0m[92m OK! [0m [90m Please, wait, processing files in parallel... [0m -[90mLoading output file centrifuge.out... [0m[92mOK! +[90mLoading output file input_dir/centrifuge_out.out... [0m[92mOK! [0m[90m Seqs read: [0m10_999 [90m[[0m4.22 Mnt[90m] [0m[90m Seqs clas: [0m10_354 [90m([0m5.86%[90m unclassified) [0m[90m Seqs pass: [0m10_354 [90m([0m0.00%[90m rejected) @@ -19,10 +20,10 @@ Info:[0m 10279 [90madditional seqs discarded ([0m99.276% [90mof accepted) [0m[93m Warning![0m 210 orphan taxids[90m (rerun with --debug for details) -[0mcentrifuge[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.0305[90m sec +[0minput_dir/centrifuge_out[94m sample [0m[92mOK! +[0m[90mLoad elapsed time: [0m0.0337[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m -[90mGenerating csv extra output ([0m[95m[test2_csv.rcf.]*.csv[0m[90m)... [0m[92mOK![0m +[90mGenerating csv extra output ([0m[95m[output.rcf.]*.csv[0m[90m)... [0m[92mOK![0m [90mTotal elapsed time:[0m 00:00:00 |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test2_csv.rcf.data.csv --- a/test-data/centrifuge_test/test2_csv.rcf.data.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/centrifuge_test/test2_csv.rcf.data.csv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -Samples,centrifuge,centrifuge,centrifuge,Details,Details +Samples,input_dir/centrifuge_out,input_dir/centrifuge_out,input_dir/centrifuge_out,Details,Details Stats,count,unassigned,score,Rank,Name Id,,,,, 1,75,0,51.07625068955332,no_rank,root |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test2_csv.rcf.stat.csv --- a/test-data/centrifuge_test/test2_csv.rcf.stat.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/centrifuge_test/test2_csv.rcf.stat.csv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -,centrifuge +,input_dir/centrifuge_out Seqs. read,10999.0 Seqs. unclass.,645.0 Seqs. class.,10354.0 |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test4_rcf.data.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_test/test4_rcf.data.tsv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -0,0 +1,11 @@ +Samples input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_out input_dir/centrifuge_out input_dir/centrifuge_out SHARED_species SHARED_species SHARED_species SHARED_genus SHARED_genus SHARED_genus SHARED_family SHARED_family SHARED_family SHARED_order SHARED_order SHARED_order SHARED_class SHARED_class SHARED_class SHARED_phylum SHARED_phylum SHARED_phylum SHARED_SUMMARY SHARED_SUMMARY SHARED_SUMMARY Details Details +Stats count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score Rank Name +Id +1 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 no_rank root +2 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 superkingdom Bacteria +1224 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 75 440.72856742250906 75 0 440.72856742250906 phylum Proteobacteria +1236 75 2 392.58666666666664 75 2 392.58666666666664 75 2 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 75 440.72856742250906 0 0 -inf 75 2 440.72856742250906 class Gammaproteobacteria +91347 73 6 390.56164383561645 73 6 390.56164383561645 73 6 390.56164383561645 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 73 442.0475236076006 0 0 -inf 0 0 -inf 73 6 442.0475236076006 order Enterobacteriales +543 67 32 400.34328358208955 67 32 400.34328358208955 67 32 400.34328358208955 31 0 488.35483870967744 35 0 489.0032653061224 67 67 446.6581994080768 0 0 -inf 0 0 -inf 0 0 -inf 67 32 446.6581994080768 family Enterobacteriaceae +561 35 4 494.0285714285714 35 4 494.0285714285714 35 4 494.0285714285714 31 0 488.35483870967744 35 35 489.0032653061224 0 0 -inf 0 0 -inf 0 0 -inf 0 0 -inf 35 4 489.0032653061224 genus Escherichia +562 31 31 488.35483870967744 31 31 488.35483870967744 31 31 488.35483870967744 31 31 488.35483870967744 0 0 -inf 0 0 -inf 0 0 -inf 0 0 -inf 0 0 -inf 31 31 488.35483870967744 species Escherichia coli |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test4_rcf.stat.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_test/test4_rcf.stat.tsv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -0,0 +1,16 @@ + input_dir/centrifuge_1_out input_dir/centrifuge_2_out input_dir/centrifuge_out +Seqs. read 10999.0 10999.0 10999.0 +Seqs. unclass. 645.0 645.0 645.0 +Seqs. class. 10354.0 10354.0 10354.0 +Seqs. filtered 10354.0 10354.0 10354.0 +Score min 23.0 23.0 23.0 +Score mean 190.73954464627033 190.73954464627033 190.73954464627033 +Score max 400.1051804377604 400.1051804377604 400.1051804377604 +Length min 70.0 70.0 70.0 +Length mean 387.0 387.0 387.0 +Length max 602.0 602.0 602.0 +Total nt read 4218210.0 4218210.0 4218210.0 +TIDs class. 215.0 215.0 215.0 +TIDs filtered 215.0 215.0 215.0 +TIDs folded 5.0 5.0 5.0 +Score limit |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/centrifuge_test/test4_tsv.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_test/test4_tsv.html Fri Aug 26 10:57:30 2022 +0000 |
