| Next changeset 1:afc795d10918 (2024-06-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 807e74c623d563166546758ae9bd435322b78b96 |
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added:
cami_amber.xml cami_amber_add_length.xml cami_amber_convert_to_biobox.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_binning.tsv test-data/test_binning2.tsv test-data/test_gold.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 6c71acde9d52 cami_amber.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cami_amber.xml Mon May 20 18:08:36 2024 +0000 |
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| b'@@ -0,0 +1,465 @@\n+<tool id="cami_amber" name="CAMI AMBER" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Evaluation package for MAGs</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ #set $path_to_html = $html.files_path\n+ #set $max = []\n+ #set $min = []\n+ #set $label = []\n+\n+ mkdir -p output inputs \'$path_to_html\' &&\n+\n+ #if $tox.ncbi.is_select == \'yes\':\n+ #if $tox.input.is_select == \'manually\':\n+ mkdir -p ncbi &&\n+ #for $file in $tox.ncbi_dir:\n+ ln -s \'$file\' \'./ncbi/$file.element_identifier\' &&\n+ #end for\n+ #end if\n+ #end if\n+\n+ #for $i, $file in enumerate($input_files):\n+ ln -s \'$file.binning_files\' \'./inputs/$file.binning_files.element_identifier\' &&\n+ #if $file.labels:\n+ $label.append($file.labels)\n+ #end if \n+ #end for\n+\n+ #if $genome.thresholds:\n+ #for $i, $arg in enumerate($genome.thresholds):\n+ #if $arg.min_completeness:\n+ $min.append($arg.min_completeness)\n+ #end if\n+ #if $arg.max_contamination:\n+ $max.append($arg.max_contamination)\n+ #end if\n+ #end for\n+ #end if\n+\n+ amber.py\n+ -g \'${gold_standard_file}\'\n+ #if $label:\n+ #set $sep = \'\'\n+ -l\n+ \'\n+ #for $lab in $label:\n+ $sep$lab\n+ #set $sep = \',\'\n+ #end for\n+ \'\n+ #end if\n+ -p ${filter}\n+ #if $min_length:\n+ -n $min_length\n+ #end if\n+ #if $desc:\n+ -d \'${desc}\'\n+ #end if\n+ #if $min:\n+ #set $sep = \'\'\n+ --min_completeness\n+ \'\n+ #for $i in $min:\n+ $sep$i\n+ #set $sep = \',\'\n+ #end for\n+ \'\n+ #end if\n+ #if $max:\n+ #set $sep = \'\'\n+ --max_contamination\n+ \'\n+ #for $i in $max:\n+ $sep$i\n+ #set$sep = \',\'\n+ #end for\n+ \'\n+ #end if\n+ #if $genome.remove_genomes:\n+ -r \'$genome.remove_genomes\'\n+ #end if\n+ #if $genome.remove.is_select == \'yes\':\n+ -k \'$genome.keyword\'\n+ #end if\n+ #if $genome.genome_coverage:\n+ --genome_coverage \'$genome.genome_coverage\'\n+ #end if\n+ #if $tox.ncbi.is_select == \'yes\':\n+ #if $tox.input.is_select == \'manually\':\n+ --ncbi_dir ncbi\n+ #else:\n+ --ncbi_dir \'$tox.ncbi_dir.fields.path\'\n+ #end if\n+ #end if\n+ -o output\n+ #for $i, $bin in enumerate($input_files):\n+ \'inputs/$bin.binning_files.element_identifier\'\n+ #end for\n+\n+ &&\n+\n+ mv \'output/heatmap_bar.png\' \'$path_to_html\'\n+\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param argument="--gold_standard_file" format="tabular" type="data"\n+ label="Mapping of contigs or reads"\n+ help="Input the gold standard file here so amber know the correct IDs for each contig/read" />\n+ <repeat name="input_files" title="Binning files and names "\n+ help="Enter multiple binning files and names (names are optional). IMPORTANT: for each binning file you use in the program you need to state one label, this mean for example for 3 binning files you need 3 labels (3 slots) not more or less!">\n+ <param name="binning_files" format="tabular" type="data"\n+ label="Input bin files here" /> \n+ <param argument="--labels" type="text" value="" optional="true"\n+ label="Name for bin" />'..b' RL|S1|C10817\tSample18_57\t20518\n+ RL|S1|C11497\tSample22_57\t37672\n+ RL|S1|C6571\tevo_1286_AP.033\t69914\n+ RL|S1|C10560\tevo_1286_AP.033\t995657\n+ RL|S1|C13546\tevo_1286_AP.033\t626775\n+\n+ Note: This file looks similar to the binning files but the only different which is also is important is the length column.\n+\n+ - Multiple binning files (biobox format)\n+\n+ Files can be created via the convert_to_biobox tool\n+\n+ .. class:: infomark\n+\n+ Example(tab separated):\n+\n+ ::\n+\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+\n+ There are also additional inputs which can be used:\n+\n+ - A genome list which should be removed(tabular format)\n+\n+ .. class:: infomark\n+\n+ Example(tab separated): \n+\n+ ::\n+\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+\n+ Note: The first column contain the BINID and the second contain any kind of string. IMPORTANT: The argument where to state a keyword has to match to the anything in the second column to filter these kind of genomes out. If there is no keyword stated it can happen if the remove list contain all genomes which should be used then AMBER will fail since there are no genomes left to use!