Mercurial > repos > iuc > ampvis2_heatmap
changeset 0:e53885a980fe draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TODO Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,6 @@ +use duplicated options instead of tokens to define defaults + + +detailed data for boxplot (see heatmap) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.xml Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,337 @@ +<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="header"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$rscript' + ]]></command> + <configfiles> + <configfile name="rscript"><![CDATA[ + #if $tax_add + #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")' + #else + #set ta='NULL' + #end if + library(ampvis2, quietly = TRUE) + d <- readRDS("$data") + #if $output_options.out_format == "tabular" + raw <- + #else + plot <- + #end if + amp_heatmap( + d + , + #if $group_by + group_by = "$group_by", + #end if + #if $facet_by + facet_by = "$facet_by", + #end if + normalise = $normalise, + tax_aggregate = "$tax_aggregate", + tax_add = $ta, + @TAX_SHOW@ + showRemainingTaxa = $showRemainingTaxa, + ## tax_class = NULL, + tax_empty = "$tax_empty", + ## TODO giving the order of the columns is difficult but "cluster" would be nice I guess + ## order_x_by = NULL, + ## order_y_by = NULL, + plot_values = $plot_values_cond.plot_values, + #if $plot_values_cond.plot_values == "TRUE" + plot_values_size = $plot_values_cond.plot_values_size, + #end if + ## plot_legendbreaks = NULL, + plot_colorscale = "$plot_colorscale", + plot_na = $plot_na, + measure = "$measure", + #if str($min_abundance) != '' + min_abundance = $min_abundance, + #end if + #if str($max_abundance) != '' + max_abundance = $max_abundance, + #end if + #if $sort_by_cond.sort_by_sel != 'no' + sort_by = "$sort_by_cond.sort_by", + #end if + ## TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 + ## #if $normalise_by_cond.normalise_by_sel != "no" + ## normalise_by = "$normalise_by_cond.normalise_by", + ## #end if + #if $scale_by + scale_by = "$scale_by", + #end if + ## color_vector = NULL + ## round = 1, + #if $output_options.out_format == "tabular" + textmap = TRUE, + #else + textmap = FALSE, + #end if + #if $plot_functions_cond.plot_functions_sel != "no" + plot_functions = TRUE, + #if $plot_functions_cond.plot_functions_sel == "file" + function_data = read.table("$plot_functions_cond.function_data", header = TRUE, sep = "\t"), + #end if + #set foo='c("' + '", "'.join(str($plot_functions_cond.functions).split(",")) + '")' + functions = $foo, + #end if + rel_widths = c(0.75, 0.25) + ) + #if $output_options.out_format != "tabular" + @OUTPUT_TOKEN@ + #else + write.table(raw, file = "$plot_raw", sep = "\t") + #end if + ]]></configfile> + </configfiles> + <inputs> + <expand macro="rds_metadata_input_macro"/> + <expand macro="metadata_select_discrete" argument="group_by" label="Group samples" help="By a categorical variable in the metadata"/> + <expand macro="metadata_select_discrete" argument="facet_by" label="Facet the samples" help="By a categorical variable in the metadata."/> + <expand macro="normalise_macro" checked="true"/> + <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> + <option value="Phylum" selected="true">Phylum</option> + </expand> + <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/> + <expand macro="tax_show_macro" value="10"/> + <param argument="showRemainingTaxa" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Display sum of remaining taxa" help="Add an additional row at the bottom displaying the sum of all remaining taxa that are not part of the top tax_show most abundant taxa."/> + <expand macro="tax_empty_macro"/> + <conditional name="plot_values_cond"> + <param argument="plot_values" type="select" label="Plot the values on the heatmap"> + <option value="TRUE">Yes</option> + <option value="FALSE">No</option> + </param> + <when value="TRUE"> + <param name="plot_values_size" type="integer" value="4" label="Size of the plotted values"/> + </when> + <when value="FALSE"/> + </conditional> + <param argument="plot_colorscale" type="select" label="Type of scale used for coloring abundances"> + <option value="sqrt">Square root (sqrt)</option> + <option value="log10" selected="true">Log (log10)</option> + </param> + <param argument="plot_na" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Color missing values with the lowest color in the scale"/> + <param argument="measure" type="select" label="Value to show across the groups"> + <option value="mean">Mean</option> + <option value="max">Maximum</option> + <option value="median">Median</option> + </param> + <param argument="min_abundance" type="float" value="0.1" min="0" optional="true" label="Maximum abundance" help="All values below this value are given the same color."/> + <param argument="max_abundance" type="float" value="" min="0" optional="true" label="Maximum abundance" help="All values above this value are given the same color." /> + + <conditional name="sort_by_cond"> + <param name="sort_by_sel" type="select" label="Sort heatmap by most abundant taxa"> + <option value="no">No</option> + <option value="group">in a group of samples</option> + <option value="sample">in a specific sample</option> + </param> + <when value="no"/> + <when value="group"> + <param argument="sort_by" type="select" optional="true" label="Group to sort by"> + <options from_dataset="metadata_list"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="param_value" column="0" ref="group_by"/> + <filter type="unique_value" column="1"/> + </options> + </param> + </when> + <when value="sample"> + <param argument="sort_by" type="select" optional="true" label="Sample to sort by"> + <options from_dataset="metadata_list"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> + <filter type="unique_value" column="1"/> + </options> + </param> + </when> + </conditional> + <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> + <!-- <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/> --> + <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/> + + <conditional name="plot_functions_cond"> + <param name="plot_functions_sel" type="select" label="Show functional information about the Genus-level OTUs" help="Produces a 2-column grid plot, showing known functional information about the Genus-level OTUs next to the heatmap. When using this feature, make sure that either tax_aggregate or tax_add is set to Genus and that Genus is the lowest level in either."> + <option value="no">No</option> + <option value="midasfieldguide">Use data from midasfieldguide.org</option> + <option value="file">Use data from a dataset in the history</option> + </param> + <when value="no"/> + <when value="file"> + <!-- neeed tsv here since tabular does not fill the column_names + metadata and therefore the data_meta filter in the functions + select would not work--> + <param argument="function_data" type="data" format="tsv" label="Tabular dataset with functional information at Genus level" help="See help"/> + <param argument="functions" type="select" multiple="true" label="Function(s) to include"> + <options> + <filter type="data_meta" ref="function_data" key="column_names"/> + <filter type="remove_value" value="Genus"/> + </options> + </param> + </when> + <when value="midasfieldguide"> + <param name="functions" type="select" multiple="true" label="Function(s) to include"> + <option value="MiDAS" selected="true">MiDAS</option> + <option value="Filamentous" selected="true">Filamentous</option> + <option value="AOB" selected="true">AOB</option> + <option value="NOB" selected="true">PAO</option> + <option value="GAO" selected="true">GAO</option> + </param> + </when> + </conditional> + <expand macro="out_format_macro"> + <option value="tabular">Table</option> + </expand> + </inputs> + <outputs> + <expand macro="out_macro"> + <filter>output_options["out_format"] != "tabular"</filter> + </expand> + <data name="plot_raw" format="tabular"> + <filter>output_options["out_format"] == "tabular"</filter> + </data> + </outputs> + <tests> + <!-- defaults --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <output name="plot" value="AalborgWWTPs-heatmap.pdf" ftype="pdf"/> + </test> + <!-- group and facet--> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="group_by" value="Plant"/> + <param name="facet_by" value="Year"/> + <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.pdf" ftype="pdf"/> + </test> + <!-- group and facet and test raw output --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="group_by" value="Plant"/> + <param name="facet_by" value="Year"/> + <param name="out_format" value="tabular"/> + <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.tsv" ftype="tabular"/> + </test> + <!-- normalise --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="normalise" value="true"/> + <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/> + </test> + <!-- normalise by a specific sample --> + <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> + <!-- <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="normalise" value="true"/> + <conditional name="normalise_by_cond"> + <param name="normalise_by_sel" value="sample"/> + <param name="normalise_by" value="16SAMP-747"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/> + </test> --> + <!-- normalise by a metadata variable --> + <!-- TODO https://github.com/MadsAlbertsen/ampvis2/issues/130 --> + <!-- <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="group_by" value="Plant"/> + <conditional name="normalise_by_cond"> + <param name="normalise_by_sel" value="variable"/> + <param name="normalise_by" value="Plant"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_variable.pdf" ftype="pdf"/> + </test> --> + <!-- tax options --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="tax_aggregate" value="Order"/> + <param name="tax_add" value="Class"/> + <param name="tax_show" value="5"/> + <param name="showRemainingTaxa" value="true"/> + <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf"/> + </test> + <!-- sort by a specific sample --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <conditional name="sort_by_cond"> + <param name="sort_by_sel" value="sample"/> + <param name="sort_by" value="16SAMP-747"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-sort_by_sample.pdf" ftype="pdf"/> + </test> + <!