| b |
| b'@@ -0,0 +1,6581 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta charset="utf-8"><link rel="shortcut icon" href="data:image/x-icon;base64,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'..b'><val></val><val></val><val></val></unassigned><tid><val href="2">2</val></tid><rank><val>superkingdom</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>440.7</val><val>440.7</val></score><node name="Proteobacteria" href="https://www.google.com/search?q=Proteobacteria"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>75</val><val></val></unassigned><tid><val href="1224">1224</val></tid><rank><val>phylum</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>440.7</val><val>440.7</val></score><node name="Gammaproteobacteria" href="https://www.google.com/search?q=Gammaproteobacteria"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val></val><val>75</val></count><unassigned><val>2</val><val>2</val><val>2</val><val></val><val></val><val></val><val></val><val>75</val><val></val><val>2</val></unassigned><tid><val href="1236">1236</val></tid><rank><val>class</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>0</val><val>440.7</val></score><node name="Enterobacteriales" href="https://www.google.com/search?q=Enterobacteriales"><count><val>73</val><val>73</val><val>73</val><val>31</val><val>35</val><val>67</val><val>73</val><val></val><val></val><val>73</val></count><unassigned><val>6</val><val>6</val><val>6</val><val></val><val></val><val></val><val>73</val><val></val><val></val><val>6</val></unassigned><tid><val href="91347">91347</val></tid><rank><val>order</val></rank><score><val>390.6</val><val>390.6</val><val>390.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>0</val><val>0</val><val>442.0</val></score><node name="Enterobacteriaceae" href="https://www.google.com/search?q=Enterobacteriaceae"><count><val>67</val><val>67</val><val>67</val><val>31</val><val>35</val><val>67</val><val></val><val></val><val></val><val>67</val></count><unassigned><val>32</val><val>32</val><val>32</val><val></val><val></val><val>67</val><val></val><val></val><val></val><val>32</val></unassigned><tid><val href="543">543</val></tid><rank><val>family</val></rank><score><val>400.3</val><val>400.3</val><val>400.3</val><val>488.4</val><val>489.0</val><val>446.7</val><val>0</val><val>0</val><val>0</val><val>446.7</val></score><node name="Escherichia" href="https://www.google.com/search?q=Escherichia"><count><val>35</val><val>35</val><val>35</val><val>31</val><val>35</val><val></val><val></val><val></val><val></val><val>35</val></count><unassigned><val>4</val><val>4</val><val>4</val><val></val><val>35</val><val></val><val></val><val></val><val></val><val>4</val></unassigned><tid><val href="561">561</val></tid><rank><val>genus</val></rank><score><val>494.0</val><val>494.0</val><val>494.0</val><val>488.4</val><val>489.0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>489.0</val></score><node name="Escherichia coli" href="https://www.google.com/search?q=Escherichia coli"><count><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></count><unassigned><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></unassigned><tid><val href="562">562</val></tid><rank><val>species</val></rank><score><val>488.4</val><val>488.4</val><val>488.4</val><val>488.4</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>488.4</val></score></node></node></node></node></node></node></node></node></krona></div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.log --- a/test-data/kraken_test/test1_csv.log Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.log Fri Aug 26 10:57:30 2022 +0000 |
| [ |