\n+\n+ - Genome coverage file (tabular format)\n+\n+ .. class:: infomark\n+\n+ Example(tab separated):\n+\n+ ::\n+\n+ @SampleID:gsa_pooled\n+ @@GENOMEID\tCOVERAGE\n+ 4378740.0\t82.85111527272727\n+ 4378740.1\t27.159305090909097\n+ denovo10559.0\t2.1596957142857143\n+ 179927.0\t1.6946866666666667\n+ denovo8373.1\t2.07144\n+ 136604.0\t9.150489565217391\n+ denovo8373.0\t1.1413460000000002\n+ 269378.0\t8.051563333333332\n+ 190114.0\t18.253119629629627\n+ 228140.0\t3.078681818181818\n+ 135956.0\t121.52672015625001\n+ 259846.0\t12.298210588235296\n+ 162576.0\t9.57867191489362\n+ 184966.0\t14.461031521739134\n+\n+ There is also an option to include the NCBI database in AMBER. This can be used when including the link which is stated in the data manager: **data_manager_fetch_ncbi_taxonomy**. This data manager download the current version of the database and store all files for you. If there are questions about data manager maybe have a look at this `Tutorial <https://usegalaxy.eu/training-material/topics/admin/tutorials/reference-genomes/tutorial.html>`_.\n+\n+ **Output**\n+\n+ AMBER will output 3 tsv files where each metrics value is stated. The important output is the HTML file where all data are included and also can be visualized with certain plots!\n+\n+ **Additional information**\n+\n+ The package **Bokeh** will create warnings which can be ignored since the only tell you that certain functions in the code are swapped with the new functions. AMBER was tested with the stated version of **Bokeh** and with the newest version of it and both generate the same output!\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 6c71acde9d52 cami_amber_add_length.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cami_amber_add_length.xml Mon May 20 18:08:36 2024 +0000 |
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| @@ -0,0 +1,90 @@ +<tool id="cami_amber_add" name="CAMI AMBER add length column" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Create gold standard file for CAMI AMBER</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + + ln -s '${gold_standard_file}' '$gold_standard_file.element_identifier' && + ln -s '${fasta_file}' '$fasta_file.element_identifier' && + + add_length_column.py + -g '$gold_standard_file.element_identifier' + -f '$fasta_file.element_identifier' + > gold_standard_file.tsv + ]]> + </command> + <inputs> + <param argument="--gold_standard_file" type="data" format="tabular" + label="Input gold standard file here" + help="Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!" /> + <param argument="--fasta_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" + label="Input fasta/fastq file here" + help="Input the file which match to the gold standard file" /> + </inputs> + <outputs> + <data name="file" format="tabular" from_work_dir="gold_standard_file.tsv" label="${tool.name}: Gold standard file" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="gold_standard_file" value="test_add.tsv" ftype="tabular" /> + <param name="fasta_file" value="test_add.fasta.gz" ftype="fasta.gz" /> + <output name="file" > + <assert_contents> + <has_size value="124000" delta="3000" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ + .. class:: infomark + + **What it does** + + This tool can create the gold standard file which has to be used for the CAMI AMBER. + + **Input** + + This tool required 2 inputs: + + - A binning file (biobox format) + + This file can be created via the convert_to_biobox tool + + .. class:: infomark + + Example(tab separated): + + :: + + #CAMI Format for Binning + @Version:0.9.0 + @SampleID:CAMI_low + @@SEQUENCEID BINID + RL|S1|C10 Bin_034 + RL|S1|C100 Bin_023 + RL|S1|C1000 Bin_034 + RL|S1|C10000 Bin_019 + RL|S1|C10002 Bin_035 + RL|S1|C10004 Bin_035 + RL|S1|C10008 Bin_034 + RL|S1|C10011 Bin_035 + RL|S1|C10012 Bin_013 + RL|S1|C10014 Bin_035 + + - A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format) + + This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER + + **Output** + + As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example! + + + ]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 6c71acde9d52 cami_amber_convert_to_biobox.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cami_amber_convert_to_biobox.xml Mon May 20 18:08:36 2024 +0000 |
