| Next changeset 1:92e77800ef2c (2024-02-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e" |
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added:
macros.xml phyloseq_from_dada2.R phyloseq_plot_ordination.R phyloseq_plot_ordination.xml phyloseq_plot_richness.R test-data/output.phyloseq test-data/sequence_table.dada2_sequencetable test-data/taxonomy_table.tabular |
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| diff -r 000000000000 -r 11d43fa12aab macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 03 13:28:30 2022 +0000 |
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| @@ -0,0 +1,27 @@ +<macros> + <token name="@TOOL_VERSION@">1.38.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-phyloseq</requirement> + <requirement type="package" version="1.7.1">r-optparse</requirement> + <requirement type="package" version="1.3.1">r-tidyverse</requirement> + </requirements> + </xml> + <xml name="phyloseq_input"> + <param name="input" type="data" format="phyloseq" label="File containing a phyloseq object"/> + </xml> + <xml name="outputs"> + <outputs> + <data name="output" format="pdf"/> + </outputs> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.18129/B9.bioc.phyloseq</citation> + <citation type="doi">10.1371/journal.pone.0061217</citation> + </citations> + </xml> +</macros> + |
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| diff -r 000000000000 -r 11d43fa12aab phyloseq_from_dada2.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_from_dada2.R Thu Mar 03 13:28:30 2022 +0000 |
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| @@ -0,0 +1,39 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) +suppressPackageStartupMessages(library("tidyverse")) + +option_list <- list( + make_option(c("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"), + make_option(c("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"), + make_option(c("--output"), action = "store", dest = "output", help = "RDS output") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); +args <- parse_args(parser, positional_arguments = TRUE); +opt <- args$options; + +# The input sequence_table is an integer matrix +# stored as tabular (rows = samples, columns = ASVs). +seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t")); + +# The input taxonomy_table is a table containing +# the assigned taxonomies exceeding the minBoot +# level of bootstrapping confidence. Rows correspond +# to sequences, columns to taxonomic levels. NA +# indicates that the sequence was not consistently +# classified at that level at the minBoot threshold. +tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t")); + +# Construct a tax_table object. The rownames of +# tax_tab must match the OTU names (taxa_names) +# of the otu_table defined below. +tax_tab <- tax_table(tax_table_matrix); + +# Construct an otu_table object. +otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE); + +# Construct a phyloseq object. +phyloseq_obj <- phyloseq(otu_tab, tax_tab); +saveRDS(phyloseq_obj, file = opt$output, compress = TRUE); |
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| diff -r 000000000000 -r 11d43fa12aab phyloseq_plot_ordination.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_ordination.R Thu Mar 03 13:28:30 2022 +0000 |
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| @@ -0,0 +1,30 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) + +option_list <- list( + make_option(c("--input"), action = "store", dest = "input", help = "Input file containing a phyloseq object"), + make_option(c("--method"), action = "store", dest = "method", help = "Ordination method"), + make_option(c("--distance"), action = "store", dest = "distance", help = "Distance method"), + make_option(c("--type"), action = "store", dest = "type", help = "Plot type"), + make_option(c("--output"), action = "store", dest = "output", help = "Output") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); +args <- parse_args(parser, positional_arguments = TRUE); +opt <- args$options; + +# Construct a phyloseq object. +phyloseq_obj <- readRDS(opt$input); + +# Transform data to proportions as appropriate for +# Bray-Curtis distances. +proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu)); +ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance); + +# Start PDF device driver and generate the plot. +dev.new(); +pdf(file = opt$output); +plot_ordination(proportions_obj, ordination_obj, type = opt$type); +dev.off(); |
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| diff -r 000000000000 -r 11d43fa12aab phyloseq_plot_ordination.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_ordination.xml Thu Mar 03 13:28:30 2022 +0000 |
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| @@ -0,0 +1,89 @@ +<tool id="phyloseq_plot_ordination" name="Phyloseq: plot ordination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +Rscript '${__tool_directory__}/phyloseq_plot_ordination.R' +--input '$input' +--method '$method' +--distance '$distance' +--type '$type' +--output '$output' + ]]></command> + <inputs> + <expand macro="phyloseq_input"/> + <param name="method" type="select" label="Ordination method"> + <option value="DCA" selected="true">DCA</option> + <option value="CCA">CCA</option> + <option value="RDA">RDA</option> + <option value="CAP">CAP</option> + <option value="NMDS">NMDS</option> + <option value="MDS">MDS</option> + <option value="PCoA">PCoA</option> + </param> + <param name="distance" type="select" label="Distance method" help="Utilized only if a distance matrix is required by the Ordination method selected above"> + <option value="bray" selected="true">bray</option> + <option value="canberra">canberra</option> + <option value="euclidean">euclidean</option> + <option value="gower">gower</option> + <option value="horn">horn</option> + <option value="jaccard">jaccard</option> + <option value="kulczynski">kulczynski</option> + <option