| @@ -1,13 +1,14 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.8.1/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +[90mKraken .krk files to analyze:[0m ['input_dir/kraken_out.krk'] [90mLoading NCBI nodes...[0m[92m OK! [0m [90mLoading NCBI names...[0m[92m OK! [0m [90mBuilding dict of parent to children taxa...[0m[92m OK! [0m [90m Please, wait, processing files in parallel... [0m -[90mLoading output file /tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b.dat... [0m[92mOK! +[90mLoading output file input_dir/kraken_out.krk... [0m[92mOK! [0m[90m Seqs read: [0m99 [90m[[0m52.81 knt[90m] [0m[90m Seqs clas: [0m99 [90m([0m0.00%[90m unclassified) [0m[90m Seqs pass: [0m99 [90m([0m0.00%[90m rejected) @@ -20,8 +21,8 @@ Info:[0m 90 [90madditional seqs discarded ([0m90.909% [90mof accepted) [0m[93m Warning![0m 11 orphan taxids[90m (rerun with --debug for details) -[0m/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.0028[90m sec +[0minput_dir/kraken_out[94m sample [0m[92mOK! +[0m[90mLoad elapsed time: [0m0.00392[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.data.csv --- a/test-data/kraken_test/test1_csv.rcf.data.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.data.csv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -Samples,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b,Details,Details +Samples,input_dir/kraken_out,input_dir/kraken_out,input_dir/kraken_out,Details,Details Stats,count,unassigned,score,Rank,Name Id,,,,, 1,9,0,13.614815253856928,no_rank,root |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.html --- a/test-data/kraken_test/test1_csv.rcf.html Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.html Fri Aug 26 10:57:30 2022 +0000 |
| b |
| b'@@ -6578,4 +6578,4 @@\n \t\tselectedNodeLast.getDepth() < selectedNode.getDepth());\n }\n */</script></head><body><img id="hiddenImage" src="data:image/png;base64,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" style="display:none"><img id="loadingImage" src="data:image/gif;base64,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" style="display:none"><img id="logo" src="data:image/png;base64,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'..b'al>9</val></count><unassigned><val></val></unassigned><tid><val href="2">2</val></tid><rank><val>superkingdom</val></rank><score><val>13.6</val></score><node name="Proteobacteria" href="https://www.google.com/search?q=Proteobacteria"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="1224">1224</val></tid><rank><val>phylum</val></rank><score><val>13.6</val></score><node name="Gammaproteobacteria" href="https://www.google.com/search?q=Gammaproteobacteria"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="1236">1236</val></tid><rank><val>class</val></rank><score><val>13.6</val></score><node name="Enterobacteriales" href="https://www.google.com/search?q=Enterobacteriales"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="91347">91347</val></tid><rank><val>order</val></rank><score><val>13.6</val></score><node name="Enterobacteriaceae" href="https://www.google.com/search?q=Enterobacteriaceae"><count><val>9</val></count><unassigned><val>9</val></unassigned><tid><val href="543">543</val></tid><rank><val>family</val></rank><score><val>13.6</val></score></node></node></node></node></node></node></krona></div></body></html>\n\\ No newline at end of file\n+" style="display:none"><noscript>Javascript must be enabled to view this page.</noscript><div style="display:none"><krona collapse="true" key="true" chart="TAXOMIC"><attributes magnitude="count"><attribute display="Count" dataAll="members" tip="Number of reads assigned to this and child taxa">count</attribute><attribute display="Unassigned" dataNode="members" tip="Number of reads assigned specifically to this taxon">unassigned</attribute><attribute display="TaxID" mono="true" hrefBase="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" tip="Taxonomic identifier">tid</attribute><attribute display="Rank" mono="true" tip="Taxonomic rank/level">rank</attribute><attribute display="Kmer coverage (%)" tip="Averaged score of reads assigned to this and child taxa">score</attribute></attributes><datasets rawSamples="1"><dataset isctr="False" sread="99" sclas="99" sfilt="99" scmin="36" scavg="99.94949494949495" scmax="347" lnmin="198 nt" lnavg="533 nt" lnmax="602 nt" tclas="13" tfilt="13" tfold="1" sclim="None" totnt="52.81 