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| @@ -0,0 +1,162 @@ +<tool id="cami_amber_convert" name="CAMI AMBER convert to biobox" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Create binning file(s) for CAMI AMBER</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + + mkdir -p output + + #for $file in $input.files: + && + ln -s '$file' './$file.element_identifier' + #end for + + #if $work == "single": + #for $file in $input.files: + && + #set $out = $file.element_identifier.split('.')[0] + '.tsv' + convert_fasta_bins_to_biobox_format.py + -o 'output/$out' + '$file.element_identifier' + #end for + #else: + && + convert_fasta_bins_to_biobox_format.py + -o 'output/binning.tsv' + #for $file in $input.files: + '$file.element_identifier' + #end for + #end if + + ]]> + </command> + <inputs> + <param name="work" type="select" label="Merge binning output files?" + help="If yes all input files will be merged into one biobox output (required input by amber). If no each input will be converted into a separate biobox output file." > + <option value="single">Each file alone</option> + <option value="all">All together</option> + </param> + <conditional name="input"> + <param name="is_select" type="select" label="Choose how to input the files" + help="You can provide each input separately or as a collection"> + <option value="manually">Manually</option> + <option value="data">Data collection</option> + </param> + <when value="manually"> + <param name="files" type="data" format="fasta" multiple="true" + label="Input fasta files" + help="Input all fasta files which this tool should convert into biobox format" /> + </when> + <when value="data"> + <param name="files" type="data_collection" collection_type="list" format="fasta" + label="Input the fasta collection" + help="Input the fasta collected which the tool should convert into biobox format" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="binning_file" format="tabular" from_work_dir="output/binning.tsv" label="${tool.name}: BINNING FILE"> + <filter>work and "all" in work</filter> + </data> + <collection name="binning_collection" type="list" label="${tool.name}: BINNING COLLECTION" > + <discover_datasets pattern="(?P<designation>.+)\.tsv" format="tabular" directory="output/" recurse="true" /> + <filter>work and "single" in work</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1" > + <param name="work" value="single" /> + <conditional name="input" > + <param name="is_select" value="manually" /> + <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" /> + </conditional> + <output_collection name="binning_collection" type="list"> + <element name="test_add1" > + <assert_contents> + <has_n_lines n="1464" /> + </assert_contents> + </element> + <element name="test_add2" > + <assert_contents> + <has_n_lines n="36" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="1" > + <param name="work" value="single" /> + <conditional name="input" > + <param name="is_select" value="data" /> + <param name="files" > + <collection name="test" type="list" > + <element name="test_add1" value="test_add1.fasta" /> + <element name="test_add2" value="test_add2.fasta" /> + </collection> + </param> + </conditional> + <output_collection name="binning_collection" type="list"> + <element name="test_add1" > + <assert_contents> + <has_n_lines n="1464" /> + </assert_contents> + </element> + <element name="test_add2" > + <assert_contents> + <has_n_lines n="36" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="1" > + <param name="work" value="all" /> + <conditional name="input" > + <param name="is_select" value="manually" /> + <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" /> + </conditional> + <output name="binning_file"> + <assert_contents> + <has_n_lines n="1496" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <param name="work" value="all" /> + <conditional name="input" > + <param name="is_select" value="data" /> + <param name="files" > + <collection name="test" type="list" > + <element name="test_add1" value="test_add1.fasta" /> + <element name="test_add2" value="test_add2.fasta" /> + </collection> + </param> + </conditional> + <output name="binning_file"> + <assert_contents> + <has_n_lines n="1496" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ + .. class:: infomark + + **What it does** + + This tool can create a tsv file in biobox format or a collection of multiple files. + + **Input** + + This tool required only fasta files. You can submit n files manually or a collection of fasta files. + + **Output** + + This tool either give out 1 binning file in biobox format or for each inputted file 1 binning file in biobox format. + + ]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 6c71acde9d52 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 20 18:08:36 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 6c71acde9d52 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 Mon May 20 18:08:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,793 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|