value="manhattan">manhattan</option> + <option value="maximum">maximum</option> + <option value="minkowski">minkowski</option> + <option value="morisita">morisita</option> + <option value="mountford">mountford</option> + </param> + <param name="type" type="select" label="Plot type"> + <option value="biplot" selected="true">biplot</option> + <option value="samples">samples</option> + <option value="scree">scree</option> + <option value="species">species</option> + <option value="split">split</option> + </param> + </inputs> + <expand macro="outputs"/> + <tests> + <test> + <param name="input" value="output.phyloseq" ftype="phyloseq"/> + <output name="output" ftype="pdf"> + <assert_contents> + <has_text text="%PDF"/> + <has_text text="%%EOF"/> + </assert_contents> + </output> + </test> + </tests> + <help> +**What it does** + +Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table, +and generates an ordination plot of the samples. + +**Options** + + **Ordination method** + + * **DCA** - Performs detrended correspondence analysis using decorana. + * **CCA** - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca. + * **RDA** - Performs redundancy analysis, or optionally principal components analysis, via vegan rda. + * **CAP** - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale. + * **NMDS** - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k). + * **MDS/PCoA** - Performs principal coordinate analysis (also called principle coordinate decomposition, multidimensional scaling (MDS), or classical scaling) of a distance matrix including two correction methods for negative eigenvalues. + + **Distance method** - Utilized only if a distance matrix is required by the Ordination method documented above. + + **Plot type** + + * **biplot** - Produces a combined plot with both taxa and samples. + * **samples** - Produces a single plot of just the samples of the ordination. + * **scree** - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis. + * **species** - Produces a single plot of just the species of the ordination. + * **split** - Produces a plot with both taxa and samples separated in two facet panels respectively. + </help> + <expand macro="citations"/> +</tool> + |
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| diff -r 000000000000 -r 11d43fa12aab phyloseq_plot_richness.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_richness.R Thu Mar 03 13:28:30 2022 +0000 |
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| @@ -0,0 +1,21 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) + +option_list <- list( + make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), + make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); +args <- parse_args(parser, positional_arguments = TRUE); +opt <- args$options; + +phyloseq_obj <- readRDS(opt$input); + +# Start PDF device driver and generate the plot. +dev.new(); +pdf(file = opt$output); +plot_richness(phyloseq_obj, x = "samples", color = "samples"); +dev.off() |
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| diff -r 000000000000 -r 11d43fa12aab test-data/output.phyloseq |
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| Binary file test-data/output.phyloseq has changed |
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| diff -r 000000000000 -r 11d43fa12aab test-data/sequence_table.dada2_sequencetable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence_table.dada2_sequencetable Thu Mar 03 13:28:30 2022 +0000 |
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@@\n+\tSRR14190457\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t178\n+GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACTGGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGTCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGGATTAGAAACCCCCGTAGTCC\t136\n+GTGTCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\t129\n+GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCCCGTAGTCC\t128\n+GTGTCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTGTGTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTATGTAACTAGAGTGTCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATCACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\t110\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\t104\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCCGTAGTCC\t97\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t90\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTCCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\t88\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t86\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t84\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAAATAAGTCTAATGTGAAAGCCCTCGGCTTAACCGAGGAACTGCATCGGAAACTGTTTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\t83\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCAGTAGTCC\t71\n+GTGTCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGAGTGGCAAGTCTGATGTGAAAACCCG'..b'CGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATAACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCC\t28\n+GTGTCAGCAGCCGCGGTAAAACGTAGGTCACAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGCAGGCGGGAAAGCAAGTTGGAAGTGAAATCCATGGGCTCAACCCATGAACTGCTTTCAAAACTGTTTTTCTTGAGTAGTGCAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTGGCGAAGGCGCCTTTCTGGACTGTGTCTGACGCTGAGATGCGAAAGCCAGGGTAGCGAACGGGATTAGATACCCCCGTAGTCC\t28\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATGGACAAGTCTGATGTGAAAGGCTGGGGCTCAACCCCGGGACTGCATTGGAAACTGCCCGTCTTGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATCACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCGCGTAGTCC\t27\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGCTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCGATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCCGTAGTCC\t27\n+GTGTCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCAGTAGTCC\t26\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCTAGTAGTCC\t26\