| Next changeset 1:d368e312aebd (2024-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a |
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added:
biobox_add_taxid.xml macros.xml test-data/cami2_mouse_gut_average_genome_coverage.tsv test-data/elated_franklin_0 test-data/goofy_hypatia_2 test-data/gsa_mapping.binning test-data/naughty_carson_2 test-data/ncbi_taxonomy.loc test-data/test-db/delnodes.dmp test-data/test-db/division.dmp test-data/test-db/gc.prt test-data/test-db/gencode.dmp test-data/test-db/merged.dmp test-data/test-db/names.dmp test-data/test-db/nodes.amber.ft test-data/test-db/nodes.dmp test-data/test-db/readme.txt test-data/test_add.fasta.gz test-data/test_add.tsv test-data/test_add1.fasta test-data/test_add2.fasta test-data/test_bat_file.tsv test-data/test_binning.tsv test-data/test_binning2.tsv test-data/test_biobox_file.tsv test-data/test_biobox_file_add_taxid_bat.tsv test-data/test_biobox_file_add_taxid_gtdb.tsv test-data/test_gold.tsv test-data/test_gtdb_file.tsv test-data/test_gtdb_to_taxdump_file.tsv test-data/test_taxonkit_file.tsv test-data/unique_common.tsv tool-data/ncbi_taxonomy.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 1e10251b9615 biobox_add_taxid.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biobox_add_taxid.xml Sun Aug 25 13:19:14 2024 +0000 |
| [ |
| @@ -0,0 +1,119 @@ +<tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Add taxid output from BAT or GTDB to biobox binning data</description> + <macros> + <import>macros.xml</import> + <token name="@SCRIPT_VERSION@">0.4</token> + </macros> + <requirements> + <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + + mkdir -p input && + + ln -s '${biobox_file}' '$biobox_file.element_identifier' && + + #for $i, $f in enumerate($tool_type.input): + ln -s '$f' 'input/${i}.tsv' && + #end for + + biobox_add_taxid.py + '$biobox_file.element_identifier' + '$tool_type.is_select' + 'input' + #if $tool_type.is_select == 'GTDB': + -g '$gtdb_to_taxdump' + -t '$taxonkit' + -c $column + #end if + && + + #if $tool_type.is_select == 'GTDB': + cp *_add_taxid_GTDB* $output + #else: + cp *_add_taxid_BAT* $output + #end if + + ]]> + </command> + <inputs> + <param name="biobox_file" type="data" format="tabular" label="CAMI amber biobox file input" help="Input the CAMI amber biobox file here which are corespond with the biner and the BAT/GTDB output which did used the biner as input! "/> + <conditional name="tool_type"> + <param name="is_select" type="select" label="Select the tool which output should be used here" help="Select BAT when you use the bin2classifier file(s) or select GTDB when using the summary file(s)"> + <option value="BAT">BAT</option> + <option value="GTDB">GTDB</option> + </param> + <when value="GTDB"> + <param argument="--gtdb_to_taxdump" type="data" format="tabular" label="Input the output from gtdb_to_taxdump here" help="Use the output from gtdb_to_taxdump here since we need the mapped names from GTDB to NCBI to get the arcoding taxids from NCBI"/> + <param argument="--taxonkit" type="data" format="tabular" label="Input the output from Taxonkit here" help="Use the output from Taxonkit here since the need the mapped NCBI names to the arcording taxids"/> + <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/> + <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here" + help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/> + </when> + <when value="BAT"> + <param name="input" type="data" multiple="true" format="tabular" label="Input bin2classifier file(s) from BAT here" + help="Use the BAT file(s) which are coresponding with the binning file!"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="tabular" label="${tool.name}: BIOBOX ADD TAXID COLUMN"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/> + <conditional name="tool_type"> + <param name="is_select" value="BAT"/> + <param name="input" ftype="tabular" value="test_bat_file.tsv"/> + </conditional> + <output name="output" file="test_biobox_file_add_taxid_bat.tsv"/> + </test> + <test expect_num_outputs="1"> + <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/> + <conditional name="tool_type"> + <param name="is_select" value="GTDB"/> + <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/> + <param name="taxonkit" ftype="tabular" value="test_taxonkit_file.tsv"/> + <param name="column" value="1"/> + <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/> + </conditional> + <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/> + </test> + </tests> + <help> + <![CDATA[ + + **USAGE OF THIS TOOL** + + This tool was desgin for using the BAT/GTDB-Tk output to expand the CAMI amber biobox file with the taxid column to access taxa evaluation with amber! + + **IMPORTAND NOTE WHEN USING GTDB OUTPUT** + + Befor using GTDB-Tk output you have to use 2 other tools to map the GTDB names to the NCBI names and then map the NCBI names to there taxids. + To map the GTDB names to the NCBI names you extract the GTDB names from the summary file and with them you can now use the gtdb_to_taxdum tool! + After using the gtdb_to_taxdum tool you have the extract the NCBI names here and then use the tool Taxonkit[name2taxid] to finaly get the taxids. + + **INPUTS** + - The CAMI amber biobox file + - BAT[bin2classifier] file(s) OR GTDB-Tk[Summary] file(s) + - The gtdb_to_taxdum output[WHEN USING GTDB-Tk] + - The Taxonkit[name2taxid] output[WHEN USING GTDB-Tk] + + **OUTPUT** + + A CAMI amber biobox file with a taxid colum + ]]> + </help> + <citations> + <citation type="bibtex">@misc{BibEntry2024Aug, + title = {{biobox{$\_$}add{$\_$}taxid}}, + author = {Santino Faack (SantaMcCloud)}, + journal = {GitHub}, + year = {2024}, + month = aug, + note = {[Online; accessed 22. Aug. 2024]}, + url = {https://github.com/SantaMcCloud/biobox_add_taxid/tree/release-0.3} + }</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 1e10251b9615 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Aug 25 13:19:14 2024 +0000 |
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| @@ -0,0 +1,17 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">cami-amber</requirement> + <yield/> + </requirements> + </xml> + <token name="@TOOL_VERSION@">2.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/gigascience/giy069</citation> + <yield/> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 1e10251b9615 test-data/cami2_mouse_gut_average_genome_coverage.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cami2_mouse_gut_average_genome_coverage.tsv Sun Aug 25 13:19:14 2024 +0000 |
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| b'@@ -0,0 +1,793 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|
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/elated_franklin_0 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/elated_franklin_0 Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,5680 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|
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/goofy_hypatia_2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/goofy_hypatia_2 Sun Aug 25 13:19:14 2024 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/gsa_mapping.binning --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gsa_mapping.binning Sun Aug 25 13:19:14 2024 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/naughty_carson_2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/naughty_carson_2 Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,8176 @@\n+#CAMI Format for Binning\n+@Version:0.9.0\n+@SampleID:CAMI_low\n+@@SEQUENCEID\tBINID\n+RL|S1|C10\tBin_034\n+RL|S1|C100\tBin_023\n+RL|S1|C1000\tBin_034\n+RL|S1|C10000\tBin_019\n+RL|S1|C10002\tBin_035\n+RL|S1|C10004\tBin_035\n+RL|S1|C10008\tBin_034\n+RL|S1|C10011\tBin_035\n+RL|S1|C10012\tBin_013\n+RL|S1|C10014\tBin_035\n+RL|S1|C10015\tBin_033\n+RL|S1|C10017\tBin_034\n+RL|S1|C1002\tBin_018\n+RL|S1|C10020\tBin_036\n+RL|S1|C10022\tBin_034\n+RL|S1|C10026\tBin_034\n+RL|S1|C10028\tBin_034\n+RL|S1|C10032\tBin_027\n+RL|S1|C10034\tBin_032\n+RL|S1|C10036\tBin_006\n+RL|S1|C10037\tBin_034\n+RL|S1|C10039\tBin_018\n+RL|S1|C1004\tBin_003\n+RL|S1|C10040\tBin_036\n+RL|S1|C10041\tBin_035\n+RL|S1|C10046\tBin_034\n+RL|S1|C10047\tBin_034\n+RL|S1|C10052\tBin_018\n+RL|S1|C10056\tBin_033\n+RL|S1|C10059\tBin_033\n+RL|S1|C1006\tBin_034\n+RL|S1|C10060\tBin_034\n+RL|S1|C10069\tBin_030\n+RL|S1|C1007\tBin_032\n+RL|S1|C10070\tBin_008\n+RL|S1|C10071\tBin_029\n+RL|S1|C10073\tBin_034\n+RL|S1|C10075\tBin_029\n+RL|S1|C10080\tBin_032\n+RL|S1|C10083\tBin_034\n+RL|S1|C10084\tBin_034\n+RL|S1|C10091\tBin_033\n+RL|S1|C10093\tBin_034\n+RL|S1|C10095\tBin_036\n+RL|S1|C10096\tBin_034\n+RL|S1|C10098\tBin_029\n+RL|S1|C101\tBin_033\n+RL|S1|C1010\tBin_036\n+RL|S1|C10103\tBin_034\n+RL|S1|C10104\tBin_034\n+RL|S1|C10108\tBin_032\n+RL|S1|C10109\tBin_033\n+RL|S1|C1011\tBin_012\n+RL|S1|C10110\tBin_036\n+RL|S1|C10113\tBin_018\n+RL|S1|C10117\tBin_036\n+RL|S1|C10122\tBin_016\n+RL|S1|C10124\tBin_034\n+RL|S1|C10127\tBin_034\n+RL|S1|C10128\tBin_018\n+RL|S1|C10129\tBin_036\n+RL|S1|C1013\tBin_034\n+RL|S1|C10132\tBin_018\n+RL|S1|C10136\tBin_032\n+RL|S1|C10143\tBin_001\n+RL|S1|C1015\tBin_036\n+RL|S1|C10150\tBin_006\n+RL|S1|C10153\tBin_034\n+RL|S1|C10154\tBin_027\n+RL|S1|C10157\tBin_036\n+RL|S1|C10162\tBin_034\n+RL|S1|C10168\tBin_034\n+RL|S1|C10170\tBin_035\n+RL|S1|C10171\tBin_034\n+RL|S1|C10173\tBin_034\n+RL|S1|C10175\tBin_034\n+RL|S1|C10179\tBin_030\n+RL|S1|C10183\tBin_036\n+RL|S1|C10184\tBin_027\n+RL|S1|C10187\tBin_036\n+RL|S1|C10188\tBin_036\n+RL|S1|C1019\tBin_019\n+RL|S1|C10193\tBin_036\n+RL|S1|C10194\tBin_004\n+RL|S1|C10197\tBin_034\n+RL|S1|C102\tBin_036\n+RL|S1|C10204\tBin_018\n+RL|S1|C10207\tBin_034\n+RL|S1|C10208\tBin_031\n+RL|S1|C10209\tBin_033\n+RL|S1|C10210\tBin_031\n+RL|S1|C10212\tBin_018\n+RL|S1|C10213\tBin_016\n+RL|S1|C1022\tBin_034\n+RL|S1|C10221\tBin_034\n+RL|S1|C10223\tBin_033\n+RL|S1|C10224\tBin_035\n+RL|S1|C10225\tBin_034\n+RL|S1|C10226\tBin_034\n+RL|S1|C10229\tBin_018\n+RL|S1|C1023\tBin_033\n+RL|S1|C10230\tBin_034\n+RL|S1|C10234\tBin_035\n+RL|S1|C10235\tBin_034\n+RL|S1|C10236\tBin_034\n+RL|S1|C10237\tBin_029\n+RL|S1|C10240\tBin_034\n+RL|S1|C10242\tBin_016\n+RL|S1|C10243\tBin_033\n+RL|S1|C10244\tBin_033\n+RL|S1|C10246\tBin_034\n+RL|S1|C1025\tBin_025\n+RL|S1|C10251\tBin_033\n+RL|S1|C10252\tBin_035\n+RL|S1|C10255\tBin_036\n+RL|S1|C10258\tBin_034\n+RL|S1|C10259\tBin_036\n+RL|S1|C1026\tBin_034\n+RL|S1|C10261\tBin_032\n+RL|S1|C10262\tBin_036\n+RL|S1|C10266\tBin_018\n+RL|S1|C10267\tBin_034\n+RL|S1|C10268\tBin_036\n+RL|S1|C10269\tBin_036\n+RL|S1|C1027\tBin_031\n+RL|S1|C10271\tBin_034\n+RL|S1|C10273\tBin_033\n+RL|S1|C10277\tBin_027\n+RL|S1|C10278\tBin_036\n+RL|S1|C10279\tBin_018\n+RL|S1|C10280\tBin_035\n+RL|S1|C10286\tBin_034\n+RL|S1|C10287\tBin_018\n+RL|S1|C10289\tBin_032\n+RL|S1|C1029\tBin_031\n+RL|S1|C10290\tBin_018\n+RL|S1|C10294\tBin_036\n+RL|S1|C10295\tBin_031\n+RL|S1|C10297\tBin_036\n+RL|S1|C10298\tBin_027\n+RL|S1|C10299\tBin_034\n+RL|S1|C1030\tBin_035\n+RL|S1|C10302\tBin_036\n+RL|S1|C10303\tBin_034\n+RL|S1|C10306\tBin_034\n+RL|S1|C10307\tBin_035\n+RL|S1|C10308\tBin_032\n+RL|S1|C10309\tBin_036\n+RL|S1|C10311\tBin_035\n+RL|S1|C10313\tBin_034\n+RL|S1|C10315\tBin_012\n+RL|S1|C10319\tBin_031\n+RL|S1|C1032\tBin_032\n+RL|S1|C10322\tBin_033\n+RL|S1|C10323\tBin_035\n+RL|S1|C10325\tBin_032\n+RL|S1|C10328\tBin_034\n+RL|S1|C10330\tBin_023\n+RL|S1|C10332\tBin_018\n+RL|S1|C10333\tBin_035\n+RL|S1|C10335\tBin_032\n+RL|S1|C10337\tBin_035\n+RL|S1|C10349\tBin_034\n+RL|S1|C1035\tBin_036\n+RL|S1|C10350\tBin_035\n+RL|S1|C10355\tBin_034\n+RL|S1|C10356\tBin_036\n+RL|S1|C10358\tBin_036\n+RL|S1|C10359\tBin_030\n+RL|S1|C10360\tBin_033\n+RL|S1|C10361\tBin_018\n+RL|S1|C10363\tBin_006\n+RL|S1|C10364\tBin_036\n+RL|S1|C10365\tBin_034\n+RL|S1|C10366\tBin_012\n+RL|S1|C10368\tBin_018\n+RL|S1|C10373\tBin_027\n+RL|S1|C10374\tBin_011\n+RL|S1|C10'..b'018\n+RL|S1|C9583\tBin_006\n+RL|S1|C9586\tBin_033\n+RL|S1|C9588\tBin_034\n+RL|S1|C9589\tBin_036\n+RL|S1|C9590\tBin_031\n+RL|S1|C9594\tBin_034\n+RL|S1|C9595\tBin_032\n+RL|S1|C9597\tBin_023\n+RL|S1|C9603\tBin_034\n+RL|S1|C9605\tBin_015\n+RL|S1|C9608\tBin_032\n+RL|S1|C961\tBin_036\n+RL|S1|C9610\tBin_036\n+RL|S1|C9613\tBin_035\n+RL|S1|C9614\tBin_030\n+RL|S1|C9618\tBin_034\n+RL|S1|C9619\tBin_034\n+RL|S1|C9622\tBin_035\n+RL|S1|C9624\tBin_016\n+RL|S1|C9625\tBin_034\n+RL|S1|C9626\tBin_035\n+RL|S1|C9627\tBin_024\n+RL|S1|C9628\tBin_036\n+RL|S1|C9632\tBin_034\n+RL|S1|C9634\tBin_036\n+RL|S1|C9636\tBin_036\n+RL|S1|C9639\tBin_033\n+RL|S1|C964\tBin_034\n+RL|S1|C9642\tBin_035\n+RL|S1|C9643\tBin_025\n+RL|S1|C9645\tBin_034\n+RL|S1|C9647\tBin_034\n+RL|S1|C9649\tBin_027\n+RL|S1|C965\tBin_020\n+RL|S1|C9653\tBin_035\n+RL|S1|C9657\tBin_035\n+RL|S1|C9659\tBin_035\n+RL|S1|C9660\tBin_036\n+RL|S1|C9661\tBin_035\n+RL|S1|C9664\tBin_034\n+RL|S1|C9667\tBin_035\n+RL|S1|C967\tBin_036\n+RL|S1|C9672\tBin_018\n+RL|S1|C9675\tBin_034\n+RL|S1|C9678\tBin_030\n+RL|S1|C9680\tBin_034\n+RL|S1|C9681\tBin_036\n+RL|S1|C9683\tBin_032\n+RL|S1|C9685\tBin_006\n+RL|S1|C9688\tBin_034\n+RL|S1|C9691\tBin_034\n+RL|S1|C9693\tBin_006\n+RL|S1|C9696\tBin_034\n+RL|S1|C9698\tBin_031\n+RL|S1|C970\tBin_034\n+RL|S1|C9700\tBin_033\n+RL|S1|C9706\tBin_034\n+RL|S1|C9708\tBin_035\n+RL|S1|C9712\tBin_036\n+RL|S1|C9713\tBin_034\n+RL|S1|C9717\tBin_036\n+RL|S1|C9719\tBin_036\n+RL|S1|C9726\tBin_034\n+RL|S1|C9732\tBin_035\n+RL|S1|C9733\tBin_033\n+RL|S1|C9734\tBin_033\n+RL|S1|C9735\tBin_004\n+RL|S1|C9736\tBin_035\n+RL|S1|C9737\tBin_035\n+RL|S1|C9740\tBin_036\n+RL|S1|C9745\tBin_035\n+RL|S1|C9747\tBin_035\n+RL|S1|C9750\tBin_028\n+RL|S1|C9752\tBin_032\n+RL|S1|C9753\tBin_032\n+RL|S1|C9754\tBin_035\n+RL|S1|C9757\tBin_034\n+RL|S1|C9763\tBin_035\n+RL|S1|C9765\tBin_033\n+RL|S1|C9766\tBin_017\n+RL|S1|C9768\tBin_036\n+RL|S1|C977\tBin_034\n+RL|S1|C9774\tBin_036\n+RL|S1|C9775\tBin_034\n+RL|S1|C9776\tBin_006\n+RL|S1|C9777\tBin_034\n+RL|S1|C9778\tBin_034\n+RL|S1|C9779\tBin_036\n+RL|S1|C9780\tBin_006\n+RL|S1|C9782\tBin_036\n+RL|S1|C9783\tBin_035\n+RL|S1|C9784\tBin_035\n+RL|S1|C9785\tBin_029\n+RL|S1|C9786\tBin_032\n+RL|S1|C9789\tBin_033\n+RL|S1|C9792\tBin_036\n+RL|S1|C9793\tBin_018\n+RL|S1|C9796\tBin_033\n+RL|S1|C9798\tBin_034\n+RL|S1|C9799\tBin_035\n+RL|S1|C980\tBin_030\n+RL|S1|C9801\tBin_035\n+RL|S1|C9803\tBin_036\n+RL|S1|C9805\tBin_034\n+RL|S1|C9806\tBin_036\n+RL|S1|C9807\tBin_036\n+RL|S1|C9809\tBin_034\n+RL|S1|C9810\tBin_036\n+RL|S1|C9815\tBin_034\n+RL|S1|C9816\tBin_034\n+RL|S1|C9818\tBin_035\n+RL|S1|C9819\tBin_017\n+RL|S1|C982\tBin_034\n+RL|S1|C9823\tBin_034\n+RL|S1|C9824\tBin_034\n+RL|S1|C9825\tBin_036\n+RL|S1|C9826\tBin_018\n+RL|S1|C983\tBin_023\n+RL|S1|C9832\tBin_030\n+RL|S1|C9834\tBin_024\n+RL|S1|C9836\tBin_036\n+RL|S1|C9837\tBin_034\n+RL|S1|C9839\tBin_033\n+RL|S1|C9841\tBin_035\n+RL|S1|C9846\tBin_034\n+RL|S1|C985\tBin_035\n+RL|S1|C9851\tBin_032\n+RL|S1|C9853\tBin_036\n+RL|S1|C9855\tBin_034\n+RL|S1|C9856\tBin_033\n+RL|S1|C9857\tBin_035\n+RL|S1|C986\tBin_034\n+RL|S1|C9868\tBin_035\n+RL|S1|C9871\tBin_036\n+RL|S1|C9877\tBin_035\n+RL|S1|C9879\tBin_031\n+RL|S1|C9882\tBin_035\n+RL|S1|C9883\tBin_012\n+RL|S1|C9885\tBin_032\n+RL|S1|C9890\tBin_034\n+RL|S1|C9891\tBin_032\n+RL|S1|C9892\tBin_035\n+RL|S1|C9894\tBin_017\n+RL|S1|C9895\tBin_017\n+RL|S1|C9897\tBin_035\n+RL|S1|C9898\tBin_018\n+RL|S1|C9899\tBin_036\n+RL|S1|C99\tBin_036\n+RL|S1|C9901\tBin_018\n+RL|S1|C9902\tBin_002\n+RL|S1|C9904\tBin_019\n+RL|S1|C9905\tBin_035\n+RL|S1|C9907\tBin_034\n+RL|S1|C9909\tBin_033\n+RL|S1|C9910\tBin_029\n+RL|S1|C9912\tBin_036\n+RL|S1|C9913\tBin_034\n+RL|S1|C9915\tBin_034\n+RL|S1|C9917\tBin_032\n+RL|S1|C992\tBin_035\n+RL|S1|C9924\tBin_033\n+RL|S1|C9925\tBin_035\n+RL|S1|C9927\tBin_034\n+RL|S1|C9928\tBin_035\n+RL|S1|C9932\tBin_007\n+RL|S1|C9941\tBin_032\n+RL|S1|C9943\tBin_034\n+RL|S1|C9947\tBin_027\n+RL|S1|C9951\tBin_034\n+RL|S1|C9956\tBin_036\n+RL|S1|C9958\tBin_036\n+RL|S1|C996\tBin_004\n+RL|S1|C9963\tBin_018\n+RL|S1|C9964\tBin_036\n+RL|S1|C9965\tBin_033\n+RL|S1|C9967\tBin_034\n+RL|S1|C9970\tBin_036\n+RL|S1|C9972\tBin_036\n+RL|S1|C9973\tBin_035\n+RL|S1|C9974\tBin_018\n+RL|S1|C9976\tBin_034\n+RL|S1|C9979\tBin_035\n+RL|S1|C998\tBin_035\n+RL|S1|C9984\tBin_032\n+RL|S1|C9986\tBin_034\n+RL|S1|C9988\tBin_031\n+RL|S1|C9990\tBin_036\n+RL|S1|C9991\tBin_035\n+RL|S1|C9994\tBin_036\n+RL|S1|C9995\tBin_018\n+RL|S1|C9997\tBin_018\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/ncbi_taxonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,1 @@ +test-db-tox Test Database ${__HERE__}/test-db \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/delnodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/delnodes.dmp Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,70000 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|
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/division.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/division.dmp Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,12 @@ +0 | BCT | Bacteria | | +1 | INV | Invertebrates | | +2 | MAM | Mammals | | +3 | PHG | Phages | | +4 | PLN | Plants and Fungi | | +5 | PRI | Primates | | +6 | ROD | Rodents | | +7 | SYN | Synthetic and Chimeric | | +8 | UNA | Unassigned | No species nodes should inherit this division assignment | +9 | VRL | Viruses | | +10 | VRT | Vertebrates | | +11 | ENV | Environmental samples | Anonymous sequences cloned directly from the environment | |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/gc.prt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/gc.prt Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,358 @@\n+--**************************************************************************\n+-- This is the NCBI genetic code table\n+-- Initial base data set from Andrzej Elzanowski while at PIR International\n+-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI\n+-- Base 1-3 of each codon have been added as comments to facilitate\n+-- readability at the suggestion of Peter Rice, EMBL\n+-- Later additions by Taxonomy Group staff at NCBI\n+--\n+-- Version 4.6\n+-- Renamed genetic code 24 to Rhabdopleuridae Mitochondrial\n+--\n+-- Version 4.5\n+-- Added Cephalodiscidae mitochondrial genetic code 33\n+--\n+-- Version 4.4\n+-- Added GTG as start codon for genetic code 3\n+-- Added Balanophoraceae plastid genetic code 32\n+--\n+-- Version 4.3\n+-- Change to CTG -> Leu in genetic codes 27, 28, 29, 30\n+--\n+-- Version 4.2\n+-- Added Karyorelict nuclear genetic code 27\n+-- Added Condylostoma nuclear genetic code 28\n+-- Added Mesodinium nuclear genetic code 29\n+-- Added Peritrich nuclear genetic code 30\n+-- Added Blastocrithidia nuclear genetic code 31\n+--\n+-- Version 4.1\n+-- Added Pachysolen tannophilus nuclear genetic code 26\n+--\n+-- Version 4.0\n+-- Updated version to reflect numerous undocumented changes:\n+-- Corrected start codons for genetic code 25\n+-- Name of new genetic code is Candidate Division SR1 and Gracilibacteria\n+-- Added candidate division SR1 nuclear genetic code 25\n+-- Added GTG as start codon for genetic code 24\n+-- Corrected Pterobranchia Mitochondrial genetic code (24)\n+-- Added genetic code 24, Pterobranchia Mitochondrial\n+-- Genetic code 11 is now Bacterial, Archaeal and Plant Plastid\n+-- Fixed capitalization of mitochondrial in codes 22 and 23\n+-- Added GTG, ATA, and TTG as alternative start codons to code 13\n+--\n+-- Version 3.9\n+-- Code 14 differs from code 9 only by translating UAA to Tyr rather than\n+-- STOP. A recent study (Telford et al, 2000) has found no evidence that\n+-- the codon UAA codes for Tyr in the flatworms, but other opinions exist.\n+-- There are very few GenBank records that are translated with code 14,\n+-- but a test translation shows that retranslating these records with code\n+-- 9 can cause premature terminations. Therefore, GenBank will maintain\n+-- code 14 until further information becomes available.\n+--\n+-- Version 3.8\n+-- Added GTG start to Echinoderm mitochondrial code, code 9\n+--\n+-- Version 3.7\n+-- Added code 23 Thraustochytrium mitochondrial code\n+-- formerly OGMP code 93\n+-- submitted by Gertraude Berger, Ph.D.\n+--\n+-- Version 3.6\n+-- Added code 22 TAG-Leu, TCA-stop\n+-- found in mitochondrial DNA of Scenedesmus obliquus\n+-- submitted by Gertraude Berger, Ph.D.\n+-- Organelle Genome Megasequencing Program, Univ Montreal\n+--\n+-- Version 3.5\n+-- Added code 21, Trematode Mitochondrial\n+-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)\n+-- Added code 16, Chlorophycean Mitochondrial\n+-- (TAG can translated to Leucine instaed to STOP in chlorophyceans\n+-- and fungi)\n+--\n+-- Version 3.4\n+-- Added CTG,TTG as allowed alternate start codons in Standard code.