knt">input_dir/kraken_out</dataset></datasets><color attribute="score" hueStart="0" hueEnd="300" valueStart="13.6" valueEnd="13.6" default="true"> </color><node name="root" href="https://www.google.com/search?q=root"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="1">1</val></tid><rank><val>no_rank</val></rank><score><val>13.6</val></score><node name="Bacteria" href="https://www.google.com/search?q=Bacteria"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="2">2</val></tid><rank><val>superkingdom</val></rank><score><val>13.6</val></score><node name="Proteobacteria" href="https://www.google.com/search?q=Proteobacteria"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="1224">1224</val></tid><rank><val>phylum</val></rank><score><val>13.6</val></score><node name="Gammaproteobacteria" href="https://www.google.com/search?q=Gammaproteobacteria"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="1236">1236</val></tid><rank><val>class</val></rank><score><val>13.6</val></score><node name="Enterobacteriales" href="https://www.google.com/search?q=Enterobacteriales"><count><val>9</val></count><unassigned><val></val></unassigned><tid><val href="91347">91347</val></tid><rank><val>order</val></rank><score><val>13.6</val></score><node name="Enterobacteriaceae" href="https://www.google.com/search?q=Enterobacteriaceae"><count><val>9</val></count><unassigned><val>9</val></unassigned><tid><val href="543">543</val></tid><rank><val>family</val></rank><score><val>13.6</val></score></node></node></node></node></node></node></krona></div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test1_csv.rcf.stat.csv --- a/test-data/kraken_test/test1_csv.rcf.stat.csv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test1_csv.rcf.stat.csv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -,/tmp/tmpz5ieggzi/files/d/5/5/dataset_d55a31f8-0f74-4938-9a4f-dce196b7467b +,input_dir/kraken_out Seqs. read,99.0 Seqs. unclass.,0.0 Seqs. class.,99.0 |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_rcf.data.tsv --- a/test-data/kraken_test/test3_rcf.data.tsv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_rcf.data.tsv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -Samples /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e Details Details +Samples input_dir/kraken_out input_dir/kraken_out input_dir/kraken_out Details Details Stats count unassigned score Rank Name Id 1 9 0 2.7230463906265316 no_rank root |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_rcf.stat.tsv --- a/test-data/kraken_test/test3_rcf.stat.tsv Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_rcf.stat.tsv Fri Aug 26 10:57:30 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ - /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e + input_dir/kraken_out Seqs. read 99.0 Seqs. unclass. 0.0 Seqs. class. 99.0 |
| b |
| diff -r 09b7b0b2e2c2 -r fe733f05c2f8 test-data/kraken_test/test3_tsv.log --- a/test-data/kraken_test/test3_tsv.log Mon Jun 27 11:03:22 2022 +0000 +++ b/test-data/kraken_test/test3_tsv.log Fri Aug 26 10:57:30 2022 +0000 |
| [ |
| @@ -1,14 +1,15 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.8.1/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= [93mCAUTION![0m --strain experimental mode activated! +[90mKraken .krk files to analyze:[0m ['input_dir/kraken_out.krk'] [90mLoading NCBI nodes...[0m[92m OK! [0m [90mLoading NCBI names...[0m[92m OK! [0m [90mBuilding dict of parent to children taxa...[0m[92m OK! [0m [90m Please, wait, processing files in parallel... [0m -[90mLoading output file /tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e.dat... [0m[92mOK! +[90mLoading output file input_dir/kraken_out.krk... [0m[92mOK! [0m[90m Seqs read: [0m99 [90m[[0m52.81 knt[90m] [0m[90m Seqs clas: [0m99 [90m([0m0.00%[90m unclassified) [0m[90m Seqs pass: [0m99 [90m([0m0.00%[90m rejected) @@ -21,8 +22,8 @@ Info:[0m 90 [90madditional seqs discarded ([0m90.909% [90mof accepted) [0m[93m Warning![0m 11 orphan taxids[90m (rerun with --debug for details) -[0m/tmp/tmpz5ieggzi/files/f/9/b/dataset_f9b4a772-d0f2-4391-a7bb-7f055b4fce1e[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.00373[90m sec +[0minput_dir/kraken_out[94m sample [0m[92mOK! +[0m[90mLoad elapsed time: [0m0.00395[90m sec [0m [90m Building the taxonomy multiple tree... [0m[92mOK![0m |