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\t25\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCC\t24\n+GTGTCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCAAAACTACTGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCGCGTAGTCC\t22\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\t22\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGAGAAACTTGAGTGCAGGAGAGGAGAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAATACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\t22\n+GTGTCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCCTGTAGTCC\t16\n+GTGTCAGCAGCCGCGGTAATACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGACTGTCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGCGGTCTTGAGTGAGCGAGAAGTACGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCGTACCGGCGCTCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGGATTAGATACCCCCGTAGTCC\t15\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTATCCGGATTCACTGGGTTTAAAGGGTGCGTAGGCGGGCGTATAAGTCAGTGGTGAAATCCTGGAGCTTAACTCCAGAACTGCCATTGATACTATATGTCTTGAATATGGTGGAGGTAAGCGGAATATGTCATGTAGCGGTGAAATGCATAGATATGACATAGAACACCTATTGCGAAGGCAGCTTACTACGCCTATATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACAGGATTAGAAACCCGAGTAGTCC\t11\n' 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| diff -r 000000000000 -r 11d43fa12aab test-data/taxonomy_table.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomy_table.tabular Thu Mar 03 13:28:30 2022 +0000 |
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| b'@@ -0,0 +1,65 @@\n+\tKingdom\tPhylum\tClass\tOrder\tFamily\tGenus\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGACTGGTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGTCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\n+GTGTCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\tBacteria\tActinobacteriota\tActinobacteria\tBifidobacteriales\tBifidobacteriaceae\tBifidobacterium\n+GTGTCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCCCGTAGTCC\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\n+GTGTCAGCAGCCGCGGTAATACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTGTGTAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTATGTAACTAGAGTGTCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATCACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\tBacteria\tFirmicutes\tClostridia\tLachnospirales\tLachnospiraceae\tTyzzerella\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tEnterobacteriaceae\tEscherichia/Shigella\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCCGTAGTCC\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCATGGCAAGCCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGGAACTGTCAGGCTAGAGTGTCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tFirmicutes\tClostridia\tLachnospirales\tLachnospiraceae\tNA\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTCCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCAGTAGTCC\tBacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae\tBacillus\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tEnterobacteriaceae\tEscherichia/Shigella\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACAC'..b'CTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tActinobacteriota\tActinobacteria\tBifidobacteriales\tBifidobacteriaceae\tBifidobacterium\n+GTGTCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGTTTGTCGCGTCGTCTGTGAAATTCTGGGGCTTAACTCCGGGCGTGCAGGCGATACGGGCATAACTTGAGTGCTGTAGGGGTAACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTTACTGGGCAGTTACTGACGCTGAGGAGCGAAAGCATGGGTAGCGAACAGGATTAGATACCCCAGTAGTCC\tBacteria\tActinobacteriota\tActinobacteria\tCorynebacteriales\tCorynebacteriaceae\tCorynebacterium\n+GTGTCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGAAAGATAAGTCTGATGTGAAAGCCCCCGGCTTAACCGAGGAATTGCATCGGAAACTGTGTTTCTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCTAGTAGTCC\tBacteria\tFirmicutes\tBacilli\tLactobacillales\tLactobacillaceae\tLactobacillus\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCCGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tEnterobacteriaceae\tEscherichia/Shigella\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tEnterobacteriaceae\tEscherichia/Shigella\n+GTGTCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCAAAACTACTGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCGCGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tPseudomonadaceae\tAzorhizophilus\n+GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCCGTAGTCC\tBacteria\tProteobacteria\tGammaproteobacteria\tEnterobacterales\tEnterobacteriaceae\tEscherichia/Shigella\n+GTGTCAGCAGCCGCGGTAATACGTAGGGGGCTAGCGTTATCCGGAATTACTGGGCGTAAAGGGTGCGTAGGTGGTTTCTTAAGTCAGAGGTGAAAGGCTACGGCTCAACCGTAGTAAGCCTTTGAAACTGAGAAACTTGAGTGCAGGAGAGGAGAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAATACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACACTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGCGTAGTCC\tBacteria\tFirmicutes\tClostridia\tPeptostreptococcales-Tissierellales\tPeptostreptococcaceae\tRomboutsia\n+GTGTCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCCTGTAGTCC\tBacteria\tActinobacteriota\tActinobacteria\tPropionibacteriales\tPropionibacteriaceae\tCutibacterium\n+GTGTCAGCAGCCGCGGTAATACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGACTGTCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGCGGTCTTGAGTGAGCGAGAAGTACGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCGTACCGGCGCTCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGGATTAGATACCCCCGTAGTCC\tBacteria\tBacteroidota\tBacteroidia\tBacteroidales\tMuribaculaceae\tNA\n+GTGTCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTATCCGGATTCACTGGGTTTAAAGGGTGCGTAGGCGGGCGTATAAGTCAGTGGTGAAATCCTGGAGCTTAACTCCAGAACTGCCATTGATACTATATGTCTTGAATATGGTGGAGGTAAGCGGAATATGTCATGTAGCGGTGAAATGCATAGATATGACATAGAACACCTATTGCGAAGGCAGCTTACTACGCCTATATTGACGCTGAGGCACGAAAGCGTGGGGATCAAACAGGATTAGAAACCCGAGTAGTCC\tBacteria\tBacteroidota\tBacteroidia\tChitinophagales\tChitinophagaceae\tAsinibacterium\n' |