\n+-- Prats et al. 1989, Hann et al. 1992\n+--\n+-- Version 3.3 - 10/13/95\n+-- Added alternate intiation codon ATC to code 5\n+-- based on complete mitochondrial genome of honeybee\n+-- Crozier and Crozier (1993)\n+--\n+-- Version 3.2 - 6/24/95\n+-- Code Comments\n+-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...\n+-- 15 Blepharisma Macro.. code added\n+-- 5 Invertebrate Mito.. GTG allowed as alternate initiator\n+-- 11 Eubacterial renamed to Bacterial as most alternate starts\n+-- have been found in Archea\n+--\n+--\n+-- Version 3.1 - 1995\n+-- Updated as per Andrzej Elzanowski at NCBI\n+-- Complete documentation in NCBI'..b'5 ,\n+ ncbieaa "FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "---M------**-----------------------M---------------M------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Pachysolen tannophilus Nuclear" ,\n+ id 26 ,\n+ ncbieaa "FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "----------**--*----M---------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Karyorelict Nuclear" ,\n+ id 27 ,\n+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "--------------*--------------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Condylostoma Nuclear" ,\n+ id 28 ,\n+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "----------**--*--------------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Mesodinium Nuclear" ,\n+ id 29 ,\n+ ncbieaa "FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "--------------*--------------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Peritrich Nuclear" ,\n+ id 30 ,\n+ ncbieaa "FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "--------------*--------------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Blastocrithidia Nuclear" ,\n+ id 31 ,\n+ ncbieaa "FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "----------**-----------------------M----------------------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Balanophoraceae Plastid" ,\n+ id 32 ,\n+ ncbieaa "FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",\n+ sncbieaa "---M------*---*----M------------MMMM---------------M------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ } ,\n+ {\n+ name "Cephalodiscidae Mitochondrial" ,\n+ id 33 ,\n+ ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",\n+ sncbieaa "---M-------*-------M---------------M---------------M------------"\n+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG\n+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG\n+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG\n+ }\n+}\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/gencode.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/gencode.dmp Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,28 @@ +0 | | Unspecified | | | +1 | | Standard | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M---------------M---------------------------- | +2 | | Vertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG | ----------**--------------------MMMM----------**---M------------ | +3 | | Yeast Mitochondrial | FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**----------------------MM---------------M------------ | +4 | | Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --MM------**-------M------------MMMM---------------M------------ | +5 | | Invertebrate Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG | ---M------**--------------------MMMM---------------M------------ | +6 | | Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear | FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- | +9 | | Echinoderm Mitochondrial; Flatworm Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ | +10 | | Euplotid Nuclear | FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- | +11 | | Bacterial, Archaeal and Plant Plastid | FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**--*----M------------MMMM---------------M------------ | +12 | | Alternative Yeast Nuclear | FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- | +13 | | Ascidian Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG | ---M------**----------------------MM---------------M------------ | +14 | | Alternative Flatworm Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG | -----------*-----------------------M---------------------------- | +15 | | Blepharisma Macronuclear | FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- | +16 | | Chlorophycean Mitochondrial | FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------*---*--------------------M---------------------------- | +21 | | Trematode Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG | ----------**-----------------------M---------------M------------ | +22 | | Scenedesmus obliquus mitochondrial | FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ------*---*---*--------------------M---------------------------- | +23 | | Thraustochytrium mitochondrial code | FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --*-------**--*-----------------M--M---------------M------------ | +24 | | Rhabdopleuridae Mitochondrial | FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M------**-------M---------------M---------------M------------ | +25 | | Candidate Division SR1 and Gracilibacteria | FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------**-----------------------M---------------M------------ | +26 | | Pachysolen tannophilus Nuclear | FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*----M---------------M---------------------------- | +27 | | Karyorelict Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- | +28 | | Condylostoma Nuclear | FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**--*--------------------M---------------------------- | +29 | | Mesodinium Nuclear | FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- | +30 | | Peritrich Nuclear | FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | --------------*--------------------M---------------------------- | +31 | | Blastocrithidia Nuclear | FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ----------**-----------------------M---------------------------- | +32 | | Balanophoraceae Plastid | FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG | ---M------*---*----M------------MMMM---------------M------------ | +33 | | Cephalodiscidae Mitochondrial | FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG | ---M-------*-------M---------------M---------------M------------ | |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/names.dmp Sun Aug 25 13:19:14 2024 +0000 |
| [ |
| @@ -0,0 +1,74 @@ +83333 | Escherichia coli K-12 | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +562 | "Bacillus coli" Migula 1895 | | authority | +562 | "Bacterium coli commune" Escherich 1885 | | authority | +562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority | +562 | ATCC 11775 | | type material | +562 | Bacillus coli | | synonym | +562 | Bacterium coli | | synonym | +562 | Bacterium coli commune | | synonym | +562 | CCUG 24 | | type material | +562 | CCUG 29300 | | type material | +562 | CIP 54.8 | | type material | +562 | DSM 30083 | | type material | +562 | Enterococcus coli | | synonym | +562 | Escherchia coli | | misspelling | +562 | Escherichia coli | | scientific name | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority | +562 | Escherichia sp. MAR | | includes | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Eschericia coli | | misspelling | +562 | JCM 1649 | | type material | +562 | LMG 2092 | | type material | +562 | NBRC 102203 | | type material | +562 | NCCB 54008 | | type material | +562 | NCTC 9001 | | type material | +562 | bacterium 10a | | includes | +562 | bacterium E3 | | includes | +561 | Escherchia | | misspelling | +561 | Escherichia | | scientific name | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +543 | Enterobacteraceae | | synonym | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae | | scientific name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae Rahn 1937 | | synonym | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria <#1> | in-part | +91347 | 'Enterobacteriales' | | synonym | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | scientific name | +91347 | enterobacteria | enterobacteria<blast91347> | blast name | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <#5> | in-part | +1236 | Gammaproteobacteria | | scientific name | +1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +1236 | g-proteobacteria | gamma proteos<blast1236> | blast name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1224 | Proteobacteria | | scientific name | +1224 | Proteobacteria Garrity et al. 2005 | | authority | +1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | authority | +1224 | not Proteobacteria Cavalier-Smith 2002 | | authority | +1224 | proteobacteria | proteobacteria<blast1224> | blast name | +1224 | purple bacteria | | common name | +1224 | purple bacteria and relatives | | common name | +1224 | purple non-sulfur bacteria | | common name | +1224 | purple photosynthetic bacteria | | common name | +1224 | purple photosynthetic bacteria and relatives | | common name | +2 | Bacteria | Bacteria <prokaryote> | scientific name | +2 | Monera | Monera <Bacteria> | in-part | +2 | Procaryotae | Procaryotae <Bacteria> | in-part | +2 | Prokaryota | Prokaryota <Bacteria> | in-part | +2 | Prokaryotae | Prokaryotae <Bacteria> | in-part | +2 | bacteria | bacteria <blast2> | blast name | +2 | eubacteria | | genbank common name | +2 | not Bacteria Haeckel 1894 | | synonym | +2 | prokaryote | prokaryote <Bacteria> | in-part | +2 | prokaryotes | prokaryotes <Bacteria> | in-part | +1 | all | | synonym | +1 | root | | scientific name | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/nodes.amber.ft |
| b |