-- sort by a group of samples --> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> + <param name="group_by" value="Period"/> + <conditional name="sort_by_cond"> + <param name="sort_by_sel" value="group"/> + <param name="sort_by" value="Winter"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-sort_by_group.pdf" ftype="pdf"/> + </test> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="tax_aggregate" value="Genus"/> + <conditional name="plot_functions_cond"> + <param name="plot_functions_sel" value="midasfieldguide"/> + <param name="functions" value="MiDAS,Filamentous,AOB,NOB,GAO"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_midas.pdf" ftype="pdf"/> + </test> + <test expect_num_outputs="1"> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="tax_aggregate" value="Genus"/> + <conditional name="plot_functions_cond"> + <param name="plot_functions_sel" value="file"/> + <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/> + <param name="functions" value="Foo,Bar"/> + </conditional> + <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf"/> + </test> + + </tests> + <help><![CDATA[ +What it does +============ + +Generates a heatmap of amplicon data by using sample metadata to aggregate +samples and taxonomy to aggregate OTUs. + +The Galaxy tool calls the `amp_heatmap +<https://madsalbertsen.github.io/ampvis2/reference/amp_heatmap.html>`_ function +of the ampvis2 package. + +@HELP_RELATIVE_ABUNDANCES@ + +Input +===== + +@HELP_RDS_INPUT@ + +@HELP_METADATA_LIST_INPUT@ + +Funtional data at genus level can be added to the plot. By default the +information is taken from `midasfieldguide <https://midasfieldguide.org/>`_ but +it can also be given by a dataset (parameter function_data): + +- The first column must be the Genus names and +- any other column(s) can be any property or metabolic function of the individual Genera. + +Output +====== + +Heatmap in the chosen output format. +If table output is chosen the data presented in the heatmap is written into a tabular dataset. + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,271 @@ +<macros> + <token name="@TOOL_VERSION@">2.7.17</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + <xml name="header"> + <xrefs> + <xref type="bio.tools">ampvis</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement> + <requirement type="package" version="2.1.1">r-readr</requirement> + </requirements> + <version_command><![CDATA[ +echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/299537</citation> + <yield/> + </citations> + </xml> + + <xml name="rds_input_macro"> + <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> + </xml> + + <xml name="rds_metadata_input_macro" token_metadata_optional="true"> + <expand macro="rds_input_macro"/> + <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list"> + <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator> + </param> + </xml> + + <token name="@SAVE_TAX_LIST@"><![CDATA[ + for(level in colnames(data\$tax)){ + for(u in unique(data\$tax[level])){ + write(u, file="$taxonomy_list_out", append=T) + } + } + ]]></token> + + <token name="@SAVE_METADATA_LIST@"><![CDATA[ + classes <- sapply(data\$metadata, class) + for(name in names(data\$metadata)){ + ## check if it is the column containing the sample names + ## the additional column in the ist file can the be used + ## to filter SampleIDs from select inputs + ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails) + if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){ + sample_names <- TRUE; + }else{ + sample_names <- FALSE; + } + for(m in unique(data\$metadata[[name]])){ + write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T); + } + } + ]]></token> + + <!-- defaults can be set by redefining an on option with selected="true" --> + <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help=""> + <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> + <option value="OTU">OTU/ASV</option> + <option value="Species">Species</option> + <option value="Genus">Genus</option> + <option value="Family">Family</option> + <option value="Order">Order</option> + <option value="Class">Class</option> + <option value="Phylum">Phylum</option> + <option value="Kingdom">Kingdom</option> + <yield/> + </param> + </xml> + + <xml name="tax_empty_macro"> + <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information"> + <option value="remove">Remove OTUs without taxonomic information</option> + <option value="best" selected="true">Use the best classification possible</option> + <option value="OTU">Display the OTU name</option> + </param> + </xml> + + <token name="@TAX_SHOW@"><![CDATA[ + #if $tax_show_cond.tax_show_sel == "number" + tax_show = $tax_show_cond.tax_show, + #else + #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")' + tax_show = $tax_show_list + #end if + ]]></token> + <xml name="tax_show_macro" token_value=""> + <conditional name="tax_show_cond"> + <param name="tax_show_sel" type="select" label="Limit the number of shown taxa"> + <option value="number">Select a number of taxa to show</option> + <option value="explicit">Manually select taxa to show</option> + </param> + <when value="number"> + <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/> + </when> + <when value="explicit"> + <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/> + <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show"> + <options from_dataset="taxonomy_list"> + <column name="name" index="0"/> + <column name="value" index="0"/> + <!-- TODO filter by tax_aggregate level? --> + </options> + </param> + </when> + </conditional> + </xml> + + <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help=""> + <param __AN__="__ARGUMENT__" type="select" optional="__OPTIONAL__" multiple="__MULTIPLE__" label="__LABEL__" help="In order to select values a metadata list needs to be selected first. __HELP__"> + <options from_dataset="metadata_list"> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + <yield name="options"/> + </options> + <yield/> + </param> + </xml> + + <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> + <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> + <token name="options"> + <filter type="static_value" column="3" value="numeric" keep="false"/> + </token> + <yield/> + </expand> + </xml> + + <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> + <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> + <token name="options"> + <filter type="static_value" column="3" value="character" keep="false"/> + <filter type="static_value" column="3" value="Date" keep="false"/> + </token> + <yield/> + </expand> + </xml> + + <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help=""> + <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@"> + <token name="options"> + <filter type="static_value" column="3" value="Date" keep="true"/> + </token> + <yield/> + </expand> + </xml> + + <xml name="metadata_sample_select" token_argument=""> + <conditional name="@ARGUMENT@_cond"> + <param name="@ARGUMENT@_sel" type="select"> + <option value="no">No</option> + <option value="variable">Metadata variable</option> + <option value="sample">Specific sample</option> + </param> + <when value="no"/> + <when value="variable"> + <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/> + </when> + <when value="sample"> + <param argument="@ARGUMENT@" type="select" optional="true"> + <options from_dataset="metadata_list"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples --> + <filter type="unique_value" column="1"/> + </options> + </param> + </when> + </conditional> + </xml> + + <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true"> + <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@"> + <options from_dataset="taxonomy_list"> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + </options> + <yield/> + </param> + </xml> + + <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help=""> + <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@"> + <option value="fixed">Same scale</option> + <option value="free">Free scale</option> + <option value="free_x">Free x-scale</option> + <option value="free_y">Free y-scale</option> + </param> + </xml> + + <token name="@OUTPUT_TOKEN@"> + ggsave("$plot", + print(plot), + device="$output_options.out_format" + #if str($output_options.plot_width) != '' + , width = $output_options.plot_width + #end if + #if str($output_options.plot_height) != '' + , height = $output_options.plot_height + #end if + ) + </token> + <xml name="out_macro" token_name="plot" token_label=""> + <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@"> + <yield/> + <change_format> + <when input="output_options.out_format" value="png" format="png" /> + <when input="output_options.out_format" value="svg" format="svg" /> + </change_format> + </data> + </xml> + <xml name="out_format_macro"> + <section name="output_options" title="Output options" expanded="false"> + <param name="out_format" type="select" label="Output format"> + <option value="pdf" selected="true">PDF</option> + <option value="png">PNG</option> + <option value="svg">SVG</option> + <yield/> + </param> + <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/> + <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/> + </section> + </xml> + + <token name="@RAREFY_TOKEN@"> + #if str($rarefy) != "" + , rarefy = $rarefy + #end if + </token> + <xml name="rarefy_macro" token_help=""> + <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/> + </xml> + + <xml name="normalise_macro" token_checked="false"> + <param argument="normalise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="@CHECKED@" label="Normalise read counts" help="Transform the OTU read counts to be in percent per sample."/> + </xml> + + <token name="@HELP_RDS_INPUT@"> + An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the + ``ampvis2: subset ...`` tools). + </token> + <token name="@HELP_METADATA_LIST_INPUT@"> + The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the + ``ampvis2: subset sample`` tool). This input is only used for providing + values to the parameters alowing to select metadata variables or values. + </token> + + <token name="@HELP_RELATIVE_ABUNDANCES@"> +Preserving relative abundances in a subset of larger data +========================================================= + +By default the raw read counts in the abundance matrix are normalised +(transformed to percentages) by some ampvis2 plotting tools (for +example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more). +If this is applied to data generated by one of the ``ampvis2: subset ...`` tools +this means that the relative +abundances shown will be calculated based on the remaining taxa after the +subset, not including the removed taxa, if any. To circumvent this, enable +``normalise`` when subsetting with the ``ampvis2: subset ...