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/elated_franklin_0 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/elated_franklin_0 Mon May 20 18:08:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,5680 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|
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/goofy_hypatia_2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/goofy_hypatia_2 Mon May 20 18:08:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,8440 @@\n+#CAMI concoct 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|
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/gsa_mapping.binning --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gsa_mapping.binning Mon May 20 18:08:36 2024 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/naughty_carson_2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/naughty_carson_2 Mon May 20 18:08:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,8176 @@\n+#CAMI Format for 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L|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 6c71acde9d52 test-data/ncbi_taxonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/delnodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/delnodes.dmp Mon May 20 18:08:36 2024 +0000 |
| b |
| b'@@ -0,0 +1,70000 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|
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/test-db/division.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/division.dmp Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/gc.prt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/gc.prt Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/gencode.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/gencode.dmp Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/names.dmp Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/nodes.amber.ft |
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| Binary file test-data/test-db/nodes.amber.ft has changed |
| b |
| diff -r 000000000000 -r 6c71acde9d52 test-data/test-db/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/nodes.dmp Mon May 20 18:08:36 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 6c71acde9d52 test-data/test-db/readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-db/readme.txt Mon May 20 18:08:36 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 6c71acde9d52 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 6c71acde9d52 test-data/test_add.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add.tsv Mon May 20 18:08:36 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 6c71acde9d52 test-data/test_add1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add1.fasta Mon May 20 18:08:36 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 6c71acde9d52 test-data/test_add2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_add2.fasta Mon May 20 18:08:36 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 6c71acde9d52 test-data/test_binning.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_binning.tsv Mon May 20 18:08:36 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 6c71acde9d52 test-data/test_binning2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_binning2.tsv Mon May 20 18:08:36 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 6c71acde9d52 test-data/test_gold.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_gold.tsv Mon May 20 18:08:36 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 6c71acde9d52 test-data/unique_common.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unique_common.tsv Mon May 20 18:08:36 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 6c71acde9d52 tool-data/ncbi_taxonomy.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ncbi_taxonomy.loc.sample Mon May 20 18:08:36 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#value name path +test-db-tox "Test Database" ${__HERE__}/test-db \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6c71acde9d52 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon May 20 18:08:36 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of taxonomy data downloaded from NCBI --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 6c71acde9d52 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon May 20 18:08:36 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> |