| Binary file test-data/test-db/nodes.amber.ft has changed |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/nodes.dmp Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,10 @@ +83333 | 562 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test-db/readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/readme.txt Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,61 @@ +*.dmp files are bcp-like dump from GenBank taxonomy database. + +General information. +Field terminator is "\t|\t" +Row terminator is "\t|\n" + +nodes.dmp file consists of taxonomy nodes. The description for each node includes the following +fields: + tax_id -- node id in GenBank taxonomy database + parent tax_id -- parent node id in GenBank taxonomy database + rank -- rank of this node (superkingdom, kingdom, ...) + embl code -- locus-name prefix; not unique + division id -- see division.dmp file + inherited div flag (1 or 0) -- 1 if node inherits division from parent + genetic code id -- see gencode.dmp file + inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent + mitochondrial genetic code id -- see gencode.dmp file + inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent + GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage + hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet + comments -- free-text comments and citations + +Taxonomy names file (names.dmp): + tax_id -- the id of node associated with this name + name_txt -- name itself + unique name -- the unique variant of this name if name not unique + name class -- (synonym, common name, ...) + +Divisions file (division.dmp): + division id -- taxonomy database division id + division cde -- GenBank division code (three characters) + division name -- e.g. BCT, PLN, VRT, MAM, PRI... + comments + +Genetic codes file (gencode.dmp): + genetic code id -- GenBank genetic code id + abbreviation -- genetic code name abbreviation + name -- genetic code name + cde -- translation table for this genetic code + starts -- start codons for this genetic code + +Deleted nodes file (delnodes.dmp): + tax_id -- deleted node id + +Merged nodes file (merged.dmp): + old_tax_id -- id of nodes which has been merged + new_tax_id -- id of nodes which is result of merging + +Citations file (citations.dmp): + cit_id -- the unique id of citation + cit_key -- citation key + pubmed_id -- unique id in PubMed database (0 if not in PubMed) + medline_id -- unique id in MedLine database (0 if not in MedLine) + url -- URL associated with citation + text -- any text (usually article name and authors). + -- The following characters are escaped in this text by a backslash: + -- newline (appear as "\n"), + -- tab character ("\t"), + -- double quotes ('\"'), + -- backslash character ("\\"). + taxid_list -- list of node ids separated by a single space |
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| diff -r 000000000000 -r 1e10251b9615 test-data/test_add.fasta.gz |
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| Binary file test-data/test_add.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_add.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,1464 @@\n+#CAMI Format for Binning\n+@Version:0.9.0\n+@SampleID:_SAMPLEID_\n+@@SEQUENCEID\tBINID\n+ERR1553846.1-ORL20E0-7-1-SSU_rRNA_eukarya/283-222\ttest_add/test_add.fasta\n+ERR1553846.10-ORL20E0-77-1-SSU_rRNA_eukarya/285-239\ttest_add/test_add.fasta\n+ERR1553846.100-ORL20E0-553-1-SSU_rRNA_eukarya/239-203\ttest_add/test_add.fasta\n+ERR1553846.10000-ORL20E0-51074-1-SSU_rRNA_eukarya/262-177\ttest_add/test_add.fasta\n+ERR1553846.100000-ORL20E0-512558-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.100001-ORL20E0-512560-1-SSU_rRNA_eukarya/278-205\ttest_add/test_add.fasta\n+ERR1553846.100003-ORL20E0-512571-1-SSU_rRNA_eukarya/252-202\ttest_add/test_add.fasta\n+ERR1553846.100005-ORL20E0-512583-1-SSU_rRNA_eukarya/261-177\ttest_add/test_add.fasta\n+ERR1553846.100006-ORL20E0-512585-1-SSU_rRNA_eukarya/286-231\ttest_add/test_add.fasta\n+ERR1553846.100007-ORL20E0-512586-1-SSU_rRNA_eukarya/263-177\ttest_add/test_add.fasta\n+ERR1553846.100008-ORL20E0-512587-1-SSU_rRNA_eukarya/259-177\ttest_add/test_add.fasta\n+ERR1553846.100013-ORL20E0-512607-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.100014-ORL20E0-512618-1-SSU_rRNA_eukarya/259-177\ttest_add/test_add.fasta\n+ERR1553846.100015-ORL20E0-512621-1-SSU_rRNA_eukarya/220-177\ttest_add/test_add.fasta\n+ERR1553846.100016-ORL20E0-512624-1-SSU_rRNA_eukarya/256-177\ttest_add/test_add.fasta\n+ERR1553846.10002-ORL20E0-51084-1-SSU_rRNA_eukarya/285-226\ttest_add/test_add.fasta\n+ERR1553846.100020-ORL20E0-512673-1-SSU_rRNA_eukarya/233-202\ttest_add/test_add.fasta\n+ERR1553846.100023-ORL20E0-512696-1-SSU_rRNA_eukarya/257-193\ttest_add/test_add.fasta\n+ERR1553846.100029-ORL20E0-512721-1-SSU_rRNA_eukarya/239-177\ttest_add/test_add.fasta\n+ERR1553846.100030-ORL20E0-512739-1-SSU_rRNA_eukarya/233-193\ttest_add/test_add.fasta\n+ERR1553846.100031-ORL20E0-512754-1-SSU_rRNA_eukarya/275-202\ttest_add/test_add.fasta\n+ERR1553846.100032-ORL20E0-512758-1-SSU_rRNA_eukarya/235-193\ttest_add/test_add.fasta\n+ERR1553846.100033-ORL20E0-512763-1-SSU_rRNA_eukarya/240-193\ttest_add/test_add.fasta\n+ERR1553846.100035-ORL20E0-512775-1-SSU_rRNA_eukarya/273-203\ttest_add/test_add.fasta\n+ERR1553846.100037-ORL20E0-512804-1-SSU_rRNA_eukarya/262-177\ttest_add/test_add.fasta\n+ERR1553846.100038-ORL20E0-512807-1-SSU_rRNA_eukarya/249-193\ttest_add/test_add.fasta\n+ERR1553846.10004-ORL20E0-51096-1-SSU_rRNA_eukarya/248-177\ttest_add/test_add.fasta\n+ERR1553846.100041-ORL20E0-512821-1-SSU_rRNA_eukarya/263-177\ttest_add/test_add.fasta\n+ERR1553846.100042-ORL20E0-512822-1-SSU_rRNA_eukarya/252-172\ttest_add/test_add.fasta\n+ERR1553846.100048-ORL20E0-512847-1-SSU_rRNA_eukarya/283-202\ttest_add/test_add.fasta\n+ERR1553846.100049-ORL20E0-512851-1-SSU_rRNA_eukarya/250-193\ttest_add/test_add.fasta\n+ERR1553846.100050-ORL20E0-512852-1-SSU_rRNA_eukarya/279-210\ttest_add/test_add.fasta\n+ERR1553846.100054-ORL20E0-512879-1-SSU_rRNA_eukarya/230-177\ttest_add/test_add.fasta\n+ERR1553846.100055-ORL20E0-512906-1-SSU_rRNA_eukarya/251-193\ttest_add/test_add.fasta\n+ERR1553846.100058-ORL20E0-512912-1-SSU_rRNA_eukarya/259-177\ttest_add/test_add.fasta\n+ERR1553846.100060-ORL20E0-512922-1-SSU_rRNA_eukarya/274-193\ttest_add/test_add.fasta\n+ERR1553846.100061-ORL20E0-512924-1-SSU_rRNA_eukarya/257-199\ttest_add/test_add.fasta\n+ERR1553846.100066-ORL20E0-512972-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.100068-ORL20E0-512984-1-SSU_rRNA_eukarya/275-205\ttest_add/test_add.fasta\n+ERR1553846.100069-ORL20E0-512993-1-SSU_rRNA_eukarya/284-203\ttest_add/test_add.fasta\n+ERR1553846.100071-ORL20E0-513003-1-SSU_rRNA_eukarya/273-205\ttest_add/test_add.fasta\n+ERR1553846.100074-ORL20E0-513010-1-SSU_rRNA_eukarya/240-199\ttest_add/test_add.fasta\n+ERR1553846.100076-ORL20E0-513032-1-SSU_rRNA_eukarya/276-193\ttest_add/test_add.fasta\n+ERR1553846.100077-ORL20E0-513033-1-SSU_rRNA_eukarya/244-88\ttest_add/test_add.fasta\n+ERR1553846.100078-ORL20E0-513038-1-SSU_rRNA_eukarya/251-193\ttest_add/test_add.fasta\n+ERR1553846.100079-ORL20E0-513041-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.10008'..b'.fasta\n+ERR1553846.102614-ORL20E0-526193-1-SSU_rRNA_eukarya/270-202\ttest_add/test_add.fasta\n+ERR1553846.102615-ORL20E0-526197-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.102618-ORL20E0-526226-1-SSU_rRNA_eukarya/269-207\ttest_add/test_add.fasta\n+ERR1553846.102620-ORL20E0-526232-1-SSU_rRNA_eukarya/259-177\ttest_add/test_add.fasta\n+ERR1553846.102623-ORL20E0-526242-1-SSU_rRNA_eukarya/256-172\ttest_add/test_add.fasta\n+ERR1553846.102624-ORL20E0-526253-1-SSU_rRNA_eukarya/239-177\ttest_add/test_add.fasta\n+ERR1553846.102625-ORL20E0-526254-1-SSU_rRNA_eukarya/284-208\ttest_add/test_add.fasta\n+ERR1553846.102626-ORL20E0-526265-1-SSU_rRNA_eukarya/211-177\ttest_add/test_add.fasta\n+ERR1553846.102628-ORL20E0-526281-1-SSU_rRNA_eukarya/282-201\ttest_add/test_add.fasta\n+ERR1553846.102632-ORL20E0-526294-1-SSU_rRNA_eukarya/259-177\ttest_add/test_add.fasta\n+ERR1553846.102634-ORL20E0-526297-1-SSU_rRNA_eukarya/250-198\ttest_add/test_add.fasta\n+ERR1553846.102636-ORL20E0-526305-1-SSU_rRNA_eukarya/283-202\ttest_add/test_add.fasta\n+ERR1553846.102637-ORL20E0-526307-1-SSU_rRNA_eukarya/244-177\ttest_add/test_add.fasta\n+ERR1553846.102638-ORL20E0-526318-1-SSU_rRNA_eukarya/247-193\ttest_add/test_add.fasta\n+ERR1553846.102641-ORL20E0-526323-1-SSU_rRNA_eukarya/286-231\ttest_add/test_add.fasta\n+ERR1553846.102642-ORL20E0-526327-1-SSU_rRNA_eukarya/256-199\ttest_add/test_add.fasta\n+ERR1553846.102643-ORL20E0-526332-1-SSU_rRNA_eukarya/262-177\ttest_add/test_add.fasta\n+ERR1553846.102644-ORL20E0-526340-1-SSU_rRNA_eukarya/236-189\ttest_add/test_add.fasta\n+ERR1553846.102645-ORL20E0-526341-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.102647-ORL20E0-526356-1-SSU_rRNA_eukarya/258-202\ttest_add/test_add.fasta\n+ERR1553846.102649-ORL20E0-526361-1-SSU_rRNA_eukarya/245-212\ttest_add/test_add.fasta\n+ERR1553846.102652-ORL20E0-526384-1-SSU_rRNA_eukarya/233-193\ttest_add/test_add.fasta\n+ERR1553846.102654-ORL20E0-526401-1-SSU_rRNA_eukarya/261-177\ttest_add/test_add.fasta\n+ERR1553846.102655-ORL20E0-526406-1-SSU_rRNA_eukarya/233-193\ttest_add/test_add.fasta\n+ERR1553846.102657-ORL20E0-526415-1-SSU_rRNA_eukarya/263-177\ttest_add/test_add.fasta\n+ERR1553846.102658-ORL20E0-526427-1-SSU_rRNA_eukarya/256-187\ttest_add/test_add.fasta\n+ERR1553846.102660-ORL20E0-526431-1-SSU_rRNA_eukarya/229-177\ttest_add/test_add.fasta\n+ERR1553846.102663-ORL20E0-526449-1-SSU_rRNA_eukarya/284-232\ttest_add/test_add.fasta\n+ERR1553846.102665-ORL20E0-526459-1-SSU_rRNA_eukarya/227-78\ttest_add/test_add.fasta\n+ERR1553846.102666-ORL20E0-526460-1-SSU_rRNA_eukarya/254-210\ttest_add/test_add.fasta\n+ERR1553846.102667-ORL20E0-526464-1-SSU_rRNA_eukarya/272-232\ttest_add/test_add.fasta\n+ERR1553846.102670-ORL20E0-526477-1-SSU_rRNA_eukarya/284-210\ttest_add/test_add.fasta\n+ERR1553846.102671-ORL20E0-526479-1-SSU_rRNA_eukarya/283-202\ttest_add/test_add.fasta\n+ERR1553846.102672-ORL20E0-526487-1-SSU_rRNA_eukarya/284-204\ttest_add/test_add.fasta\n+ERR1553846.102673-ORL20E0-526491-1-SSU_rRNA_eukarya/246-177\ttest_add/test_add.fasta\n+ERR1553846.102675-ORL20E0-526502-1-SSU_rRNA_eukarya/260-177\ttest_add/test_add.fasta\n+ERR1553846.102676-ORL20E0-526503-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.102680-ORL20E0-526508-1-SSU_rRNA_eukarya/259-203\ttest_add/test_add.fasta\n+ERR1553846.102682-ORL20E0-526514-1-SSU_rRNA_eukarya/284-203\ttest_add/test_add.fasta\n+ERR1553846.102683-ORL20E0-526528-1-SSU_rRNA_eukarya/264-177\ttest_add/test_add.fasta\n+ERR1553846.102687-ORL20E0-526545-1-SSU_rRNA_eukarya/263-177\ttest_add/test_add.fasta\n+ERR1553846.10269-ORL20E0-52574-1-SSU_rRNA_eukarya/237-192\ttest_add/test_add.fasta\n+ERR1553846.102691-ORL20E0-526566-1-SSU_rRNA_eukarya/214-177\ttest_add/test_add.fasta\n+ERR1553846.102693-ORL20E0-526588-1-SSU_rRNA_eukarya/277-193\ttest_add/test_add.fasta\n+ERR1553846.102694-ORL20E0-526594-1-SSU_rRNA_eukarya/281-201\ttest_add/test_add.fasta\n+ERR1553846.102695-ORL20E0-526600-1-SSU_rRNA_eukarya/281-199\ttest_add/test_add.fasta\n+ERR1553846.102696-ORL20E0-526601-1-SSU_rRNA_eukarya/277-208\ttest_add/test_add.fasta\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_add1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add1.fasta Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,3836 @@\n+>ERR1553846.1-ORL20E0-7-1-SSU_rRNA_eukarya/283-222\n+TCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCA\n+TT\n+>ERR1553846.10-ORL20E0-77-1-SSU_rRNA_eukarya/285-239\n+AAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.100-ORL20E0-553-1-SSU_rRNA_eukarya/239-203\n+ACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.10000-ORL20E0-51074-1-SSU_rRNA_eukarya/262-177\n+GGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAGAGTCGTAACAAGGTTTCC\n+GTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100000-ORL20E0-512558-1-SSU_rRNA_eukarya/264-177\n+CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT\n+CCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100001-ORL20E0-512560-1-SSU_rRNA_eukarya/278-205\n+GTTCAAACTTGGGCATTTAGATGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCT\n+GCGGCAGGATCATT\n+>ERR1553846.100003-ORL20E0-512571-1-SSU_rRNA_eukarya/252-202\n+AAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.100005-ORL20E0-512583-1-SSU_rRNA_eukarya/261-177\n+GCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCG\n+TTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100006-ORL20E0-512585-1-SSU_rRNA_eukarya/286-231\n+AGAGGAAGGTGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.100007-ORL20E0-512586-1-SSU_rRNA_eukarya/263-177\n+GGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC\n+GGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100008-ORL20E0-512587-1-SSU_rRNA_eukarya/259-177\n+CGGAAAGTTATCCAAACTTGGTCATTTAGAGGAATTAAAAGTCGTAACAAGGTTTCCGTT\n+GGTGAACTAGCGGAAGGATCATT\n+>ERR1553846.100013-ORL20E0-512607-1-SSU_rRNA_eukarya/264-177\n+CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT\n+CCGTTGGCGAACCAGCGGAAGGATCATT\n+>ERR1553846.100014-ORL20E0-512618-1-SSU_rRNA_eukarya/259-177\n+CGGAAAGTTATCCAAACTTGGGCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTT\n+GGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100015-ORL20E0-512621-1-SSU_rRNA_eukarya/220-177\n+AGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100016-ORL20E0-512624-1-SSU_rRNA_eukarya/256-177\n+AAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGT\n+GAACCAGCGGAAGGATCATT\n+>ERR1553846.10002-ORL20E0-51084-1-SSU_rRNA_eukarya/285-226\n+ATTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.100020-ORL20E0-512673-1-SSU_rRNA_eukarya/233-202\n+GTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.100023-ORL20E0-512696-1-SSU_rRNA_eukarya/257-193\n+CGGTCGTTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGA\n+TCATT\n+>ERR1553846.100029-ORL20E0-512721-1-SSU_rRNA_eukarya/239-177\n+GTCAATTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATC\n+ATT\n+>ERR1553846.100030-ORL20E0-512739-1-SSU_rRNA_eukarya/233-193\n+CGTAACAAGGTCTCCGTTGGTGAAACAGCGGAGGGATCATT\n+>ERR1553846.100031-ORL20E0-512754-1-SSU_rRNA_eukarya/275-202\n+GTTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCT\n+GCGGAAGGATCATT\n+>ERR1553846.100032-ORL20E0-512758-1-SSU_rRNA_eukarya/235-193\n+GTCGTAACAAGGTCTCTGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.100033-ORL20E0-512763-1-SSU_rRNA_eukarya/240-193\n+TAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.100035-ORL20E0-512775-1-SSU_rRNA_eukarya/273-203\n+CAAACTTGGTTATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGGGAACCTGCG\n+GAAGGATCATT\n+>ERR1553846.100037-ORL20E0-512804-1-SSU_rRNA_eukarya/262-177\n+GGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCC\n+GTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100038-ORL20E0-512807-1-SSU_rRNA_eukarya/249-193\n+TAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.10004-ORL20E0-51096-1-SSU_rRNA_eukarya/248-177\n+CCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGC\n+GGAAGGATCATT\n+>ERR1553846.100041-ORL20E0-512821-1-SSU_rRNA_eukarya/263-177\n+GGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC\n+CGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.100042-ORL20E0-512822-1-SSU_rRNA_eukarya/252-172\n+GGGAAATTGCCCAAACTTGCTTATTTAGAGGAAGTACAAGTCGTAACAAGGTTTCCGTAG\n+GTGAACCTGCGGAAGGATCAT\n+>ERR1553846.100048-ORL20E0-512847-1-SSU_rRNA_eukarya/283-202\n+GGAAAGTTGTTCAAACTTGGGCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAG\n+GTGAACCTGCGGAAGGATCATT\n+>ERR1553846.100049-ORL20E0-512851-1-SS'..b'ACAAGGTCTCCGGAGGTGAACCTGCGGAGGGATCATT\n+>ERR1553846.102645-ORL20E0-526341-1-SSU_rRNA_eukarya/264-177\n+CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT\n+CCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102647-ORL20E0-526356-1-SSU_rRNA_eukarya/258-202\n+TGGTGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.102649-ORL20E0-526361-1-SSU_rRNA_eukarya/245-212\n+AGGTAACCGGAGGTGAACCTGCGGTTGGATCATT\n+>ERR1553846.102652-ORL20E0-526384-1-SSU_rRNA_eukarya/233-193\n+CGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.102654-ORL20E0-526401-1-SSU_rRNA_eukarya/261-177\n+GCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCG\n+TTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102655-ORL20E0-526406-1-SSU_rRNA_eukarya/233-193\n+CGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.102657-ORL20E0-526415-1-SSU_rRNA_eukarya/263-177\n+AGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC\n+CGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102658-ORL20E0-526427-1-SSU_rRNA_eukarya/256-187\n+AAACTCGGTCATTTAGAGGAAGTAAAAGTCGTAACGAGGTTTCCGTAGGTGAACCTGCGG\n+AAGGATCATT\n+>ERR1553846.102660-ORL20E0-526431-1-SSU_rRNA_eukarya/229-177\n+GGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102663-ORL20E0-526449-1-SSU_rRNA_eukarya/284-232\n+GGAAGTAAAAGTCGTAAAAAGGTTTCTGTAGGTGAACCTGCAGAAGGATCATT\n+>ERR1553846.102665-ORL20E0-526459-1-SSU_rRNA_eukarya/227-78\n+ACACCGCCCGTCGCTCCTACCGATTTCGAGTGATGAGGTGAACCCTCCGGACTGTGCGCG\n+CAAGCGTTGGGAAGTTGAGTAAACCTTATCACTTAGAGGAAGGAGAAGTCGTAACAAGGT\n+ATCTGTAGGTGAACCTGCAGATGGATCATT\n+>ERR1553846.102666-ORL20E0-526460-1-SSU_rRNA_eukarya/254-210\n+AAGTCGTAACAAGGTCTCCGTAGGTGAACCTGCTGAGGGATCATT\n+>ERR1553846.102667-ORL20E0-526464-1-SSU_rRNA_eukarya/272-232\n+CGTAACAAGGTTTCTGTAGGTGAACCTGCAGAAGGATCATT\n+>ERR1553846.102670-ORL20E0-526477-1-SSU_rRNA_eukarya/284-210\n+TGATCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACC\n+TGCGGAAGGATCATT\n+>ERR1553846.102671-ORL20E0-526479-1-SSU_rRNA_eukarya/283-202\n+GGAAAGCTGTCCAAACTGTGTCATTTAGAGGAAGGAAAAGTCGTAACAAGGTTTCCGTAG\n+GTGAACCTGCGGAAGGATCATT\n+>ERR1553846.102672-ORL20E0-526487-1-SSU_rRNA_eukarya/284-204\n+GAAAGTTGTTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGG\n+TGAACCTGCGGAAGGATCATT\n+>ERR1553846.102673-ORL20E0-526491-1-SSU_rRNA_eukarya/246-177\n+AAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGG\n+AAGGATCAGT\n+>ERR1553846.102675-ORL20E0-526502-1-SSU_rRNA_eukarya/260-177\n+CCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGT\n+TGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102676-ORL20E0-526503-1-SSU_rRNA_eukarya/264-177\n+CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGAAAAAGTCGTAACAAGGTTT\n+CCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102680-ORL20E0-526508-1-SSU_rRNA_eukarya/259-203\n+TAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT\n+>ERR1553846.102682-ORL20E0-526514-1-SSU_rRNA_eukarya/284-203\n+GGAAAGTTATTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTG\n+GTGAACCAGCGGAAGGGTCATT\n+>ERR1553846.102683-ORL20E0-526528-1-SSU_rRNA_eukarya/264-177\n+CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT\n+CCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102687-ORL20E0-526545-1-SSU_rRNA_eukarya/263-177\n+GGGCCGGAAAGTTATCCAAACTTGGGCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC\n+CGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.10269-ORL20E0-52574-1-SSU_rRNA_eukarya/237-192\n+AAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.102691-ORL20E0-526566-1-SSU_rRNA_eukarya/214-177\n+AACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATCATT\n+>ERR1553846.102693-ORL20E0-526588-1-SSU_rRNA_eukarya/277-193\n+GCCGGAAAGCTATCCAAACTCGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCG\n+TTGGTGAACCAGCGGAGGGATCATT\n+>ERR1553846.102694-ORL20E0-526594-1-SSU_rRNA_eukarya/281-201\n+GAGAGGTTGGTCAAACTTGGTCATTTAGATGAACTAAAGTCGTAACAAGGTAACCGTAGG\n+TGAACCTGCGGTTGGATCATT\n+>ERR1553846.102695-ORL20E0-526600-1-SSU_rRNA_eukarya/281-199\n+CGGAAAGTTGTCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTA\n+GGTGAACCTGCGGAGGGATCATT\n+>ERR1553846.102696-ORL20E0-526601-1-SSU_rRNA_eukarya/277-208\n+AAACTTGGTCATTTAGAGGAACTAAAAGTCGTAACAAGGTAACCGTAGGTGAACCTGCGG\n+TTGGATCATT\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_add2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add2.fasta Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,84 @@ +>ERR1553846.1-ORL20E0-7-1-SSU_rRNA_eukarya/283-222 +TCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCA +TT +>ERR1553846.10-ORL20E0-77-1-SSU_rRNA_eukarya/285-239 +AAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT +>ERR1553846.100-ORL20E0-553-1-SSU_rRNA_eukarya/239-203 +ACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT +>ERR1553846.10000-ORL20E0-51074-1-SSU_rRNA_eukarya/262-177 +GGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAGAGTCGTAACAAGGTTTCC +GTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100000-ORL20E0-512558-1-SSU_rRNA_eukarya/264-177 +CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT +CCGTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100001-ORL20E0-512560-1-SSU_rRNA_eukarya/278-205 +GTTCAAACTTGGGCATTTAGATGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCT +GCGGCAGGATCATT +>ERR1553846.100003-ORL20E0-512571-1-SSU_rRNA_eukarya/252-202 +AAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT +>ERR1553846.100005-ORL20E0-512583-1-SSU_rRNA_eukarya/261-177 +GCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCG +TTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100006-ORL20E0-512585-1-SSU_rRNA_eukarya/286-231 +AGAGGAAGGTGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATT +>ERR1553846.100007-ORL20E0-512586-1-SSU_rRNA_eukarya/263-177 +GGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC +GGTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100008-ORL20E0-512587-1-SSU_rRNA_eukarya/259-177 +CGGAAAGTTATCCAAACTTGGTCATTTAGAGGAATTAAAAGTCGTAACAAGGTTTCCGTT +GGTGAACTAGCGGAAGGATCATT +>ERR1553846.100013-ORL20E0-512607-1-SSU_rRNA_eukarya/264-177 +CGGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTT +CCGTTGGCGAACCAGCGGAAGGATCATT +>ERR1553846.100014-ORL20E0-512618-1-SSU_rRNA_eukarya/259-177 +CGGAAAGTTATCCAAACTTGGGCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTT +GGTGAACCAGCGGAAGGATCATT +>ERR1553846.100015-ORL20E0-512621-1-SSU_rRNA_eukarya/220-177 +AGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100016-ORL20E0-512624-1-SSU_rRNA_eukarya/256-177 +AAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGT +GAACCAGCGGAAGGATCATT +>ERR1553846.10002-ORL20E0-51084-1-SSU_rRNA_eukarya/285-226 +ATTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT +>ERR1553846.100020-ORL20E0-512673-1-SSU_rRNA_eukarya/233-202 +GTTTCCGTAGGTGAACCTGCGGAAGGATCATT +>ERR1553846.100023-ORL20E0-512696-1-SSU_rRNA_eukarya/257-193 +CGGTCGTTTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGA +TCATT +>ERR1553846.100029-ORL20E0-512721-1-SSU_rRNA_eukarya/239-177 +GTCAATTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGCGGAAGGATC +ATT +>ERR1553846.100030-ORL20E0-512739-1-SSU_rRNA_eukarya/233-193 +CGTAACAAGGTCTCCGTTGGTGAAACAGCGGAGGGATCATT +>ERR1553846.100031-ORL20E0-512754-1-SSU_rRNA_eukarya/275-202 +GTTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCT +GCGGAAGGATCATT +>ERR1553846.100032-ORL20E0-512758-1-SSU_rRNA_eukarya/235-193 +GTCGTAACAAGGTCTCTGTTGGTGAACCAGCGGAGGGATCATT +>ERR1553846.100033-ORL20E0-512763-1-SSU_rRNA_eukarya/240-193 +TAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT +>ERR1553846.100035-ORL20E0-512775-1-SSU_rRNA_eukarya/273-203 +CAAACTTGGTTATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGGGAACCTGCG +GAAGGATCATT +>ERR1553846.100037-ORL20E0-512804-1-SSU_rRNA_eukarya/262-177 +GGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCC +GTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100038-ORL20E0-512807-1-SSU_rRNA_eukarya/249-193 +TAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT +>ERR1553846.10004-ORL20E0-51096-1-SSU_rRNA_eukarya/248-177 +CCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTTGGTGAACCAGC +GGAAGGATCATT +>ERR1553846.100041-ORL20E0-512821-1-SSU_rRNA_eukarya/263-177 +GGGCCGGAAAGTTATCCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTC +CGTTGGTGAACCAGCGGAAGGATCATT +>ERR1553846.100042-ORL20E0-512822-1-SSU_rRNA_eukarya/252-172 +GGGAAATTGCCCAAACTTGCTTATTTAGAGGAAGTACAAGTCGTAACAAGGTTTCCGTAG +GTGAACCTGCGGAAGGATCAT +>ERR1553846.100048-ORL20E0-512847-1-SSU_rRNA_eukarya/283-202 +GGAAAGTTGTTCAAACTTGGGCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAG +GTGAACCTGCGGAAGGATCATT +>ERR1553846.100049-ORL20E0-512851-1-SSU_rRNA_eukarya/250-193 +TTAGAGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATT +>ERR1553846.100050-ORL20E0-512852-1-SSU_rRNA_eukarya/279-210 +AAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAG +AAGGATCATT \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_bat_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bat_file.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,39 @@ +# bin classification reason lineage lineage scores +1.FASTA taxid assigned based on 4161/4187 ORFs 1;131567;2;1783272;201174;1760;85007;182102;85043;1736349 1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.99;0.31 +10.FASTA taxid assigned based on 1895/1915 ORFs 1;131567;2;1224;1236;135614;32033;2370;2371 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.94 +11.FASTA taxid assigned based on 4793/4923 ORFs 1;131567;2;1783272;1239;186801;186802;31979;1884934;191027* 1.00;1.00;1.00;0.99;0.99;0.98;0.98;0.83;0.81;0.81 +12.FASTA taxid assigned based on 4056/4136 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;398041;462367 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 +13.FASTA taxid assigned based on 3575/3644 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +14.FASTA taxid assigned based on 245/248 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736522 1.00;1.00;1.00;0.99;0.91;0.91;0.91;0.89;0.35 +15.FASTA taxid assigned based on 3834/3853 ORFs 1;131567;2;1224;28211;204455;31989;1097466;404881 1.00;1.00;1.00;1.00;1.00;0.99;0.97;0.96;0.96 +16.FASTA taxid assigned based on 2824/2869 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +17.FASTA taxid assigned based on 2646/2678 ORFs 1;131567;2;1783272;1239;186801;186802;186804;214904;227138 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.90 +18.FASTA taxid assigned based on 6183/6302 ORFs 1;131567;2;1783272;200795;388447;388448;768649;768650* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +19.FASTA taxid assigned based on 8855/8930 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +2.FASTA taxid assigned based on 3440/3461 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +20.FASTA taxid assigned based on 4264/4287 ORFs 1;131567;2;1224;28216;206351;1499392;397275;1121000 1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.97 +21.FASTA taxid assigned based on 5835/5867 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736522 1.00;1.00;1.00;1.00;0.98;0.98;0.98;0.97;0.59 +22.FASTA taxid assigned based on 2576/2598 ORFs 1;131567;2;1783270;68336;976;117743;200644;49546;363408;328515 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.97;0.97;0.96;0.89 +23.FASTA taxid assigned based on 5759/5763 ORFs 1;131567;2 1.00;0.74;0.73 +24.FASTA taxid assigned based on 6458/6478 ORFs 1;131567;2;1224;28211;204455;31989;265;266 1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.95;0.46 +25.FASTA taxid assigned based on 4145/4341 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;398041;462367 1.00;1.00;1.00;0.99;0.99;0.99;0.93;0.93;0.93;0.89;0.88 +26.FASTA taxid assigned based on 2208/2231 ORFs 1;131567;2;1783272;1239;186801;186802;1491775;42447;182411 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.97;0.97;0.72 +27.FASTA taxid assigned based on 4557/4633 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.88 +28.FASTA taxid assigned based on 1856/1860 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +29.FASTA taxid assigned based on 3780/3817 ORFs 1;131567;2;1783272;1239;91061;1385;539002;539742;33986* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +3.FASTA taxid assigned based on 205/207 ORFs 1;131567;2;1783272;1239;909932;909929;1843491;55506;55507* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 +30.FASTA taxid assigned based on 6218/6259 ORFs 1;131567;2;1224;28216;80840;75682;149698;1736532 1.00;1.00;1.00;1.00;0.98;0.98;0.98;0.97;0.57 +31.FASTA taxid assigned based on 2720/2744 ORFs 1;131567;2;1224;28216;80840;80864;198705;198706 1.00;1.00;1.00;1.00;0.99;0.99;0.98;0.97;0.97 +32.FASTA taxid assigned based on 3222/3245 ORFs 1;131567;2;1783272;201174;1760;85006;85021;99479;1736399 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.96;0.53 +33.FASTA taxid assigned based on 292/297 ORFs 1;131567;2;1224;28211;204455;31989 1.00;1.00;0.99;0.89;0.84;0.50;0.49 +34.FASTA taxid assigned based on 3557/3604 ORFs 1;131567;2;1783272;1239;186801;186802;186803;653683;264463* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.99 +35.FASTA taxid assigned based on 2175/2205 ORFs 1;131567;2;1783272;1239;909932;909929;1843491;55506;55507* 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.99;0.99 +36.FASTA taxid assigned based on 3370/3422 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.87 +37.FASTA taxid assigned based on 4212/4264 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.92;0.92;0.92;0.92;0.91 +38.FASTA taxid assigned based on 8008/8038 ORFs 1;131567;2;1224;28211;204455;31989;265;266 1.00;1.00;1.00;1.00;1.00;0.99;0.99;0.98;0.40 +4.FASTA taxid assigned based on 8568/8682 ORFs 1;131567;2;1783270;68336;976;1853228;1853229;563835;1004300;1004304 1.00;1.00;1.00;1.00;1.00;1.00;0.92;0.92;0.92;0.92;0.90 +5.FASTA taxid assigned based on 2948/2952 ORFs 1;131567;2;1224;28211;204455;31989;205889;990712 1.00;1.00;1.00;1.00;1.00;0.87;0.87;0.86;0.86 +6.FASTA taxid assigned based on 2846/2901 ORFs 1;131567;2;1224;1236;135614;32033;68;1736549 1.00;1.00;1.00;0.96;0.94;0.92;0.85;0.65;0.52 +7.FASTA taxid assigned based on 5030/5081 ORFs 1;131567;2;1224;68525;28221;213118;213119;218207;259354 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.38 +8.FASTA taxid assigned based on 2537/2579 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +9.FASTA taxid assigned based on 1648/1673 ORFs 1;131567;2;1783272;544448;31969;186332;186333;2086;2088 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_binning.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_binning.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +@Version:0.9.1 +@SampleID:gsa + +@@SEQUENCEID BINID TAXID +RH|P|C37126 Sample6_89 45202 +RH|P|C3274 Sample9_91 32644 +RH|P|C26099 1053046 765201 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_binning2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_binning2.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +@Version:0.9.1 +@SampleID:gsa + +@@SEQUENCEID BINID TAXID +RH|P|C35075 1053046 765201 +RH|P|C20873 1053046 765201 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_biobox_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_biobox_file.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +#CAMI Format for Binning +@Version:0.9.0 +@SampleID:gsa +@@SEQUENCEID BINID +RL|S1|C1198 1 +RL|S1|C3912 1 +RL|S1|C131 10 +RL|S1|C1410 10 +RL|S1|C2929 10 +RL|S1|C3754 10 +RL|S1|C1335 11 +RL|S1|C1344 11 +RL|S1|C1352 11 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_biobox_file_add_taxid_bat.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_biobox_file_add_taxid_bat.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +#CAMI Format for Binning +@Version:0.9.0 +@SampleID:_SAMPLEID_ +@@SEQUENCEID BINID TAXID +RL|S1|C1198 1 1736349 +RL|S1|C3912 1 1736349 +RL|S1|C131 10 2371 +RL|S1|C1410 10 2371 +RL|S1|C2929 10 2371 +RL|S1|C3754 10 2371 +RL|S1|C1335 11 191027 +RL|S1|C1344 11 191027 +RL|S1|C1352 11 191027 |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_biobox_file_add_taxid_gtdb.