``` tools, +and then disable ``normalise`` in the plotting tool. This will +transform the OTU counts to relative abundances BEFORE the subset. + </token> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs-functions.tsv Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,80 @@ +Genus Foo Bar +g__Acetitomaculum A Z +g__Ruminococcaceae UCG-005 A Z +g__Dyadobacter A Z +g__Nitrosomonas A Z +g__Tetrasphaera A Z +g__Desulforegula A Z +g__Rummeliibacillus A Z +g__ A Z +g__Fusicatenibacter A Z +g__Ruminiclostridium 1 A Z +g__uncultured A Z +g__Brooklawnia A Z +g__Sulfuritalea A Z +g__Lactobacillus A Z +g__Flavobacterium A Z +g__Acidicaldus A Z +g__Candidatus Defluviifilum A Z +g__Ruminococcaceae UCG-010 A Z +g__SBR2113 A Z +g__Subdoligranulum A Z +g__Ramlibacter B Z +g__Bosea B Z +g__Desulfobulbus B Z +g__Nocardioides B Z +g__Fusibacter B Z +g__SM1F10 B Z +g__Hyphomicrobium B Z +g__Meiothermus B Z +g__Trichococcus B Y +g__oca15 B Y +g__Simplicispira B Y +g__Sandaracinus B Y +g__OM27 clade B Y +g__Collinsella B Y +g__MNG7 B Y +g__Roseomonas B Y +g__Pirellula B Y +g__Clostridium sensu stricto 1 B Y +g__Acetoanaerobium B Y +g__Nitrospira B Y +g__Propioniciclava B Y +g__Parabacteroides C Y +g__Actinomyces C Y +g__Aeromicrobium C Y +g__Clostridium sensu stricto 6 C Y +g__Reyranella C Y +g__Proteiniclasticum C Y +g__B1-K1A-105 C Y +g__Prevotellaceae UCG-004 C Y +g__Haliangium C Y +g__Ureibacillus C Y +g__Ruminococcus 2 C Y +g__CYCU-0281 C Y +g__Parafilimonas C Y +g__Aestuariimicrobium C Y +g__Diaminobutyricimonas C Y +g__K2-78 C Y +g__Erysipelatoclostridium C Y +g__CL500-29 marine group C Y +g__Bacteroides C Y +g__Tessaracoccus C Y +g__Gordonia C Y +g__Senegalimassilia C Y +g__Atopobium C Y +g__Proteiniphilum C Y +g__Uliginosibacterium C Y +g__WCHB1-50 C Y +g__Christensenellaceae R-7 group C X +g__Fodinibacter C X +g__Defluviicoccus C X +g__Acidovorax C X +g__Salana C X +g__Propionimicrobium C X +g__Litorilinea C X +g__Faecalitalea C X +g__Ruminiclostridium 5 C X +g__Rivicola C X +g__[Eubacterium] coprostanoligenes group C X +g__Lewinella C X
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs-heatmap-group-facet.tsv Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,11 @@ +"Aalborg East 2006" "Aalborg East 2007" "Aalborg East 2008" "Aalborg East 2009" "Aalborg East 2010" "Aalborg East 2011" "Aalborg East 2012" "Aalborg East 2013" "Aalborg East 2014" "Aalborg East 2015" "Aalborg West 2006" "Aalborg West 2007" "Aalborg West 2008" "Aalborg West 2009" "Aalborg West 2010" "Aalborg West 2011" "Aalborg West 2012" "Aalborg West 2013" "Aalborg West 2014" "Aalborg West 2015" +"Proteobacteria" 38.1319941850736 35.9175566196596 35.3239223028173 34.9909501829368 36.3283102328281 38.9915608421962 53.8529383953324 51.3460117968074 72.8722023985104 57.4344068148402 54.2087542087542 36.4326282804544 38.4757369086407 38.3005233882427 37.9516676472635 40.6258026017424 38.6472843550883 44.6513837857578 60.526398421492 45.2994925859604 +"Actinobacteria" 16.1262929321795 18.8003924243249 19.7958105485988 12.3985441180767 11.9508628506455 11.9822773321894 12.658277703168 9.86692802463733 4.41749530915451 5.99609488982366 17.8451178451178 30.1393785089437 27.2165206926683 27.0923034080929 28.0991209423852 18.3670127700203 20.8878481743068 14.4816058069532 5.78450375894784 6.93249190968154 +"Chloroflexi" 18.3131199353417 13.271226587611 18.1723687926502 29.7622211645584 27.2162188095204 27.4083281864652 13.3425292037346 12.0421436922346 2.84378751176108 1.05381359276388 5.72390572390572 9.29625277451364 13.2781161639047 9.09181786374769 8.90144026478223 13.2039431913116 11.6630983081279 10.2302102712301 9.44167249733746 12.9289629664804 +"Bacteroidetes" 15.238944647955 17.0944898458844 4.80841552255416 6.79789110506974 7.21184338673076 12.2970476460921 12.0216954506151 19.8089694348484 15.1180034568227 26.7842680520852 10.4377104377104 7.90899595247421 4.19318035043356 6.73335761055059 5.58986985476623 11.2276978159685 11.4612545797781 15.2032565168297 14.8111317970807 21.1241394277011 +"Firmicutes" 6.65926307960792 8.08826902584616 13.5323428478027 11.135420901698 12.2381391019829 5.3065353223222 4.15566119372564 5.39379512409247 2.50275820445282 2.65696422748934 6.73400673400673 7.45201723462593 6.59801488988521 10.8497740076687 7.68965190921149 4.23883518319609 4.98282022116985 5.50491710923881 2.78564846131452 2.80406275115902 +"Acidobacteria" 1.84522886779123 3.19309844412278 0.579562724509533 1.22263018757176 1.22019363164889 1.8556042232708 2.61733996209427 0.818911905713214 1.77946201792775 4.74365552197578 3.03030303030303 3.46814205509858 2.58723846405261 4.34169469257189 7.1137753294489 6.57976369495166 6.87742567426134 6.0700195803001 4.28737081122707 9.42431811091215 +"Planctomycetes" 0.746563781302169 0.25464448503398 0.987168692856751 0.411589894060679 0.492479742080341 0.564736695897598 0.0730994152046784 0.152535023867842 0.0235849056603774 0.0250752256770311 1.34680134680135 3.09766288027158 4.52112645443821 1.78687459389214 2.47741727664007 2.23035684449218 1.84033791082559 1.3257701894156 1.01973806934665 0.584070896715898 +"Deinococcus-Thermus" 1.45963179413928 1.00870720718181 5.11548610677814 1.03259577383117 0.684345869495339 0.424454945159917 0.0955583622050142 0 0.0474171268233897 0.685625086716673 0 0 0 0 0 0 0 0 0 0 +"Hydrogenedentes" 0.134770889487871 0.244052637669659 0.152267354395014 0.155400155400155 0.199004975124378 0.308893572463899 0.402906470230555 0.0861326442721792 0.0747487181080226 0.185094894105122 0 0.120772946859903 0.4920049200492 0.562660211783019 0.404258953481751 0.500747105859888 1.36061070732636 0.873921616081284 0.298532298518384 0.373761440277151 +"WCHB1-60" 0.789762842230565 0.41040519763924 0.129960317460317 0.0556483027267668 0.136612021857924 0 0.0730994152046784 0 0 0 0 0.233385559472516 0.879805929046964 0.21706688373355 0.836894586894587 1.25864184270199 1.14445526079798 0.629254175715777 0.0949491695303551 0.148135364082208
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs-metadata.list Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,125 @@ +SampleID 16SAMP-747 TRUE character +SampleID 16S-AMP-1168 TRUE character +SampleID 16SAMP-4603 TRUE character +SampleID 16S-AMP-1149 TRUE character +SampleID 16SAMP-537 TRUE character +SampleID 16S-AMP-1114 TRUE character +SampleID 16SAMP-3893 TRUE character +SampleID 16SAMP-703 TRUE character +SampleID 16SAMP-638 TRUE character +SampleID 16SAMP-2611 TRUE character +SampleID 16S-AMP-1100 TRUE character +SampleID 16SAMP-608 TRUE character +SampleID 16SAMP-636 TRUE character +SampleID 16SAMP-13288 TRUE character +SampleID 16SAMP-719 TRUE character +SampleID 16S-AMP-1098 TRUE character +SampleID 16SAMP-536 TRUE character +SampleID 16S-AMP-1169 TRUE character +SampleID 16SAMP-635 TRUE character +SampleID 16SAMP-637 TRUE character +SampleID 16SAMP-717 TRUE character +SampleID 16S-AMP-1148 TRUE character +SampleID 16SAMP-735 TRUE character +SampleID 16SAMP-729 TRUE character +SampleID 16SAMP-738 TRUE character +SampleID 16SAMP-2613 TRUE character +SampleID 16SAMP-10925 TRUE character +SampleID 16SAMP-3913 TRUE character +SampleID 16SAMP-716 TRUE character +SampleID 16SAMP-726 TRUE character +SampleID 16SAMP-728 TRUE character +SampleID 16SAMP-625 TRUE character +SampleID 16SAMP-736 TRUE character +SampleID 16SAMP-13281 TRUE character +SampleID 16SAMP-626 TRUE character +SampleID 16SAMP-704 TRUE character +SampleID 16SAMP-2612 TRUE character +SampleID 16SAMP-746 TRUE character +SampleID 16SAMP-522 TRUE character +SampleID 16SAMP-516 TRUE character +SampleID 16S-AMP-1170 TRUE character +SampleID 16S-AMP-1099 TRUE character +SampleID 16SAMP-10932 TRUE character +SampleID 16SAMP-740 TRUE character +SampleID 16SAMP-739 TRUE character +SampleID 16SAMP-4597 TRUE character +SampleID 16SAMP-535 TRUE character +SampleID 16SAMP-3941 TRUE character +SampleID 16SAMP-3953 TRUE character +SampleID 16SAMP-720 TRUE character +SampleID 16SAMP-705 TRUE character +SampleID 16SAMP-10907 TRUE character +SampleID 16SAMP-538 TRUE character +SampleID 16SAMP-10911 TRUE character +SampleID 16SAMP-737 TRUE character +SampleID 16SAMP-4591 TRUE character +SampleID 16SAMP-745 TRUE character +SampleID 16SAMP-706 TRUE character +SampleID 16SAMP-3946 TRUE character +SampleID 16S-AMP-1101 TRUE character +SampleID 16SAMP-10896 TRUE character +SampleID 16SAMP-10891 TRUE character +SampleID 16SAMP-748 TRUE character +SampleID 16SAMP-725 TRUE character +SampleID 16SAMP-730 TRUE character +SampleID 16S-AMP-1107 TRUE character +SampleID 16SAMP-727 TRUE character +Plant Aalborg East FALSE character +Plant Aalborg West FALSE character +Date 14644 FALSE Date +Date 15831 FALSE Date +Date 16301 FALSE Date +Date 16006 FALSE Date +Date 14840 FALSE Date +Date 15740 FALSE Date +Date 16107 FALSE Date +Date 13183 FALSE Date +Date 15641 FALSE Date +Date 15009 FALSE Date +Date 15571 FALSE Date +Date 15275 FALSE Date +Date 15466 FALSE Date +Date 16475 FALSE Date +Date 13744 FALSE Date +Date 15374 FALSE Date +Date 14735 FALSE Date +Date 15936 FALSE Date +Date 13548 FALSE Date +Date 14005 FALSE Date +Date 14110 FALSE Date +Date 14279 FALSE Date +Date 15205 FALSE Date +Date 16735 FALSE Date +Date 16254 FALSE Date +Date 16476 FALSE Date +Date 13274 FALSE Date +Date 14370 FALSE Date +Date 14910 FALSE Date +Date 14545 FALSE Date +Date 16195 FALSE Date +Date 16300 FALSE Date +Date 16386 FALSE Date +Date 13814 FALSE Date +Date 13379 FALSE Date +Date 16671 FALSE Date +Date 14180 FALSE Date +Date 16105 FALSE Date +Date 13449 FALSE Date +Date 16387 FALSE Date +Date 16559 FALSE Date +Date 13913 FALSE Date +Year 2010 FALSE integer +Year 2013 FALSE integer +Year 2014 FALSE integer +Year 2006 FALSE integer +Year 2012 FALSE integer +Year 2011 FALSE integer +Year 2015 FALSE integer +Year 2007 FALSE integer +Year 2008 FALSE integer +Year 2009 FALSE integer +Period Winter FALSE character +Period Spring FALSE character +Period Summer FALSE character +Period Fall FALSE character