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_biobox_file_add_taxid_gtdb.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +#CAMI Format for Binning +@Version:0.9.0 +@SampleID:_SAMPLEID_ +@@SEQUENCEID BINID TAXID +RL|S1|C1198 1 12908 +RL|S1|C3912 1 12908 +RL|S1|C131 10 2371 +RL|S1|C1410 10 2371 +RL|S1|C2929 10 2371 +RL|S1|C3754 10 2371 +RL|S1|C1335 11 191027 +RL|S1|C1344 11 191027 +RL|S1|C1352 11 191027 |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_gold.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gold.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,9 @@ +@Version:0.9.1 +@SampleID:gsa + +@@SEQUENCEID BINID TAXID LENGTH +RH|P|C37126 Sample6_89 45202 25096 +RH|P|C3274 Sample9_91 32644 10009 +RH|P|C26099 1053046 765201 689201 +RH|P|C35075 1053046 765201 173282 +RH|P|C20873 1053046 765201 339258 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_gtdb_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gtdb_file.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,39 @@\n+user_genome\tclassification\tfastani_reference\tfastani_reference_radius\tfastani_taxonomy\tfastani_ani\tfastani_af\tclosest_placement_reference\tclosest_placement_radius\tclosest_placement_taxonomy\tclosest_placement_ani\tclosest_placement_af\tpplacer_taxonomy\tclassification_method\tnote\tother_related_references(genome_id,species_name,radius,ANI,AF)\tmsa_percent\ttranslation_table\tred_value\twarnings\n+1\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\tGCF_000964005.1\t95.0\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\t95.01\t0.891\tGCF_000964005.1\t95.0\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__Williamsia_A herbipolensis\t95.01\t0.891\td__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCF_014635305.1, s__Williamsia_A phyllosphaerae, 95.0, 82.43, 0.702; GCA_016462415.1, s__Williamsia_A sp016462415, 95.0, 82.15, 0.649; GCF_018474015.1, s__Williamsia_A sp018474015, 95.0, 80.23, 0.523\t96.49\t11\tN/A\tN/A\n+10\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\tGCF_011801475.1\t95.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\t99.99\t1.0\tGCF_011801475.1\t95.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__Xylella fastidiosa\t99.99\t1.0\td__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCF_013177435.1, s__Xylella taiwanensis, 95.0, 82.85, 0.849\t85.13\t11\tN/A\tN/A\n+11\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\tGCF_900142245.1\t95.0\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\t99.97\t0.872\tGCF_900142245.1\t95.0\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter;s__Paramaledivibacter caminithermalis\t99.97\t0.872\td__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tN/A\t78.49\t11\tN/A\tGenome has more than 10.0% of markers with multiple hits\n+12\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\tGCF_900129295.1\t95.0\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\t100.0\t0.999\tGCF_900129295.1\t95.0\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__Flavisolibacter ginsengisoli\t100.0\t0.999\td__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017745135.1, s__Flavisolibacter sp017745135, 95.0, 77.32, 0.1; GCA_013327885.1, s__Flavisolibacter sp013327885, 95.0, 77.25, 0.081; GCF_007970805.1, s__Flavisolibacter ginsenosidimutans, 95.0, 76.92, 0.056; GCF_003628535.1, s__Flavisolibacter nicotianae, 95.0, 76.88, 0.08; GCA_014163555.1, s__Flavisolibacter sp014163555, 95.0, 76.86, 0.077; GCA_002050435.1, s__Flavisolibacter sp002050435, 95.0, 76.62, 0.139\t97.8\t11\tN/A\tN/A\n+13\td__Bacteria;p__Fir'..b'eae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t99.22\t0.892\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t99.22\t0.892\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017388605.1, s__Anaeroplasma sp017388605, 95.0, 83.89, 0.71; GCA_017449215.1, s__Anaeroplasma sp017449215, 95.0, 78.37, 0.262; GCA_017441525.1, s__Anaeroplasma sp017441525, 95.0, 78.17, 0.272; GCA_002449755.1, s__Anaeroplasma sp002449755, 95.0, 78.14, 0.275; GCA_017462645.1, s__Anaeroplasma sp017462645, 95.0, 78.0, 0.236; GCA_017524905.1, s__Anaeroplasma sp017524905, 95.0, 77.92, 0.242; GCA_016280975.1, s__Anaeroplasma sp016280975, 95.0, 77.86, 0.273; GCA_017444645.1, s__Anaeroplasma sp017444645, 95.0, 77.57, 0.26; GCA_900770055.1, s__Anaeroplasma sp900770055, 95.0, 77.54, 0.192; GCA_902783745.1, s__Anaeroplasma sp902783745, 95.0, 77.5, 0.231; GCA_016282815.1, s__Anaeroplasma sp016282815, 95.0, 77.44, 0.216; GCA_017542485.1, s__Anaeroplasma sp017542485, 95.0, 77.43, 0.189; GCA_016288855.1, s__Anaeroplasma sp016288855, 95.0, 77.42, 0.212; GCA_015059145.1, s__Anaeroplasma sp015059145, 95.0, 77.4, 0.199; GCA_900767915.1, s__Anaeroplasma sp900767915, 95.0, 77.38, 0.187; GCA_017454375.1, s__Anaeroplasma sp017454375, 95.0, 77.11, 0.128; GCA_902796895.1, s__Anaeroplasma sp902796895, 95.0, 76.99, 0.242; GCA_018715825.1, s__Anaeroplasma faecigallinarum, 95.0, 76.73, 0.118; GCA_905236965.1, s__Anaeroplasma sp905236965, 95.0, 76.07, 0.2; GCA_905236105.1, s__Anaeroplasma sp905236105, 95.0, 76.05, 0.133\t57.15\t11\tN/A\tGenome has more than 10.0% of markers with multiple hits\n+9\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t100.0\t1.0\tGCF_003550015.1\t95.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__Anaeroplasma bactoclasticum\t100.0\t1.0\td__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma;s__\ttaxonomic classification defined by topology and ANI\ttopological placement and ANI have congruent species assignments\tGCA_017388605.1, s__Anaeroplasma sp017388605, 95.0, 84.15, 0.658; GCA_002449755.1, s__Anaeroplasma sp002449755, 95.0, 78.65, 0.256; GCA_017441525.1, s__Anaeroplasma sp017441525, 95.0, 78.34, 0.265; GCA_017449215.1, s__Anaeroplasma sp017449215, 95.0, 78.33, 0.263; GCA_017524905.1, s__Anaeroplasma sp017524905, 95.0, 78.01, 0.244; GCA_017462645.1, s__Anaeroplasma sp017462645, 95.0, 78.0, 0.23; GCA_016280975.1, s__Anaeroplasma sp016280975, 95.0, 77.96, 0.23; GCA_017542485.1, s__Anaeroplasma sp017542485, 95.0, 77.74, 0.195; GCA_017444645.1, s__Anaeroplasma sp017444645, 95.0, 77.7, 0.258; GCA_900767915.1, s__Anaeroplasma sp900767915, 95.0, 77.52, 0.172; GCA_016288855.1, s__Anaeroplasma sp016288855, 95.0, 77.51, 0.196; GCA_902783745.1, s__Anaeroplasma sp902783745, 95.0, 77.5, 0.209; GCA_016282815.1, s__Anaeroplasma sp016282815, 95.0, 77.5, 0.201; GCA_900770055.1, s__Anaeroplasma sp900770055, 95.0, 77.43, 0.184; GCA_015059145.1, s__Anaeroplasma sp015059145, 95.0, 77.28, 0.183; GCA_902796895.1, s__Anaeroplasma sp902796895, 95.0, 77.2, 0.221; GCA_017454375.1, s__Anaeroplasma sp017454375, 95.0, 77.19, 0.129; GCA_018715825.1, s__Anaeroplasma faecigallinarum, 95.0, 76.79, 0.111; GCA_905236965.1, s__Anaeroplasma sp905236965, 95.0, 76.42, 0.19; GCA_905236105.1, s__Anaeroplasma sp905236105, 95.0, 76.12, 0.118\t66.58\t11\tN/A\tN/A\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_gtdb_to_taxdump_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gtdb_to_taxdump_file.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,25 @@ +ncbi_taxonomy gtdb_taxonomy lca_frac target_tax_level lineage +s__Williamsia_A herbipolensis unclassified NA NA NA +s__Xylella fastidiosa s__Xylella fastidiosa 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__xanthomonadales;f__xanthomonadaceae;g__xylella;s__xylella fastidiosa +s__Paramaledivibacter caminithermalis s__Paramaledivibacter caminithermalis 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__peptostreptococcales;f__caminicellaceae;g__paramaledivibacter;s__paramaledivibacter caminithermalis +s__Flavisolibacter ginsengisoli s__Flavisolibacter ginsengisoli 1.0 species d__bacteria;p__bacteroidota;c__bacteroidia;o__chitinophagales;f__chitinophagaceae;g__flavisolibacter;s__flavisolibacter ginsengisoli +s__Anaeroplasma bactoclasticum c__Bacilli 1.0 class d__bacteria;p__bacillota;c__bacilli +s__Pseudoduganella sp001425045 unclassified NA NA NA +s__Albidovulum denitrificans unclassified NA NA NA +s__Tepidibacter formicigenes s__Tepidibacter formicigenes 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__peptostreptococcales;f__peptostreptococcaceae;g__tepidibacter;s__tepidibacter formicigenes +s__Thermosporothrix hazakensis unclassified NA NA NA +s__Exiguobacterium_A sp001423965 unclassified NA NA NA +s__Andreprevotia lacus s__Andreprevotia lacus 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__burkholderiales;f__chitinibacteraceae;g__andreprevotia;s__andreprevotia lacus +s__Nonlabens dokdonensis g__Nonlabens 1.0 genus d__bacteria;p__bacteroidota;c__bacteroidia;o__flavobacteriales;f__flavobacteriaceae;g__nonlabens +s__Pseudomonas aeruginosa s__Pseudomonas aeruginosa 0.99 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__pseudomonadales;f__pseudomonadaceae;g__pseudomonas;s__pseudomonas aeruginosa +s__Paracoccus denitrificans g__Paracoccus 1.0 genus d__bacteria;p__pseudomonadota;c__alphaproteobacteria;o__rhodobacterales;f__rhodobacteraceae;g__paracoccus +N/A unclassified NA NA NA +s__Anaerobranca californiensis s__Anaerobranca californiensis 1.0 species d__bacteria;p__bacillota_d;c__proteinivoracia;o__proteinivoracales;f__proteinivoraceae;g__anaerobranca;s__anaerobranca californiensis +s__Hydrotalea sandarakina s__Hydrotalea sandarakina 1.0 species d__bacteria;p__bacteroidota;c__bacteroidia;o__chitinophagales;f__chitinophagaceae;g__hydrotalea;s__hydrotalea sandarakina +s__Schwartzia succinivorans f__Selenomonadaceae 1.0 family d__bacteria;p__bacillota_c;c__negativicutes;o__selenomonadales;f__selenomonadaceae +s__Pseudoduganella sp001425265 unclassified NA NA NA +s__Lampropedia hyalina s__Lampropedia hyalina 1.0 species d__bacteria;p__pseudomonadota;c__gammaproteobacteria;o__burkholderiales;f__burkholderiaceae_b;g__lampropedia;s__lampropedia hyalina +s__Phycicoccus sp001428065 unclassified NA NA NA +s__Anaerosporobacter mobilis s__Anaerosporobacter mobilis 1.0 species d__bacteria;p__bacillota_a;c__clostridia;o__lachnospirales;f__lachnospiraceae;g__anaerosporobacter;s__anaerosporobacter mobilis +s__Meinhardsimonia xiamenensis s__Meinhardsimonia xiamenensis 1.0 species d__bacteria;p__pseudomonadota;c__alphaproteobacteria;o__rhodobacterales;f__rhodobacteraceae;g__meinhardsimonia;s__meinhardsimonia xiamenensis +s__Desulfatibacillum alkenivorans s__Desulfatibacillum alkenivorans 1.0 species d__bacteria;p__desulfobacterota;c__desulfobacteria;o__desulfobacterales;f__desulfatibacillaceae;g__desulfatibacillum;s__desulfatibacillum alkenivorans |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/test_taxonkit_file.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_taxonkit_file.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,25 @@ +unclassified 12908 +Xylella fastidiosa 2371 +Paramaledivibacter caminithermalis 191027 +Flavisolibacter ginsengisoli 462367 +Bacilli 91061 +unclassified 12908 +unclassified 12908 +Tepidibacter formicigenes 227138 +unclassified 12908 +unclassified 12908 +Andreprevotia lacus 1121000 +Nonlabens 363408 +Pseudomonas aeruginosa 287 +Paracoccus 265 +Paracoccus 249411 +unclassified 12908 +Anaerobranca californiensis 182411 +Hydrotalea sandarakina 1004304 +Selenomonadaceae 1843491 +unclassified 12908 +Lampropedia hyalina 198706 +unclassified 12908 +Anaerosporobacter mobilis 264463 +Meinhardsimonia xiamenensis 990712 +Desulfatibacillum alkenivorans 259354 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 test-data/unique_common.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unique_common.tsv Sun Aug 25 13:19:14 2024 +0000 |