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stroke-linecap: butt;' /> +<text x='29.72' y='445.60' text-anchor='end' style='font-size: 8.80px;fill: #4D4D4D; font-family: "DejaVu Sans";' textLength='5.59px' lengthAdjust='spacingAndGlyphs'>0</text> +<text x='29.72' y='416.95' text-anchor='end' style='font-size: 8.80px;fill: #4D4D4D; font-family: "DejaVu Sans";' textLength='11.19px' lengthAdjust='spacingAndGlyphs'>10</text> +<text x='29.72' y='388.30' text-anchor='end' style='font-size: 8.80px;fill: #4D4D4D; font-family: "DejaVu Sans";' textLength='11.19px' lengthAdjust='spacingAndGlyphs'>20</text> +<text x='29.72' y='359.66' text-anchor='end' style='font-size: 8.80px;fill: #4D4D4D; font-family: "DejaVu Sans";' textLength='11.19px' lengthAdjust='spacingAndGlyphs'>30</text> +<polyline points='31.91,442.39 34.65,442.39 ' style='stroke-width: 1.07; stroke: #333333; stroke-linecap: butt;' /> +<polyline points='31.91,413.74 34.65,413.74 ' style='stroke-width: 1.07; stroke: #333333; stroke-linecap: butt;' /> +<polyline points='31.91,385.10 34.65,385.10 ' style='stroke-width: 1.07; stroke: #333333; stroke-linecap: butt;' /> +<polyline points='31.91,356.45 34.65,356.45 ' style='stroke-width: 1.07; stroke: #333333; stroke-linecap: butt;' /> +<text x='266.59' y='496.23' text-anchor='middle' style='font-size: 11.00px; font-family: "DejaVu Sans";' textLength='84.97px' lengthAdjust='spacingAndGlyphs'>Minimum reads</text> +<text transform='translate(13.50,234.73) rotate(-90)' text-anchor='middle' style='font-size: 11.00px; font-family: "DejaVu Sans";' textLength='137.95px' lengthAdjust='spacingAndGlyphs'>Number of distinct OTU's</text> +</g> +</svg>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs-taxonomy.list Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,495 @@ +k__Bacteria +p__Firmicutes +p__Bacteroidetes +p__Proteobacteria +p__Actinobacteria +p__Hydrogenedentes +p__Parcubacteria +p__Planctomycetes +p__Acidobacteria +p__Chloroflexi + +p__Saccharibacteria +p__Candidate division SR1 +p__Cyanobacteria +p__Synergistetes +p__Deinococcus-Thermus +p__Chlorobi +p__Verrucomicrobia +p__GOUTA4 +p__Nitrospirae +p__WCHB1-60 +p__Elusimicrobia +p__SM2F11 +p__TM6 +p__Armatimonadetes +p__Fusobacteria +p__Tenericutes +p__Lentisphaerae +p__Microgenomates +c__Clostridia +c__Cytophagia +c__Betaproteobacteria +c__Actinobacteria +c__Gammaproteobacteria +c__Deltaproteobacteria +c__Bacilli +c__ +c__Sphingobacteriia +c__Planctomycetacia +c__Holophagae +c__Chloroflexia +c__Caldilineae + +c__Anaerolineae +c__Flavobacteriia +c__Negativicutes +c__Alphaproteobacteria +c__Unknown Class +c__Cyanobacteria +c__Synergistia +c__Thermoleophilia +c__Acidimicrobiia +c__Bacteroidia +c__Phycisphaerae +c__WCHB1-50 +c__Deinococci +c__Ignavibacteria +c__Verrucomicrobiae +c__Coriobacteriia +c__TA18 +c__Acidobacteria +c__Nitrospira +c__Chlorobia +c__Elusimicrobia +c__Erysipelotrichia +c__BSV13 +c__Thermomicrobia +c__OPB35 soil group +c__Fusobacteriia +c__Mollicutes +c__PBS-III-20 +c__Chloroplast +o__Clostridiales +o__Cytophagales +o__Nitrosomonadales +o__Micrococcales +o__Xanthomonadales +o__Desulfobacterales +o__Bacillales +o__ +o__Sphingobacteriales +o__Planctomycetales +o__Holophagales +o__Propionibacteriales +o__Chloroflexales +o__PeM15 +o__Caldilineales +o__Rhodocyclales + +o__Myxococcales +o__Lactobacillales +o__Anaerolineales +o__Flavobacteriales +o__Selenomonadales +o__Rhodospirillales +o__Unknown Order +o__SubsectionIII +o__Burkholderiales +o__Rickettsiales +o__Rhizobiales +o__Synergistales +o__Gaiellales +o__Acidimicrobiales +o__Bacteroidales +o__Phycisphaerales +o__WCHB1-50 +o__Thermales +o__Ignavibacteriales +o__Bdellovibrionales +o__Verrucomicrobiales +o__Coriobacteriales +o__Subgroup 6 +o__Nitrospirales +o__WD2101 soil group +o__Actinomycetales +o__Chlorobiales +o__Subgroup 10 +o__Lineage IIb +o__Oligoflexales +o__Solirubrobacterales +o__Erysipelotrichales +o__Corynebacteriales +o__JG30-KF-CM45 +o__FW73 +o__Fusobacteriales +o__Mollicutes RF9 +o__Neisseriales +o__GR-WP33-30 +f__Lachnospiraceae +f__Ruminococcaceae +f__Cytophagaceae +f__Nitrosomonadaceae +f__Intrasporangiaceae +f__Xanthomonadaceae +f__Desulfobacteraceae +f__Planococcaceae +f__ +f__Dermatophilaceae +f__AKYH767 +f__Planctomycetaceae +f__Holophagaceae +f__Propionibacteriaceae +f__Roseiflexaceae +f__PeM15 +f__Caldilineaceae +f__Rhodocyclaceae + +f__Blfdi19 +f__Lactobacillaceae +f__Anaerolineaceae +f__Flavobacteriaceae +f__Veillonellaceae +f__Acetobacteraceae +f__mle1-27 +f__SBR2060 +f__FamilyI +f__Microbacteriaceae +f__Saprospiraceae +f__Comamonadaceae +f__TK34 +f__Bradyrhizobiaceae +f__Synergistaceae +f__Desulfobulbaceae +f__BVA77 +f__env.OPS 17 +f__Nocardioidaceae +f__DUNssu044 +f__Prevotellaceae +f__Family XII +f__Phycisphaeraceae +f__Chitinophagaceae +f__WCHB1-50 +f__Hyphomicrobiaceae +f__Thermaceae +f__Carnobacteriaceae +f__PHOS-HE36 +f__Family XIII +f__Sandaracinaceae +f__Bdellovibrionaceae +f__Mitochondria +f__Verrucomicrobiaceae +f__Coriobacteriaceae +f__Nordellaceae +f__Clostridiaceae 1 +f__Peptostreptococcaceae +f__Holosporaceae +f__Nitrospiraceae +f__Porphyromonadaceae +f__Actinomycetaceae +f__Family XI +f__Chlorobiaceae +f__NS9 marine group +f__Rhodospirillales Incertae Sedis +f__ABS-19 +f__Haliangiaceae +f__Bacillaceae +f__480-2 +f__Erysipelotrichaceae +f__Acidimicrobiaceae +f__Bacteroidaceae +f__Nocardiaceae +f__bacteriap25 +f__Christensenellaceae +f__Rhodospirillaceae +f__Beutenbergiaceae +f__Leptotrichiaceae +f__Oligoflexaceae +f__Neisseriaceae +f__AKIW1012 +f__Microthricaceae +f__OPB56 +g__Acetitomaculum +g__Ruminococcaceae UCG-005 +g__Dyadobacter +g__Nitrosomonas +g__Tetrasphaera + +g__Desulforegula +g__Rummeliibacillus +g__ +g__Fusicatenibacter +g__Ruminiclostridium 1 +g__uncultured +g__Brooklawnia +g__Sulfuritalea +g__Lactobacillus +g__Flavobacterium +g__Acidicaldus +g__Candidatus Defluviifilum +g__Ruminococcaceae UCG-010 +g__SBR2113 +g__Subdoligranulum +g__Ramlibacter +g__Bosea +g__Desulfobulbus +g__Nocardioides +g__Fusibacter +g__SM1F10 +g__Hyphomicrobium +g__Meiothermus +g__Trichococcus +g__oca15 +g__Simplicispira +g__Sandaracinus +g__OM27 clade +g__Collinsella +g__MNG7 +g__Roseomonas +g__Pirellula +g__Clostridium sensu stricto 1 +g__Acetoanaerobium +g__Nitrospira +g__Propioniciclava +g__Parabacteroides +g__Actinomyces +g__Aeromicrobium +g__Clostridium sensu stricto 6 +g__Reyranella +g__Proteiniclasticum +g__B1-K1A-105 +g__Prevotellaceae UCG-004 +g__Haliangium +g__Ureibacillus +g__Ruminococcus 2 +g__CYCU-0281 +g__Parafilimonas +g__Aestuariimicrobium +g__Diaminobutyricimonas +g__K2-78 +g__Erysipelatoclostridium +g__CL500-29 marine group +g__Bacteroides +g__Tessaracoccus +g__Gordonia +g__Senegalimassilia +g__Atopobium +g__Proteiniphilum +g__Uliginosibacterium +g__WCHB1-50 +g__Christensenellaceae R-7 group +g__Fodinibacter +g__Defluviicoccus +g__Acidovorax +g__Salana +g__Propionimicrobium +g__Litorilinea +g__Faecalitalea +g__Ruminiclostridium 5 +g__Rivicola +g__[Eubacterium] coprostanoligenes group +g__Lewinella +s__ + +s__sublineage I +s__cluster I +OTU_8735 +OTU_13382 +OTU_5516 +OTU_8315 +OTU_10522 +OTU_11040 +OTU_7263 +OTU_13379 +OTU_1418 +OTU_556 +OTU_6869 +OTU_10171 +OTU_2830 +OTU_4232 +OTU_12831 +OTU_613 +OTU_3625 +OTU_3605 +OTU_11148 +OTU_656 +OTU_4382 +OTU_3834 +OTU_13127 +OTU_4528 +OTU_4485 +OTU_12265 +OTU_11820 +OTU_4093 +OTU_8360 +OTU_15123 +OTU_11928 +OTU_11334 +OTU_4511 +OTU_3265 +OTU_2991 +OTU_522 +OTU_11832 +OTU_6358 +OTU_3611 +OTU_1408 +OTU_7471 +OTU_14124 +OTU_13012 +OTU_8113 +OTU_11414 +OTU_2232 +OTU_13504 +OTU_173 +OTU_11006 +OTU_9035 +OTU_8165 +OTU_1707 +OTU_4805 +OTU_7801 +OTU_6106 +OTU_9681 +OTU_4039 +OTU_4338 +OTU_1634 +OTU_684 +OTU_496 +OTU_3941 +OTU_4193 +OTU_9455 +OTU_7842 +OTU_13494 +OTU_1285 +OTU_132 +OTU_10641 +OTU_236 +OTU_462 +OTU_161 +OTU_13660 +OTU_9412 +OTU_7504 +OTU_318 +OTU_7070 +OTU_288 +OTU_2415 +OTU_95 +OTU_3982 +OTU_4278 +OTU_2887 +OTU_5684 +OTU_4220 +OTU_7051 +OTU_11398 +OTU_4669 +OTU_4697 +OTU_6765 +OTU_1066 +OTU_5907 +OTU_4933 +OTU_8885 +OTU_4226 +OTU_1821 +OTU_1794 +OTU_3925 +OTU_3353 +OTU_7163 +OTU_541 +OTU_1521 +OTU_14421 +OTU_2972 +OTU_8291 +OTU_289 +OTU_1306 +OTU_4839 +OTU_11689 +OTU_12665 +OTU_2085 +OTU_448 +OTU_6935 +OTU_190 +OTU_4458 +OTU_927 +OTU_5113 +OTU_1875 +OTU_9228 +OTU_1845 +OTU_6255 +OTU_1479 +OTU_14146 +OTU_6507 +OTU_7542 +OTU_13718 +OTU_4593 +OTU_2343 +OTU_8708 +OTU_2677 +OTU_9665 +OTU_81 +OTU_6422 +OTU_1612 +OTU_3216 +OTU_9248 +OTU_5187 +OTU_7882 +OTU_1543 +OTU_11775 +OTU_233 +OTU_4015 +OTU_8260 +OTU_9548 +OTU_5643 +OTU_1586 +OTU_3782 +OTU_2934 +OTU_14570 +OTU_11781 +OTU_3700 +OTU_6318 +OTU_2148 +OTU_2244 +OTU_7867 +OTU_14248 +OTU_12704 +OTU_364 +OTU_8245 +OTU_10847 +OTU_1151 +OTU_1998 +OTU_10321 +OTU_4721 +OTU_6237 +OTU_1972 +OTU_11364 +OTU_1816 +OTU_14842 +OTU_6533 +OTU_8887 +OTU_12690 +OTU_3097 +OTU_3257 +OTU_3161 +OTU_11903 +OTU_7508 +OTU_10969 +OTU_1801 +OTU_3488 +OTU_933 +OTU_3824 +OTU_777 +OTU_3169 +OTU_12385 +OTU_1496 +OTU_11294 +OTU_1968 +OTU_8832 +OTU_8652 +OTU_13621 +OTU_3043 +OTU_10760 +OTU_14173 +OTU_10746 +OTU_284 +OTU_5049 +OTU_2397 +OTU_2913 +OTU_9512
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.fa Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,1879 @@ +>OTU_8735 +gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc gatggcgtac taatggaaga +agcttcggca gaaaaccggt gtacgccaga gcggcggatg ggtgagtaac gcgtggacaa +cctgccctgc actgggggat aacagctgga aacggctgtt aataccgcat atgcgcacga +tgccgcatgg cagagggcgg aaagatttat cggtgcagga tgggtccgcg tcggattagc +cagttggcgg ggtaacggcc caccaaagcg atgatccgta gccggcctga gagggcgatc +ggccacattg ggactgagac acggcccaaa ctcctacggg aggcagcagt gggggatatt +gcacaatggg ggaaaccctg atgcagcgac gccgcgtgag cgatgaagtg cttcggcatg +taaagctcta tcagcgggga agaagatgac ggtacccgac taagaagccc cggctaacta +cgtg +>OTU_13382 +gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac ggacgaggcc ccttcgggga +ccgagttagt ggcgaacggg tgagtaacgc gtgagcaacc tgcctttcag tgggggacaa +cagttggaaa cgactgctaa taccgcataa aactctaaga ggacatcctc agtgagtcaa +agatttattg ctgaaagatg ggctcgcgtc tgattagcta gttggcgggg taacggccca +ccaaggcgac gatcagtagc cggactgaga ggttgaacgg ccacattggg actgagatac +ggcccagact cctacgggag gcagcagtgg ggaatattgg gcaatggggg aaaccctgac +ccagcaacgc cgcgtgaagg aagaaggctt tcgggttgta aacttctttt accagggacg +aaggacgtga cggtacctgg agaaaaagcc acggctaact acgtg +>OTU_5516 +gatgaacgct agcggcaggc ttaatacatg caaggcgagg gggcatttcg gtgtcaccgt +cgtacgggtg cgtaacgcgt atgcaaccta cctttaactg ggggatagcc cggggaaacc +cggattaata ccgcatgaca ctgtgatttc acctgagatt ataagttaaa gatttatcgg +ttaaagatgg gcatgcgttc gattagctag ttggcggggt aatggcccac caaggcgacg +atcgataggg gagctgagag gttgatcccc cacacgggca ctgagatacg ggcccgactc +ctacgggagg cagcagtagg gaatattggg caatggatgc aagtctgacc cagccatgcc +gcgtgccgga cgaaggccct cagggttgta aacggctttt attcgggaag aagagcaggg +atgcgtcctt gtgtgacggt accgaatgaa taagcaccgg ctaactccgt g +>OTU_8315 +attgaacgct ggcggcatgc tttacacatg caagtcgaac ggcagcacga gtgcttgcac +ttggtggcga gtggcggacg ggtgagtaat acatcggaac gtatcctaaa gtgggggata +acgcatcgaa agatgtgcta ataccgcata tactctgagg aggaaagtag gggatcgaaa +gaccttatgc ttttggagcg gccgatgtct gattagctag ttggtaaggt aatggcttac +caaggcaacg atcagtagtt ggtctgagag gacgaccagc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaattttgga caatgggcgc aagcctgatc +cagcaatgcc gcgtgagtga agaaggcctt cgggttgtaa agctctttca gttgagaaga +aaagattgta actaataatt gcgatccann acngnatcaa canannannc accnnctaac +tacgtg +>OTU_10522 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtgacgagg agcttgctcc +tctgatcagt ggcgaacggg tgagtaacac gtgagtaacc tgccccagac tctgggataa +cagttggaaa cagctgctaa taccggatac gagacggaga ggcatctcta ccgtctggaa +agtttttcgg tctgggatgg actcgcggcc tatcagcttg ttggtgaggt aatggctcac +caaggcgacg acgggtagcc ggcctgagag ggcgaccggc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaatattgca caatgggcgc aagcctgatg +cagcgacgcc gcgtgaggga tgacggcctt cgggttgtaa accgctttcg acagggaaga +aaatgacggt acctgtagaa gaagccccgg ccaactacgt g +>OTU_11040 +attgaacgct ggcggcatgc ctaacacatg caagtcgaac ggcagcgcgg gtagcaatac +ctggcggcga gtggcggacg ggtgagtaat gcatcgggat ctacccagac gtgggggata +acgtagggaa acttacgcta ataccgcata cgtcctacgg gagaaagcgg gggctcgcaa +gacctcgcgc ggttggacga accgatgtgc gattagctag ttggtggggt aatggcccac +caaggcgacg atcgctagct ggtctgagag gatgatcagc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaatattgga caatgggcgc aagcctgatc +cagcaatgcc gcgtgtgtga agaaggcctt cgggttgtaa agcactttta tcaggagcga +aatgccattg gttaataccc ggtggagctg acggtacctg aggaataagc accggctaac +ttcgtg +>OTU_7263 +aatgaacgct ggcggcgtgc ttaacacatg caagtcgtac gcgaaaggcg ctttcgggtg +ctgagtagag tggcgcacgg gtgagtaacg cgtgggtaat ctacccttgg atcttggata +acacatcgaa aggtgtgcta atacgggatg aagtctgcgg agatgcgttt ttgcagatga +aaggccgcgc aagcggttgt ccgaggatga gcctgcgtcc cattagctag ttggcggggt +aaaggcccac caaggctgag atgggtagct ggtctgagag gatgatcagc cacactggaa +ctggaacacg gtccagactc ctacgggagg cagcagtgag gaattttgcg caatggggga +aaccctgacg cagcaacgcc gcgtgagtga tgaaggcctt cgggtcgtaa agctctgtcg +agtgggaaga aaccgttcag attaataacc tgaaccttga cggtaccact aaaggaagca +ccggctaact ccgtg +>OTU_13379 +gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc gcatgacgag gagcttgctc +ctctgattga gcggcggacg ggtgagtaac acgtgggcaa cctgccctgt agacggggat +aacttcggga aaccggagct aataccggat aatcctcttc cccacatggg gaagagttga +aaggcgcttt tgcgtcacta caggatgggc ccgcggtgca ttagctagtt ggtggggtaa +cggcctacca aggcgacgat gcatagccga cctgagaggg tgatcggcca cattgggact +gagacacggc ccaaactcct acgggaggca gcagtaggga atcttccaca atggacgaaa +gtctgatgga gcaacgccgc gtgagtgatg aaggttttcg gatcgtaaaa ctctgttgta +agggaagaac cagtacgtca ggcaatggac gtaccttgac ggtaccttat tagaaagcca +cggctaacta cgtg +>OTU_1418 +aatgaacgct ggcggcgtgg attaggcatg caagtcgaac gggcattagc aatagtgtca +gtggcgacct ggtcagtaca aattgggtta cgtgcccgga agtgggggat aacgccgtga +aaacggcgct aataccgcat gtggacgaaa gtctaaagca gcagtgcgct tccggatcgg +cccaatcctc attagcttgt tggcggtgta aaagaccacc aaggcatcga tgagtaggcg +acgtgagagc gcgaccgccg acacgaggac tgagatacgg cctcgactcc tacggggggc +agcagtctag aagcttcgtc aatgggcgaa agcctgaacg agcgacgccg cgtgtgggat +gacgcccttt ggggtgtaaa ccactttcga ctgggaagaa ggtccggatg gtgaattcgg +atttgacggt accagtggaa gaagcaccgg ctaactccgt g +>OTU_556 +gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc gaagcggctg aattgattct +tcggatgatt ttcagttgac tgagcggcgg acgggtgagt aacgcgtggg tgacctgccc +cataccgggg gataacagct ggaaacggct gctaataccg cataagcgca cagagctgca +tggctcggtg tgaaaaactc cggtggtatg ggatgggccc gcgtctgatt aggcagttgg +cggggtaacg gcccaccaaa ccgacgatca gtagccggcc tgagagggcg accggccaca +ttgggactga gacacggccc aaactcctac gggaggcagc agtggggaat attgcacaat +gggggaaacc ctgatgcagc gacgccgcgt gagcgaagaa gtatttcggt atgtaaagct +ctatcagcag ggaagataat gacggtacct gactaagaag ccccggctaa ctacgtg +>OTU_6869 +gatgaacgct ggcggcgtgg ataaggcatg caagtcaagg ggcccgcaag ggcaccggca +gacgaggtag taataagtag gtaccaaccc caaagtcagg gatacctcat cgaaagatga +gttaatactt gatggtctct tcggagtaaa gatttatcgc tttgggatgg gcctgctcgg +tatcagctag ttggtaaggt aacggcttac caaggctatg acacctaggg gacctgagag +ggtgaccccc accgatggaa ctgagacacg gtccatacac ctacgggtgg ccgcagtcga +gaatcttccg caatgggcga aagcctgacg gagcgacgcc gcgtgattga tgaagctctt +cggagcgtaa aaatcttttg ccagggaaaa agtatattga ttgtacttgg cgaataagag +gttgctaaac tcgtg +>OTU_10171 +gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc ggagatatta gtaatagtat +cttagcggcg gacgggtgag taacgcgtgg gcaacctacc ttcaactggg ggataacaca +gggaaacttg tgctaatacc gcataacatc gctaagtgac atcacttaat gatcaaagga +gtaatccggt ggaagatggg cccgcgtccg attagctagt tggtgatgta acggaccacc +aaggcgacga tcggtagccg aactgagagg ttgatcggcc acattgggac tgagacacgg +cccagactcc tacgggaggc agcagtgggg aatattgcgc aatggaggga actctgacgc +agcaacgccg cgtgaaggat gaaggctttc gggttgtaaa cttctttgat gagggacgaa +acaaatgacg gtacctcaaa aacaagccac ggctaactac gtg +>OTU_2830 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac gatgaagccc tttcgggggt +ggattagtgg cgaacgggtg agtaacacgt gagtaacctg cccttcactt ctggataact +ctcggaaacg ggggctaata caggatatga ctcaagcctg catgggtttg ggtggaaaga +ttttttggtg ggggatgggc tcgcggccta tcagcttgat ggtggggtga tggcctacca +tggcgacgac gggtagccgg cctgagaggg cgatcggcca cactgggact gagacacggc +ccagactcct gcgggaggca gcagtgggga atattgcaca atgggcgaaa gcctgatgca +gcgacgccgc gtgagggatg aaggccttcg ggttgtaaac ctctttcgtc agggaagaag +cctttcgggg tgacggtacc tggagaagaa gcaccggcta actacgtg +>OTU_4232 +gattaacgct agcggcaggc ctaatacatg caagtcgagg ggcagcaggg tgtagcaata +catcgctggc gaccggcgca cgggtgcgta acacgtatgc aacctacctt taactgggga +atagccctcc gaaaggagga ttaacaccgc ataacatcac gagacggcat cgccttgtga +tcaaacctcc gggggttaaa gatgggcatg cgtccgatta gctagttggc ggggtaacgg +cccaccaagg cgacgatcgg tagggggtct gagaggatga tcccccacac tggtactgag +acacggacca gactcctacg ggaggcagca gtaaggaata ttggacaatg gtcgcaagac +tgatccagcc atgccgcgtg caggatgaac gatctatgat ctgtaaactg cttttgttcg +ggaataaacc ccttcacgtg tggagggctg aatgtaccga aagaataagg gtcggctaac +ttcgtg +>OTU_12831 +aatgaacgtt ggcggcgtgg attaggcatg caagtcgagc gagaaccgta gcaatacggg +gacagcggcg aaagggagag gaccacgtgg atacgtaccc tcgggttcag gatagccatg +ggaaactatg ggtaatactg aatgacatct ccggatcaaa ggtgagattc cgcccgggga +gcggtccgcg tcctattagc tagttggtga ggtaacggct caccaaggcg aagatgggta +tgggatgtga gagcatgatc ccactcactg ggactgagac actgcccaga cacctacggg +tggctgcagt cgagaatctt cggcaatggg ggcaaccctg accgagcgac gccgcgtgcg +agatgaaggc cttcgggttg taaatcgctg tcagagggga ggaaatgtcg gtgggttctc +ccatcgattt gacctatcct cagaggaagg acgggctaag ttcgtg +>OTU_613 +aatgaacgct ggcggcgtgc ctaacacatg caagtcgaat gtgccgcaag gtgcatggca +gacgggtgag taacgcgtgg gcaatctacc ttctcgtggg gaataacgct ccgaaaggag +tggtaatacc gcataagacc gatggctggg atgctgtcgg tgaaacctgg ggaccgcaag +gcctggggcg agaagaggag cctgcgtctg attagctagt tggtggggta atggcctacc +aaggcatcga tcagtagccg gcctgagagg gtgatcggcc acactggaac tgagacacgg +tccagactcc tacgggaggc agcagtgggg aattttgcgc aatgggcgaa agcctgacgc +agcaacgccg cgtgggtgat gaaggtcttc ggatcgtaaa accctgtcgt tggggacgaa +ggtagggcgg ttaatagccg ttttgcttga cggtacccgg agaggaagcc ccggctaact +ctgtg +>OTU_3625 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtaaggccc ttcggggtac +acgagtggcg aacgggtgag taacgcgtga gtaacctgcc cttgactctg ggataacaga +tagaaatgtc tgctaatacc ggatactcag cctcgcaggc atctgtgagg ctggaaagct +ccggcggtca aggatggact cgcgtcctat cagcttgttg gtggggtaat ggcctaccaa +ggcgacgacg ggtagccggc ctgagagggc gaccggccac attgggactg agatacggcc +caaactccta cgggaggcag cagtggggaa tattgcacaa tgggcgaaag cctgatgcag +caacgccgcg tgcgggatga cggccttcgg gttgtaaacc gctttcagca gggacgaagc +gcaagtgacg gtacctgcag aagaagcacc ggctaactac gtg +>OTU_3605 +gacgaacgct ggcggcgtgc ctaatgcatg caagtcgcac gcgccgcctt cgggcggtga +gtggcgcacg gctgaggatc acgtgggaac atgcctcgtg gtgggggaca acagcgcgaa +agcgctgcta atcccgcata cgctcgcgca agcgaggaaa gcggtaacgc gccgcgagag +tggcccgcgg cccatcaggt cgtaggtggg gtaacggcct acctagccga tgacgggtag +ctggtctgtg aggacagaca gccagactgg gactgagaca cggcccagac tcctacggga +ggcagcagca aggaattttc gtcaatgggc gcaagcctga acgagcaacg ccgcgtggag +gatgacggcc ttcgggttgt aaactccttt tgggggggac gataatgacg gtaccccttg +aataaggctc ggctaactct gtg +>OTU_11148 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtgacgcgc cttcgggcgc +tgatcagtgg cgaacgggtg agtaacacgt gggcaacctg cccctagctc tgggataacc +cctcgaaaga ggagctaata ccggatatca ccgctccaga catctggtgc ggttgaaagt +ttttcggcta gggatgggcc cgcggcctat cagcttgttg gtggggtaac ggcccaccaa +ggcgacgacg ggtagccggc ctgagagggc gaccggccac actgggactg agacacggcc +cagactccta cgggaggcag cagtggggaa tattgcgcaa tgggcgaaag cctgacgcag +caacgccgcg tgagggacga cggcccttgg gttgtaaacc tctttcagca gggacgaaaa +tgactgtacc tgcagaagaa gcgccggcta actacgtg +>OTU_656 +gatgaacgct ggcggcgtgc ctaacacatg taagtcgaac gtgagagact agcaatagtc +ttgaaagtgg cgaacgggtg agtaacacgt aggaacctgc cctggagtgg gggataacca +ctggaaacgg tggctaatac cgcatacgcc tgtgaagatg ggagtctttg cagggaaaga +gcgattgctc caggaggggt ctgcgtccga ttagctagat ggtggggtaa aggcctacca +tggcgatgat cggtagctgg tctgagagga tgatcagcca cacgggaact gagacacggt +cccgactcct acggggggca gcagtgagga atattgcaca atgggggaaa ccctgatgca +gcaacgccgc gtggaggatt gacggtcttt ggattgtaaa ctccttttct gtgggacgag +cgaggacggt accacaggaa tcagtcacgg ctaactacgt g +>OTU_4382 +attgaacgct ggcggaatgc tttacacatg caagtcgagc ggcagcgcgg gggcaaccct +ggcggcgagc ggcgaacggg tgagtaacat atcggaacgt accctgtcgt gggggataac +acatcgaaag gtgtgctaat accgcatacg acctgagggt gaaagcgggg gatcgcaaga +cctcgcgcga caggagcggc cgatatcgga ttagctagtt ggtgaggtaa aggctcacca +aggcgacgat ccgtagcggg tctgagagga cgacccgcca cactggaact gagacacggt +ccagactcct acgggaggca gcagtgggga attttggaca atgggggcaa ccctgatcca +gccattccgc gtgagtgaag aaggccttcg ggttgtaaag ctctttcagc aggaacgaaa +cggtggcccc taatacgggc tactaatgac ggtacctgaa gaagaagcac cggctaacta +cgtg +>OTU_3834 +gatgaacgct agcggcaggc ctaatacatg caagtcgaac ggtaaggccc tttcgggggt +acacgagtgg cggacgggtg cgtaacgcgt atgcaacata ccttccagcg ggggatatgc +cagggaaact tggtgcaata ccccatggta tcattgtttc acatgggacg atgattaaaa +ctccggtgct gggagattgg catgcgtgac attagctagt tggcggggta acggcccacc +aaggcgacga tgtctagctg gtctgagagg atgatcagcc acactgggac tgagacacgg +cccagactcc tacgggaggc agcagtaggg aatattggac aatgggggga accctgatcc +agccatgccg cgtgagggaa gaaggtcctc tggattgtaa acctcttttg gcgggggaca +aacctgtgct acacgcacag ctgagggtac ccgcagaata agcaccggct aactccgtg +>OTU_13127 +gacgaacgct ggcggcatgc ctaacacatg caagtcgaac ggagaatagt attaagttta +cttgatacta aacttagtgg cggacgggtg agtaacgcgt ggataacctg cctgttagac +cgggataact tcgggaaacc gtagctaata ccggatacag actatatact gcatagtaaa +tagttgaaaa gaatattgct aacagatggg tccgcgtccc attagctagt tggtggggta +acggcctacc aaggcagcga tgggtagccg gcctgagagg gtggacggcc acactgggac +tgagacacgg cccagactcc tacgggaggc agcagtgggg aatattccgc aatgggggga +accctgacgg agcaatgccg cgtgagggac gaatgccttc gggttgtaaa cctttgttct +atgggaagat aatgacggta ccataggagt aagccccggc taactacgtg +>OTU_4528 +gatgaacgct agcgggaggc ctaatacatg caagtcgaac ggtaaggtcc ttcgggatac +acgagtggca aacgggtgcg taacgcgtac ggaacatgcc tctatcagag agatagccct +gggaaactgg gtataatacc tcatagtatt gtattgccgc atggtattta caattaaagc +tccggcggat agagattgtc gtgcgtccca ttagctagtt ggtaaggtaa cggcttacca +aggcgacgat gggtaactgg tttgagagga tgatcagtca cactggaact gagacacggt +ccagactcct acgggaggca gcagtaggga atattggaca atggacgcaa gtctgatcca +gccatcccgc gtgcaggatt aaggccctct gggttgtaaa ctgcttttat tagagaagaa +aacctcagat ttatctgaac ttgacggtat ctaatgaata agcaccggct aactccgtg +>OTU_4485 +aacgaacgct ggcggcatgc ttaacacatg caagttgtgc gagaaccaag gggcttgctc +tttggggaaa gcagcgcacg ggtgagtaac gcgtggataa cgtgccctag ggttggggat +aacccgccga aaggtggact aataccgaat gtgttccaat aaggtgcgcc tatttggaag +aaagcggggc aacccgcgcc caaggatcgg tccgcgttcc atcagctagt tggtgaggta +atggctcacc aaggctacga cggatagctg gtctgagagg atgatcagcc acactgggac +tgagatacgg cccagactcc tacgggaggc agcagtgggg aatattggtc aatgggcgaa +agcctgaacc agcaatgccg cgtgagtgat gaaggcctta gggttgtaaa gctctgtcag +tgggaacgaa taagtcgatt aatacccgat gatgacggta cccacaaagg aagcaccggc +taactctgtg +>OTU_12265 +gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc gagcggaact aacagattta +cttcggtaat gacgttagga aagcgagcgg cggatgggtg agtaacacgt ggggaacctg +ccccatagtc tgggatacca cttggaaaca ggtgctaata ccggataaga aagcagatcg +catgatcagc ttttaaaagg cggcgtaagc tgtcgctatg ggatggcccc gcggtgcatt +agctagttgg taaggtaaag gcttaccaag gcgatgatgc atagccgagt tgagagactg +atcggccaca ttgggactga gacacggccc aaactcctac gggaggcagc agtagggaat +cttccacaat ggacgcaagt ctgatggagc aacgccgcgt gagtgaagaa ggttttcgga +tcgtaaagct ctgttgttgg tgaagaagga tagaggtagt aactggcctt tatttnacng +naatcaacna gnanntcacn nctaactang tg +>OTU_11820 +gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc ggagataaga agagtacttg +tacaattttt atcttagcgg cggacgggtg agtaacacgt gagtaacctg cctttcactg +gggaataaca tcgagaaatc ggtgctaata ccgcataatg tcaagacatc acctggtgac +ttgaccaaag gagaaatccg gtaaaagatg gactcgcgtc cgattaggta gttggtgagg +taatggccca ccaagcctac gatcggtagc cgaactgaga ggttgatcgg ccacattggg +actgagacac ggcccagact cctacgggag gcagcagtgg ggaatattgg gcaatgggcg +aaagcctgac ccagcaacgc cgcgtgaagg aagaaggtct tcggattgta aacttctttg +acgagggacg aaaaaaatga cggtacctcg aaaacaagcc acggctaact acgtg +>OTU_4093 +gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtgatagca atatcacagt +ggcgcacggg tgaggaacac gtagctcatc tgccccaaag tgtgggataa cggtccgaaa +ggattgctaa taccgcataa gctcccggac tgtagaggtc tgagagaaaa ggcgcaagtc +gctttgggag gaggctgcgg cccatcaggt agttggtgtg gtaacggcgc accaagccaa +cgacgggtag gggacctgag agggtgaccc cccacactgg gactgagaca cggcccagac +tcctacggga ggcagcagtg aggaatattg cccaatggac gcaagtctga ggcagcgacg +ccgcgtgggt gaagaaggcc ttcgggtcgt aaagcccttt tctgtgtgac gagaacggac +ggtagcacag gaaaaagtct cggctaacta cgtg +>OTU_8360 +gatgaacgct agcggcaggc ttaacacatg caagtcgagg ggtaaatagt tttcggatta +ttgagaccgg cgcacgggtg cgtaacgcgt atgcaatcta ccttttacag agggatagcc +cagagaaatt tggattaata cctcatagta tagttgaatg gcatcattta attattaaag +ttccaacggt aaaagatgag catgcgtccc attagttagt tggtaaggta acggcttacc +aagacaatga tgggtagggg tcctgagagg gagatccccc acactggtac tgagacacgg +accagactcc tacgggaggc agcagtgagg aatattggac aatgggcgca agcctgatcc +agccatgccg cgtgcaggaa gaagcatcta tggtgtgtaa actgcttttg tacgggaaga +aacatcacta cgtgtagtga cttgacggta ccgtaagaat aaggatcggc taactccgtg +>OTU_15123 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac gaggattttt atttcggtaa +aaatccgagt ggcaaacggg tgagtaacgc gtaggcaacc tgcctttctg atggggacaa +cagttcgaaa ggactgctaa taccgaatga cgtatatttc tcgcatgaga gacataccaa +agatggcctc tgaatatgct atcacagaaa gatgggcctg cgtctgatta gctggttggt +ggggtaacgg cctaccaagg cgacgatcag tagccggtct gagaggatga acggccacat +tgggactgag acacggccca gactcctacg ggaggcagca gtggggaatc ttccacaatg +gacgaaagtc tgatggagca acgccgcgtg agtgaagaag gttttcgaat cgtaaagctc +tgttgtcagg gacgaatgtt gagactgaga atattggttt caaatgacgg tacctgacga +ggaagccacg gctaactacg tg +>OTU_11928 +aatgaacgct ggcggcgtgc ttaacacatg caagtcgcac gagaacgctt ctgcttgcag +gggctagtaa agtggcgcac gggtgagtaa cgcgtgggta atctaccccc ggatctggga +taaccctccg aaaggggtgc taataccgga tgaagtcatt gagactgcgg ttttgatgat +gaaaggtggc ctctccatgg aagctactgt ttggggatga gcccgcgtac cattagctag +ttggtggggt aacggcctac caaggcagcg atggttagct ggtctgagag gatgatcagc +cacactggaa ctgacacacg gtccagactc ctacgggagg cagcagtgag gaattttgcg +caatgggggg aaccctgacg cagcaacgcc gcgtgagtga agaaggcctt cgggtcgtaa +agctctgtcg agtgggaaga acattttcat ggtgaacatc catggggatt gacggtacca +cagaaggaag caccggctaa ctccgtg +>OTU_11334 +agcgaacgct ggcggcatgc ttaacacatg caagtcgcac ggtcgggggc aacctcggca +gtggcggacg ggtgagtaac gcgtaggcat ctatccttgg atgggggaca accgtgggaa +actacggcta ataccgcatg aagcctgagg gctaaagctc gcgagagcgt ctggggcgga +gcctgcgtcc gattagctag ttggtggggt aaaggcctac caaggcgatg atcggtagct +ggtctgagag gatgatcagc cacactggga ctgagacacg gcccagactc ctacgggagg +cagcagtggg gaatattgga caatgggcgc aagcctgatc cagcaatgcc gcgtgggtga +agaaggtctt cggattgtaa agccctttcg acggggacga tgatgacggt acccgtagaa +gaagccccgg ctaacttcgt g +>OTU_4511 +agcgaacgtt agcggcgcgc ctaacacatg caagtcgcac gagaaagggc ttcggccccg +gtaaagtggc gcacgggtga gtaacacgtg ggcaacctgc ccaaccctgg gggataacct +gccgaaaggc gggctaatac cgcgtacgag ggctctactt cggtagggtt ctgaaagcag +gcctctgtat acaagcttgc ggggttggat gggcccgcgc tccatcagct agttggtgag +gtaagagctc accaaggcta cgacggatag ctggtctgag aggatgatca gccacactgg +aactgagaca cggtccagac tcctacggga ggcagcagtg gggaatcttg cgcaatgggc +gaaagcctga cgcagcgacg ccgcgtgggt 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atcagtagtt ggtctgagag gacgaccagc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaattttgga caatgggcgc aagcctgatc +cagcaatgcc gcgtgagtga agaaggcctt cgggttgtaa agctctttca gcagggacga +aactgacggt acctgcagaa gaagcaccgg ctaactacgt g +>OTU_6358 +gatgaacgct ggcggcgtgc ttaacacatt caagtcgaac ggagaacggg gagcttgctc +cccgggatca gtggcggacg ggtgagtaac gcgtgagcaa cctgcctgtg tgtgggggat +aacacccgga aacgggtgct aataccgcat aacgcaacgg agccgcatga ctttgttgcc +aaagatatat tgcgcacaga tgggctcgcg tctgattaga tagttggtga ggtaacggct +caccaagtcg acgatcagta gccggactga gaggttgaac ggccacattg gaactgagat +acggtccaga ctcctacggg aggcagcagt ggggaatatt gggcaatggg cgaaagcctg +acccagcgac gccgcgtgag ggaagaaggt cttcggattg taaaccttag tcaacaggga +agaagaaagt gacggtacct gtggaggaag ccacggctaa ctacgtg +>OTU_3611 +aatgaacgct ggcggcgtgc ctaatacatg caagtcgagc gccccttcat agtactgatg +agtaatcata agtcctgtga tggggagcgg cggacgggtg agtaacgcgt gggaacatac +cccagactga gggataagca ccagaaatgg tgtctaatac cgcataacct ctacggagaa +aagcttcggc 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agcattatgg tgtgtaaact tcttttctgg gggacgaaga +atgacggtac ctcaggaata agggacggct aactacgtg +>OTU_11414 +gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggacccttcg gggttagtgg +cggacgggtg agtaacgcgt gaggatctgc ccttaggagg ggaacaacag ttggaaacga +ctgctaatgc cccatatgcc gagaggtgaa aagttatatc gcctagggat gaactcgcgt +ctgattagct agttggtggg gtaaaggctc accaaggcga cgatcagtag ctggtctaag +aggatgatca gccacactgg gactgagaca cggcccagac tcctacggga ggcagcagtg +gggaattttc cgcaatgggc gaaagcctga cggagcaacg ccgcgtgagg gacgaaggcc +ttagggttgt aaacctcttt tctctgggaa gaagaactga cggtaccaga ggaataagcc +tcggctaact ccgtg +>OTU_2232 +gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtgaagcca agcttgcttg +gtggatcagt ggcgaacggg tgagtaacac gtgagtaacc tgccccagac tctgggataa +gcgctggaaa cggcgtctaa taccggatac gagacgagac cgcatggtca ttgtctggaa +agaatttcgg tctgggatgg actcgcggcc tatcagcttg ttggtgaggt aatggctcac +caaggcgtcg acgggtagcc ggcctgagag ggtgaccggc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaatattgca caatgggcgc aagcctgatg +cagcaacgcc gcgtgaggga cgaaggcctt cgggttgtaa acctctttta gcagggaaga +agcgaaagtg acggtacctg cagaaaaagc gccggctaac tacgtg +>OTU_13504 +gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac gaatcttggt gaatgaattg +gagtgcttgc acaaagaggc atttacaatg agatgagtgg cggacgggtg agtaacacgt +gggtaacctg ccctgaagtg ggggataaca tttggaaaca gatgctaata ccgcataaca +atgagagtca catgactttt atttgaaaga tggagcaatc tatcacttca ggatggacct +gcggcgtatt agctagttgg taaggtaaag gcttaccaag gcgatgatac gtagccgact +tgagagagtg atcggccaca ttgggactga gacacggccc aaactcctac gggaggcagc +agtagggaat cttccacaat ggacgaaagt ctgatggagc aacgccgcgt gagtgaagaa +gggtttcggc tcgtaaaact ctgttattgg agaagaagga taaggtaagt aactgtactt +tatttgacgg tacccaacca gaaagtcacg gctaactacg tg +>OTU_173 +gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac gtgaaggggt acttgtatcc +ctgaaagtgg cgaacgggtg agtaacacgt aggtgaccta cctcaaagaa ggggataact +actggaaacg gtggctaata ccctatggtt ctgacgactg tggaggttgt cagataaaga +ctccggtgct ttgagagggg cctgcgtccg attaggtagt tggtggggta aaggcctacc 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ttgtaataaa ggtaaataat +taaaactacg gtgcttatag attggtgtgc gtctgattag ctagttggcg aggtaacggc +tcaccaaggc gacgatcagt agggggcgtg agagcgtgaa cccccacacg ggtactgaga +cacggacccg actcctacgg gaggcagcag taaggaatat tggtcaatgg agggaactct +gaaccagcca tgccgcgtgc aggatgaaag ccctctgggt tgtaaactgc ttttaacagg +gaagaaaatg ctatacgtga tatagtacnn gcngnncctg agnnntnnnc accnnctaac +tccntg +>OTU_8165 +gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac gaaccagtca gattgatttc +ttcggaatga aatcagacac ggttagtggc ggacgggtga gtaacacgtg ggtaatttac +ctcttagaca gggataacac tgggaaactg gtgctaatac ctgataaagt ttatataagg +catcttaaat agatgaaatg gaggcctctc aaagaagctc ccgctaagag atgaacccgc +ggctgattag ctagttggta aggtaatggc ttaccaaggc aacgatcagt agccggcctg +agagggtgat cggccacact gggactgaga cacggcccag actcctacgg gaggcagcag +tggggaatat tgcgcaatgg gggaaaccct gacgcagcaa cgccgcgtga gtgaagaagg +tcttcggatt gtaaagctct gtcaattggg aagaaggctt acaggtaaat agcctgtgag +atgacggtac ctaagaagga agctccggct aactacgtg +>OTU_1707 +attgaacgct ggcggaatgc tttacacatg caagtcgaac ggcagcacgg gggcaaccct +ggtggcgagt ggcgaacggg tgagtaacac atcggaacgt gcccagtcgt gggggataac +gtagcgaaag ctacgctaat accgcatacg aactctggtt gaaagcgggg gactcgcaag +ggcctcgcgc gattggagcg gccgatggca gattaggtag ttggtggggt aaaggctcac +caagccgacg atctgtagct ggtctgagag gacgaccagc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaattttgga caatgggcgc aagcctgatc +cagccattcc gcgtgcagga tgaaggccct cgggttgtaa actgcttttg tacggaacga +aacggtctga gttaatacct cgggctaatg acggtaccgt aagaataagc accggctaac +tacgtg +>OTU_4805 +aacgaacgct ggcggcatgc ctaacacatg caagtcgaac gccccgcaag gggagtggcg +aacgggtgag taacgcgtgg gaacctaccc agcagttggg gataaccgcg ggaaactgcg +gctaataccg aatacgtcct tagggagaaa gatttatcgc tgttggaggg gcccgcgtcg +gattagctag ttggtgaggt aacggctcac caaggcgacg atccgtagct ggtctgagag +gatgatcagc cacactggga cttagacacg gcccagactc ctacgggagg cagcagtggg +gaatattgga caatgggggc aaccctgatc cagcaatgcc gcgtgagtga tgaaggcctt +agggttgtaa agctctttta ccggggacga tgatgacggt acccggagaa taagccccgg 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cgaacgggtg agtaacacgt gggtaacctg ccgcgcagag ggggataacg +actggaaacg gtcgctaata ccgcatggta ccaagaggaa tggtctcctt ttggttaaaa +ctttggtgct gcgcgagggg cctgcgcccg attagctagt tggtgaggta aaggctcacc +aaggcgatga tcggtagcta gtctgagagg atgattagcc acacgggaac tgagacacgg +tcccgactcc tacggggggc agcagtgagg aatattgcac aatggacgaa agtctgatgc +agcaacgccg cgtggaggat gaaggccctt gggttgtaaa ctcctttttt cagggaagag +aatggacggt acctgaagaa taagtcacgg ctaactacgt g +>OTU_7882 +gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc ggagattgca gtaatgtaat +cttagcggcg gacgggtgag taacgcgtgg gcaacctacc tataactggg ggataacaca +gggaaacttg tgctaatacc gcataacatc atgaagtgac atcactttat gatcaaagga +gcaatccggt gatagatggg cccgcgtccg attagctagt tggtggggta atggctcacc +aaggcgacga tcggtagccg aactgagagg ttgatcggcc acattgggac tgagacacgg +cccagactcc tacgggaggc agcagtgggg aatattgcgc aatgggggaa accctgacgc +agcaacgccg cgtgaaggat gaaggttttc ggatcgtaaa cttctttgat tggggacgaa +taatgacggt acccaaaaaa caagccacgg ctaactacgt g +>OTU_1543 +gatgaacgct ggcggcgtgc 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actacgtg +>OTU_233 +gacgaacgct ggcggtgtgc ttaacacatg caagtggtgc gacgaaccag gcttcggcct +ggggcaaagc cgcgaacggg tgagtaacac gtgggtaatc tgccccgatg accgggacaa +cccgaggaaa ctcgggctaa taccggatgt ggtgcccaga cttaagtctg gtcactaaag +gtagcttcgg cttccgcatt gggaggggcc cgcggcccat tagcttgttg gtggggtcaa +ggcctaccaa ggcaacgatg ggtagctggt ctgagaggac gatcagccac actgggactg +agacacggcc cagactccta cgggaggcag cagtggggaa tcttgcgcaa tgcgcgaaag +cgtgacgcag caacaccgcg tgagggaaga cggccttagg gttgtaaacc tctttcagat +gggacgaagg tcatccggtg aatagccgag gtgattgacg gtaccgtcag aagaagctcc +ggctaactac gtg +>OTU_4015 +gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac gcgagcactt gtgctcgagt +ggcgaacggg tgagtaatac ataagtaacc tgccctagac agggggataa ctattggaaa +cgatagctaa gaccgcatag gtacggacac tgcatggtga ccgtattaaa agtgcctcaa +agcactggta gaggatggac ttatggcgca ttagctggtt ggcggggtaa cggcccacca +aggcgacgat gcgtagccga cctgagaggg tgaccggcca cactgggact gagacacggc +ccagactcct acgggaggca gcagtaggga attttcggca atgggggaaa ccctgaccga +gcaacgccgc 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tgatcagcca cactgggact +gagacacggc ccagactcct acgggaggca gcagtgggga atcttgcgca atgggcgaaa +gcctgacgca gcaacgccgc gtgcgggaag aaggctctcg ggttgtaaac cgctttcagc +aggaacgaaa atgacggtac ctgcagaaga agccccggct aactacgtg +>OTU_5643 +gatgaacgct agctacaggc ttaacacatg caagtcgagg ggcagcattt tagtttgctt +gcaaactaaa gatggcgacc ggcgcacggg tgagtaacac gtatccaacc tgccgataac +tcggggatag cctttcgaaa gaaagattaa tatccgatag tatattaaaa ccgcatggtt +ttactattaa agaatttcgg ttatcgatgg ggatgcgttc cattagtttg ttggcggggt +aacggcccac caagactacg atggataggg gttctgagag gaaggtcccc cacattggaa +ctgagacacg gtccaaactc ctacgggagg cagcagtgag gaatattggt caatggacga +gagtctgaac cagccaagta gcgtgaagga tgactgccct atgggttgta aacttctttt +atatgggaat aaagtattcc acgtgtggga ttttgtatgt accatatgaa taaggatcgg +ctaactccgt g +>OTU_1586 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggtaaggccc tttcgggggt +acacgagtgg cgaacgggtg agtaacacgt gagtaacctg ccccagactc tgggataaca +gccggaaacg gttgctaata ccggatattc agcttcctgc gcatgtgggt tgttggaaag +tttttgcggt ttgggatggg ctcgcggtct atcagcttgt tggtggggta gtggctcacc +aaggcttcga cgggtagccg gcctgagagg gtgaccggcc acattgggac tgagatacgg +cccaaactcc tacgggaggc agcagtgggg aatattgcac aatggacgga agtctgatgc +agcaacgccg cgtgcgggat gacggccttc gggttgtaaa ccgctttcat ccatgacgaa +gcgaaagtga cggtagtggg agaagaagca ccggctaact acgtg +>OTU_3782 +gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac ggaaaggcct agcttgctag +gtactcgagt ggcgaacggg tgagtaacac gtgggtgatc tgccctcaac ttcgggataa +gcttgggaaa ctgggtctaa taccggatat gaccaggagc tgcatggctt ctggtggaaa +gccttgtgcg gttggggatg ggcccgcggc ctatcagttt gttggtgggg taatggccta +ccaaggcgac gacgggtagc cggcctgaga gggtgaccgg tcacactggg actgagacac +ggcccagact cctacgggag gcagcagtgg ggaatattgc acaatgggcg caagcctgat +gcagcgacgc cgcgtgaggg acgacggcct tcgggttgta aacctctttc gccagggacg +aagcgcaagt gacggtacct ggagaagaag caccggccaa ctacgtg +>OTU_2934 +gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc gatgaaaccg ccctcgggcg +gacatgaagc ggcgaacggg tgagtaacac gtgaccgacc tgccccccgc ccagggacag +ccccccgaaa 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cgggttgtaa agctctttca gacggaaaga +aatggctccg gataatacct ggagtcgatg acggtaccgt aagaagaagc accggctaac +tacgtg +>OTU_2244 +gatgaacgct ggcggcgtgc ctaacccatg taagtcgggc gatctttgta gcaatacgga +gagagcggcg gaagggtgag taacacgtag aagacctacc tcactgcagg gaacaacttc +gcgaaagcgg agctaatacc caaaaggttc ggacattcaa ttgttcgagc agagttcgca +agagcgtagt gagagggttc tgcggcccat cagctagttg gtagggtagt ggcctaccaa +ggcaacgacg ggtagggggt ctgagaggac gatcccccac actggaactg aaacacggtc +cagacgccta cgggtggcag cagggaggaa tattgggcaa tgggcgaaag cctgacccag +caacgccgcg tgaaggatga aagccttcgg gttgtaaact tcttttgagg gagacgagaa +aggacggtat ccctcgaata agcaacggct aactacgtg +>OTU_7867 +gatgaacgct agcgggaggc ttaacacatg caagtcgagg ggtatttgta gcaatacaga +gagaccggcg cacgggtgag taacgcgtat gcaacctgcc ctttactgga ggatagcccg +tagaaatgcg gattaatacc ccatagtaat atcggatcgc atgatttgat atttaaagtt +tcggcggtaa aggatgggca tgcgtgacat tagctagttg gtaaggtaac ggcttaccaa +ggcttcgatg tctaggggtt ctgagaggaa gatcccccac actggtactg agacacggac +cagactccta cgggaggcag cagtgaggaa tattggtcaa tgggcgagag cctgaaccag +ccatcccgcg tgcaggaaga atgccctatg ggttgtaaac tgctttttcg catgaagaac +acccctgacg tgtcaggggc tgacggtaat gcgtgaataa gcaccggcta actccgtg +>OTU_14248 +gccgcccgct ttctttttgc ttaacacctt ccctttttgc gacgaaccag agcttgctct +ggggcaaagc cgcgaacggg tgagtaacac gtgggtaatc taccccgatg accgggacaa +cccgaggaaa ctcgggctaa taccggatgt ggtacggaga cataagtctc tttactaaag +gtagcttcgg cttccgcatt gggaggggcc cgcggcccat tagctagttg gtggggtcaa +ggcctaccaa ggcaacgatg ggtagctggt ctgagaggac gatcagccac actgggactg +agacacggcc cagactccta cgggaggcag cagtggggaa tcttgcgcaa tgcgcgaaag +cgtgacgcag caacaccgcg tgagggaaga cggccttagg gttgtaaacc tctttcagat +gggacgaagg tgatgcggtg aatagccgat gtcattgacg gtaccgtcag aagaagctcc +ggctaactac gtg +>OTU_12704 +aacgaacgct ggcggcgtgc ctaacacatg caagtctaac gggctgtagc aatacagtca +gtggcgcacg ggtgagtaat gcatgagtaa tctgccctca agatggggat aacctgccga +aaggcgggct aataccaaat aagaccacgg gatctgcgga ttctgaggtt aaaggtggcc +tctatttata agctatcgct tgaggatgag ctcatgtccc atcagctagt tggtgaggta +atagcttacc aaggctaaga cgggtagctg atctgagagg atgatcagcc acactggaac +tgagatacgg tccagactcc tacgggaggc agcagtgggg aatattgcgc aatggacgaa +agtctgacgc agcaacgccg cgtgggtgat gaaggccttc gggttgtaaa gccctgtcga +cagggaaaaa tgtcctgcat gctaatatca tgcaggagtg atggtacctg taaaggaagc +accggctaac tccgtg +>OTU_364 +gatcaacgct ggcggcgtgc ctaatgcatg caagtcgagc ggggtgggtt tcggcccact +tacgcggcgg acgggtgcgg aacacgtggg caacctgccc cgaggtgggg gatagccggt +ggaaacaccg ggtaattccg catgaggtca ctgatcggag gatcagtgag gaaagggttt +tcggacccgc cttgggaggg gcctgcggcc gattagctag acggtggggt aacggcctac +cgtggcgatg atcggtagct ggtctgagag gacggccagc cacacgggga ctgagacacg +gccccgactc ctacgggagg cagcagcaag gaatcttccg caatgggcga aagcctgacg +gagcaacgcc gcgtgtggga tgacgccttt cggggtgtaa accacttttc tcggggaaga +agcactgacg gtacctgagg aataaggacc ggctaactac gtg +>OTU_8245 +gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac ggagatatga tttcggttat +atcttagtgg cgaacgggtg agtaacgcgt gagcaacctg accttcagag ggggataaca +tttggaaaca 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aagcaccggc taactacgtg +>OTU_10321 +aacgaacgct ggcggcatgc ttaacacatg caagtcgaac ggatgtcttg gctttggctg +gggcatcagt ggcgcacggg tgagtaacgc gtgggaacct gtccttaggt ggggaacaac +cgctggaaac ggcggctaat accgcatgat cccttcggtg agagccgttg ggcaaaggct +ttcgagccgc ctgaggaggg gcccgcgtcc gattagcttg ttggtggggt aacggcctac +caaggcatcg atcggtagct ggtctgagag gacgatcagc cacactggga ctgagacacg +gcccagactc ctacgggagg cagcagtggg gaatattgga caatgggggc aaccctgatc +cagcaatgcc gcgtgagtga tgaaggcctt agggttgtaa agctctttcg cccgagacga +tgatgacggt atcgggagaa gaagccccgg ctaattccgt g +>OTU_4721 +attgaacgct ggcggcatgc cttacacatg caagtcgaac ggtaacaggt cttcggatgc +tgacgagtgg cgaacgggtg agtaatacat cggaacgtgc ccagacgtgg gggataacga +ggcgaaagct ttgctaatac cgcatacgat ctaaggatga aagcagggga ccgaaaggcc +ttgcgcgttt ggagcggccg atggcagatt aggtagttgg tgggataaaa gcttaccaag +ccgacgatct gtagctggtc tgagaggacg accagccaca ctgggactga gacacggccc +agactcctac gggaggcagc agtggggaat tttggacaat gggcgaaagc ctgatccagc +aatgccgcgt gcaggacgaa ggccttcggg 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tcggtagccg aactgagagg ttgatcggcc gcattgggac +tgagacacgg cccagactcc tacgggaggc agcagtgggg gatattggtc aatgggggaa +accctgaacc agcaatgccg cgtgagggaa gaaggtcttc ggattgtaaa cctaagtagt +cagggacgaa agaaatgacg gtacctgaag agtaagctcc ggctaactac gtg +>OTU_10969 +aacgaacgct ggcggcgtgc ctaacacatg caagtcgaac gtgaaaacct tcgggtgagt +aaagtggcag acgggtgagt aacacgtggg taatctaccc cagagtctgg gataacctgc +cgaaaggcgg gctaataccg gataaatccc aggtgaacca taatcggttt tcttggaaaa +gggagctggc aacagccctt gctttgggag gagcctgcgc ctcattagct agttggtaag +gtaatggctt accaaggctt cgatgagtag ctggtctaag aggacgacca gtcacactgg +aactgaaaca cggtccagac tcctacggga ggcagcagtg gggaatattg cgcaatggac +gaaagtctga cgcagcaacg ccgcgtgagt gaagaaggcc ttcgggttgt aaagctctgt +cggaagggaa gaaaagcctt ggagtgataa gcttcagggt ttgacggtac cttcaaagga +agcaccggct aactccgtg +>OTU_1801 +aacgaacgct ggcggcgtgc ctaacacatg caagtcgcac gagaaagtcc ttcgggatga +gtagagtggc gcacgggtga gtaatccata ggaacgtgcc ttcaagaggg ggataaccac +tggaaacggt ggctaatacc gcatacagac gtaagtcgaa 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gttccggggt aaataatccc ggaatttgat agtaccggag +gaggaagcca cggctaactc tgtg +>OTU_777 +aacgaacgct ggcggcatgc ctaacacatg caagttgaac gaagatgcag cttcggctgt +agactgagtg gcgcacgggt gagtaacgcg tgggaattta cctattggtg ggggacaact +gttggaaacg acagctaata ccgcataagc tctacggagg aaagatttat cgccaatgga +taagcccgcg tcggattagg tagttggtag ggtaatggcc taccaagcca atgatctgta +gctggtctga gaggatgatc agccacactg ggactgagac acggcccaga ctcctacggg +aggcagcagt ggggaatatt agacaatggg ggaaaccctg atctagcaat gccgcgtgaa +tgaagaaggc cttagggttg taaagttctt tcgcctttga agatgatgac tgtagaagga +taagaagcac cggctaactc cgtg +>OTU_3169 +aataaacgct ggcggcgtgc ctaacacatg caagtcgagc gagaaaattc cttcgggaat +tagtacagcg gcggacgggt gagcaacgcg tgagaacctt ccctttagtg aagaatacct +ccgagaaatc ggagacaata ctgcatacgt cccttcgggg agaaaggtgg ctttatgctg +ccgctaaagg atgggcttgc gtactattag ctagttggta gggtaatggc ctaccaaggc +gatgatggtt aaccggcctg agagggtgta cggtcacact ggaactgaga cacggtccag +actcctacgg gaggcagcag tggggaatat tgcgcaatgg gcgaaagcct gacgcagcga 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.nwk Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,1 @@ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.otu.csv Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,201 @@ +OTU 16SAMP-747 16S-AMP-1168 16SAMP-4603 16S-AMP-1149 16SAMP-537 16S-AMP-1114 16SAMP-3893 16SAMP-703 16SAMP-638 16SAMP-2611 16S-AMP-1100 16SAMP-608 16SAMP-636 16SAMP-13288 16SAMP-719 16S-AMP-1098 16SAMP-536 16S-AMP-1169 16SAMP-635 16SAMP-637 16SAMP-717 16S-AMP-1148 16SAMP-735 16SAMP-729 16SAMP-738 16SAMP-2613 16SAMP-10925 16SAMP-3913 16SAMP-716 16SAMP-726 16SAMP-728 16SAMP-625 16SAMP-736 16SAMP-13281 16SAMP-626 16SAMP-704 16SAMP-2612 16SAMP-746 16SAMP-522 16SAMP-516 16S-AMP-1170 16S-AMP-1099 16SAMP-10932 16SAMP-740 16SAMP-739 16SAMP-4597 16SAMP-535 16SAMP-3941 16SAMP-3953 16SAMP-720 