| b |
| b'@@ -0,0 +1,1366 @@\n+evo_1035930.029\tcommon strain\n+1035930\tcommon strain\n+evo_1035930.032\tcommon strain\n+evo_1035930.011\tcommon strain\n+evo_1286_AP.033\tcommon strain\n+1286_AP\tcommon strain\n+evo_1286_AP.026\tcommon strain\n+evo_1286_AP.037\tcommon strain\n+evo_1286_AP.008\tcommon strain\n+1052944\tcommon strain\n+1053058\tcommon strain\n+1052947\tcommon strain\n+evo_1049056.013\tcommon strain\n+evo_1049056.031\tcommon strain\n+evo_1049056.011\tcommon strain\n+1049056\tcommon strain\n+evo_1049056.039\tcommon strain\n+evo_1049056.015\tcommon strain\n+1048783\tunique strain\n+1220_AD\tunique strain\n+1036608\tunique strain\n+1036728\tunique strain\n+1036743\tunique strain\n+1036539\tunique strain\n+1139_AG\tunique strain\n+1285_BH\tunique strain\n+1036707\tunique strain\n+1030755\tunique strain\n+1048993\tunique strain\n+1036755\tunique strain\n+1049005\tunique strain\n+1036554\tunique strain\n+1030752\tunique strain\n+1035900\tunique strain\n+1030878\tunique strain\n+1030836\tunique strain\n+1049089\tunique strain\n+1220_AJ\tunique strain\n+1365_A\tunique strain\n+1036641\tunique strain\n+evo_1030728.011\tcommon strain\n+evo_1030728.001\tcommon strain\n+1030728\tcommon strain\n+evo_1030728.035\tcommon strain\n+evo_1030728.009\tcommon strain\n+evo_1030728.038\tcommon strain\n+1052977\tcommon strain\n+1052974\tcommon strain\n+evo_1035921.028\tcommon strain\n+1035921\tcommon strain\n+evo_1035921.030\tcommon strain\n+evo_1035921.008\tcommon strain\n+evo_1035921.007\tcommon strain\n+1053034\tcommon strain\n+1053037\tcommon strain\n+1286_AO\tcommon strain\n+1286_Y\tcommon strain\n+1139_T\tcommon strain\n+1139_AW\tcommon strain\n+1220_BB\tcommon strain\n+1021_AS\tcommon strain\n+1021_AQ\tcommon strain\n+evo_1139_Y.018\tcommon strain\n+evo_1139_Y.035\tcommon strain\n+1139_Y\tcommon strain\n+1220_BD\tcommon strain\n+1053028\tcommon strain\n+1053022\tcommon strain\n+1053025\tcommon strain\n+1052968\tcommon strain\n+1048966\tcommon strain\n+1021_P\tcommon strain\n+1220_AX\tcommon strain\n+1139_B\tcommon strain\n+1287_N\tcommon strain\n+1052992\tcommon strain\n+1052995\tcommon strain\n+1285_BO\tcommon strain\n+1285_CK\tcommon strain\n+1285_AC\tcommon strain\n+1287_BD\tcommon strain\n+1220_AR\tcommon strain\n+1286_BU\tcommon strain\n+1285_BV\tcommon strain\n+1286_BD\tcommon strain\n+1286_G\tcommon strain\n+evo_1286_G.034\tcommon strain\n+evo_1286_G.010\tcommon strain\n+1052965\tcommon strain\n+1052959\tcommon strain\n+1287_BC\tcommon strain\n+1021_C\tcommon strain\n+1053004\tcommon strain\n+1052998\tcommon strain\n+1053055\tunique strain\n+1052953\tunique strain\n+1286_AF\tunique strain\n+1030905\tunique strain\n+1053031\tunique strain\n+1048861\tunique strain\n+1036782\tunique strain\n+1048870\tunique strain\n+1139_CO\tunique strain\n+1030776\tunique strain\n+1030740\tunique strain\n+1285_BD\tunique strain\n+1139_BF\tunique strain\n+1035939\tunique strain\n+1139_CJ\tunique strain\n+1030782\tunique strain\n+1036695\tunique strain\n+1139_CF\tunique strain\n+1285_BF\tunique strain\n+1030881\tunique strain\n+1048978\tunique strain\n+1036803\tunique strain\n+1052950\tunique strain\n+1036629\tunique strain\n+1035993\tunique strain\n+1220_E\tunique strain\n+1285_CF\tunique strain\n+1036614\tunique strain\n+1030896\tunique strain\n+1049035\tunique strain\n+1030869\tunique strain\n+1035906\tunique strain\n+1036011\tunique strain\n+1048942\tunique strain\n+1035969\tunique strain\n+1035981\tunique strain\n+1030806\tunique strain\n+1036635\tunique strain\n+1049032\tunique strain\n+1287_W\tunique strain\n+1030800\tunique strain\n+1030716\tunique strain\n+1053049\tunique strain\n+1287_BO\tunique strain\n+1021_AP\tunique strain\n+1035951\tunique strain\n+1220_CF\tunique strain\n+1030968\tunique strain\n+1030812\tunique strain\n+1287_BN\tunique strain\n+1139_AL\tunique strain\n+1036557\tunique strain\n+1285_AD\tunique strain\n+1286_BV\tunique strain\n+1036716\tunique strain\n+1036566\tunique strain\n+1053040\tunique strain\n+1220_AO\tunique strain\n+1049011\tunique strain\n+1048945\tunique strain\n+1036731\tunique strain\n+1036701\tunique strain\n+1139_AA\tunique strain\n+1220_A\tunique strain\n+1048885\tunique strain\n+1220_X\tunique strain\n+1049083\tunique strain\n+1139_AF\tunique strain\n+1052941\tunique strain\n+1036785\tunique strain\n+1036704\tunique strain\n+1'..b'ircular element\n+Sample18_70\tcircular element\n+Sample18_82\tcircular element\n+Sample18_83\tcircular element\n+Sample18_86\tcircular element\n+Sample18_87\tcircular element\n+Sample18_90\tcircular element\n+Sample18_91\tcircular element\n+Sample18_94\tcircular element\n+Sample18_97\tcircular element\n+Sample19_105\tcircular element\n+Sample19_106\tcircular element\n+Sample19_117\tcircular element\n+Sample19_13\tcircular element\n+Sample19_146\tcircular element\n+Sample19_153\tcircular element\n+Sample19_175\tcircular element\n+Sample19_180\tcircular element\n+Sample19_19\tcircular element\n+Sample19_209\tcircular element\n+Sample19_21\tcircular element\n+Sample19_212\tcircular element\n+Sample19_215\tcircular element\n+Sample19_220\tcircular element\n+Sample19_241\tcircular element\n+Sample19_242\tcircular element\n+Sample19_247\tcircular element\n+Sample19_254\tcircular element\n+Sample19_275\tcircular element\n+Sample19_280\tcircular element\n+Sample19_286\tcircular element\n+Sample19_293\tcircular element\n+Sample19_315\tcircular element\n+Sample19_32\tcircular element\n+Sample19_350\tcircular element\n+Sample19_366\tcircular element\n+Sample19_367\tcircular element\n+Sample19_37\tcircular element\n+Sample19_39\tcircular element\n+Sample19_391\tcircular element\n+Sample19_392\tcircular element\n+Sample19_62\tcircular element\n+Sample19_67\tcircular element\n+Sample19_75\tcircular element\n+Sample19_77\tcircular element\n+Sample19_78\tcircular element\n+Sample19_89\tcircular element\n+Sample20_1\tcircular element\n+Sample20_10\tcircular element\n+Sample20_101\tcircular element\n+Sample20_108\tcircular element\n+Sample20_122\tcircular element\n+Sample20_124\tcircular element\n+Sample20_130\tcircular element\n+Sample20_131\tcircular element\n+Sample20_136\tcircular element\n+Sample20_145\tcircular element\n+Sample20_154\tcircular element\n+Sample20_158\tcircular element\n+Sample20_175\tcircular element\n+Sample20_20\tcircular element\n+Sample20_24\tcircular element\n+Sample20_25\tcircular element\n+Sample20_33\tcircular element\n+Sample20_37\tcircular element\n+Sample20_40\tcircular element\n+Sample20_43\tcircular element\n+Sample20_5\tcircular element\n+Sample20_58\tcircular element\n+Sample20_70\tcircular element\n+Sample20_78\tcircular element\n+Sample20_79\tcircular element\n+Sample20_80\tcircular element\n+Sample20_85\tcircular element\n+Sample20_94\tcircular element\n+Sample6_102\tcircular element\n+Sample6_107\tcircular element\n+Sample6_110\tcircular element\n+Sample6_125\tcircular element\n+Sample6_130\tcircular element\n+Sample6_16\tcircular element\n+Sample6_171\tcircular element\n+Sample6_173\tcircular element\n+Sample6_180\tcircular element\n+Sample6_183\tcircular element\n+Sample6_186\tcircular element\n+Sample6_188\tcircular element\n+Sample6_206\tcircular element\n+Sample6_217\tcircular element\n+Sample6_219\tcircular element\n+Sample6_224\tcircular element\n+Sample6_227\tcircular element\n+Sample6_260\tcircular element\n+Sample6_273\tcircular element\n+Sample6_306\tcircular element\n+Sample6_33\tcircular element\n+Sample6_333\tcircular element\n+Sample6_342\tcircular element\n+Sample6_35\tcircular element\n+Sample6_389\tcircular element\n+Sample6_39\tcircular element\n+Sample6_391\tcircular element\n+Sample6_40\tcircular element\n+Sample6_421\tcircular element\n+Sample6_423\tcircular element\n+Sample6_47\tcircular element\n+Sample6_485\tcircular element\n+Sample6_506\tcircular element\n+Sample6_508\tcircular element\n+Sample6_535\tcircular element\n+Sample6_553\tcircular element\n+Sample6_564\tcircular element\n+Sample6_566\tcircular element\n+Sample6_588\tcircular element\n+Sample6_590\tcircular element\n+Sample6_608\tcircular element\n+Sample6_632\tcircular element\n+Sample6_634\tcircular element\n+Sample6_670\tcircular element\n+Sample6_72\tcircular element\n+Sample6_746\tcircular element\n+Sample6_752\tcircular element\n+Sample6_793\tcircular element\n+Sample6_823\tcircular element\n+Sample6_837\tcircular element\n+Sample6_84\tcircular element\n+Sample6_843\tcircular element\n+Sample6_863\tcircular element\n+Sample6_89\tcircular element\n+Sample6_894\tcircular element\n+Sample6_936\tcircular element\n+Sample6_94\tcircular element\n+Sample6_96\tcircular element\n' |
| b |
| diff -r 000000000000 -r 1e10251b9615 tool-data/ncbi_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#value name path +test-db-tox "Test Database" ${__HERE__}/test-db \ No newline at end of file |
| b |
| diff -r 000000000000 -r 1e10251b9615 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 1e10251b9615 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sun Aug 25 13:19:14 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables> |