16SAMP-705 16SAMP-10907 16SAMP-538 16SAMP-10911 16SAMP-737 16SAMP-4591 16SAMP-745 16SAMP-706 16SAMP-3946 16S-AMP-1101 16SAMP-10896 16SAMP-10891 16SAMP-748 16SAMP-725 16SAMP-730 16S-AMP-1107 16SAMP-727 +OTU_95 1 132 382 37 2 29 317 2 241 5 15 379 422 111 1 47 0 101 603 151 2 350 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.tax Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,201 @@ +Kingdom Phylum Class Order Family Genus Species OTU +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae g__Acetitomaculum s__ OTU_8735 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcaceae UCG-005 s__ OTU_13382 +k__Bacteria p__Bacteroidetes c__Cytophagia o__Cytophagales f__Cytophagaceae g__Dyadobacter s__ OTU_5516 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Nitrosomonadales f__Nitrosomonadaceae g__Nitrosomonas s__ OTU_8315 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Intrasporangiaceae g__Tetrasphaera s__ OTU_10522 +k__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Xanthomonadales f__Xanthomonadaceae OTU_11040 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobacteraceae g__Desulforegula s__ OTU_7263 +k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Planococcaceae g__Rummeliibacillus s__ OTU_13379 +k__Bacteria p__Hydrogenedentes c__ o__ f__ g__ s__ OTU_1418 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae g__Fusicatenibacter s__ OTU_556 +k__Bacteria p__Parcubacteria c__ o__ f__ g__ s__ OTU_6869 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 1 s__ OTU_10171 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Dermatophilaceae g__uncultured s__ OTU_2830 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__AKYH767 g__ s__ OTU_4232 +k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae OTU_12831 +k__Bacteria p__Acidobacteria c__Holophagae o__Holophagales f__Holophagaceae OTU_613 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Brooklawnia s__ OTU_3625 +k__Bacteria p__Chloroflexi c__Chloroflexia o__Chloroflexales f__Roseiflexaceae g__ s__ OTU_3605 +k__Bacteria p__Actinobacteria c__Actinobacteria o__PeM15 f__PeM15 g__ s__ OTU_11148 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_656 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae g__Sulfuritalea s__ OTU_4382 +k__Bacteria OTU_3834 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales OTU_13127 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales OTU_4528 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Blfdi19 g__ s__ OTU_4485 +k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_12265 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_11820 +k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_4093 +k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__Flavobacteriaceae g__Flavobacterium s__ OTU_8360 +k__Bacteria p__Firmicutes c__Negativicutes o__Selenomonadales f__Veillonellaceae OTU_15123 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobacteraceae OTU_11928 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__Acidicaldus s__ OTU_11334 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__mle1-27 g__ s__ OTU_4511 +k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_3265 +k__Bacteria p__Actinobacteria OTU_2991 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Candidatus Defluviifilum s__ OTU_522 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Nitrosomonadales f__Nitrosomonadaceae g__Nitrosomonas s__ OTU_11832 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcaceae UCG-010 s__ OTU_6358 +k__Bacteria p__Saccharibacteria c__Unknown Class o__Unknown Order f__SBR2060 g__SBR2113 s__ OTU_3611 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales OTU_1408 +k__Bacteria p__Bacteroidetes OTU_7471 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Subdoligranulum s__ OTU_14124 +k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_13012 +k__Bacteria p__Candidate division SR1 c__ o__ f__ g__ s__ OTU_8113 +k__Bacteria p__Cyanobacteria c__Cyanobacteria o__SubsectionIII f__FamilyI OTU_11414 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Microbacteriaceae OTU_2232 +k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_13504 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_173 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Lachnospiraceae OTU_11006 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_9035 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales OTU_8165 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Ramlibacter s__ OTU_1707 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__TK34 g__ s__ OTU_4805 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Bradyrhizobiaceae g__Bosea s__ OTU_7801 +k__Bacteria p__Hydrogenedentes c__ o__ f__ g__ s__ OTU_6106 +k__Bacteria p__Synergistetes c__Synergistia o__Synergistales f__Synergistaceae g__uncultured s__ OTU_9681 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Desulfobacterales f__Desulfobulbaceae g__Desulfobulbus s__ OTU_4039 +k__Bacteria p__Actinobacteria c__Thermoleophilia o__Gaiellales f__BVA77 g__ s__ OTU_4338 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae OTU_1634 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__env.OPS 17 g__ s__ OTU_684 +k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales OTU_496 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Nocardioidaceae g__Nocardioides s__ OTU_3941 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__DUNssu044 g__ s__ OTU_4193 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__uncultured s__ OTU_9455 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XII g__Fusibacter s__ OTU_7842 +k__Bacteria p__Planctomycetes c__Phycisphaerae o__Phycisphaerales f__Phycisphaeraceae g__uncultured s__ OTU_13494 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__uncultured s__ OTU_1285 +k__Bacteria p__Chloroflexi c__WCHB1-50 o__WCHB1-50 f__WCHB1-50 g__SM1F10 s__ OTU_132 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae g__Hyphomicrobium s__ OTU_10641 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae OTU_236 +k__Bacteria p__Deinococcus-Thermus c__Deinococci o__Thermales f__Thermaceae g__Meiothermus s__ OTU_462 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae g__Hyphomicrobium s__ OTU_161 +k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Carnobacteriaceae g__Trichococcus s__ OTU_13660 +k__Bacteria p__Chlorobi c__Ignavibacteria o__Ignavibacteriales f__PHOS-HE36 g__oca15 s__ OTU_9412 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales OTU_7504 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Simplicispira s__ OTU_318 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XIII OTU_7070 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Hyphomicrobiaceae OTU_288 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Sandaracinaceae g__Sandaracinus s__ OTU_2415 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Bdellovibrionales f__Bdellovibrionaceae g__OM27 clade s__ OTU_95 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__Mitochondria g__ s__ OTU_3982 +k__Bacteria p__Verrucomicrobia c__Verrucomicrobiae o__Verrucomicrobiales f__Verrucomicrobiaceae g__uncultured s__ OTU_4278 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae OTU_2887 +k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_5684 +k__Bacteria OTU_4220 +k__Bacteria OTU_7051 +k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Collinsella s__ OTU_11398 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhizobiales f__Nordellaceae g__MNG7 s__ OTU_4669 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__Roseomonas s__ OTU_4697 +k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae OTU_6765 +k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__Pirellula s__ OTU_1066 +k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__uncultured s__ OTU_5907 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Clostridium sensu stricto 1 s__ OTU_4933 +k__Bacteria p__Firmicutes c__Bacilli o__Lactobacillales f__Lactobacillaceae g__Lactobacillus s__ OTU_8885 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Candidatus Defluviifilum s__ OTU_4226 +k__Bacteria p__Proteobacteria c__TA18 o__ f__ g__ s__ OTU_1821 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Peptostreptococcaceae g__Acetoanaerobium s__ OTU_1794 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__env.OPS 17 g__ s__ OTU_3925 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae OTU_3353 +k__Bacteria p__GOUTA4 c__ o__ f__ g__ s__ OTU_7163 +k__Bacteria p__Acidobacteria c__Acidobacteria o__Subgroup 6 f__ g__ s__ OTU_541 +k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__Flavobacteriaceae g__Flavobacterium s__ OTU_1521 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__Holosporaceae g__uncultured s__ OTU_14421 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_2972 +k__Bacteria p__Nitrospirae c__Nitrospira o__Nitrospirales f__Nitrospiraceae g__Nitrospira s__sublineage I OTU_8291 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__uncultured s__ OTU_289 +k__Bacteria p__WCHB1-60 c__ o__ f__ g__ s__ OTU_1306 +k__Bacteria p__Planctomycetes c__Phycisphaerae o__WD2101 soil group f__ g__ s__ OTU_4839 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Propioniciclava s__ OTU_11689 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Parabacteroides s__ OTU_12665 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae OTU_2085 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__uncultured s__ OTU_448 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__ OTU_6935 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Nocardioidaceae g__Aeromicrobium s__ OTU_190 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Family XI g__uncultured s__ OTU_4458 +k__Bacteria OTU_927 +k__Bacteria p__Chlorobi c__Chlorobia o__Chlorobiales f__Chlorobiaceae g__ s__ OTU_5113 +k__Bacteria p__Bacteroidetes c__Flavobacteriia o__Flavobacteriales f__NS9 marine group g__ s__ OTU_1875 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Clostridium sensu stricto 6 s__ OTU_9228 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Rhodospirillales Incertae Sedis g__Reyranella s__ OTU_1845 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Proteiniclasticum s__ OTU_6255 +k__Bacteria p__Acidobacteria c__Holophagae o__Subgroup 10 f__ABS-19 g__B1-K1A-105 s__ OTU_1479 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Prevotellaceae g__Prevotellaceae UCG-004 s__ OTU_14146 +k__Bacteria p__Elusimicrobia c__Elusimicrobia o__Lineage IIb f__ g__ s__ OTU_6507 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__Haliangiaceae g__Haliangium s__ OTU_7542 +k__Bacteria p__Firmicutes c__Bacilli o__Bacillales f__Bacillaceae g__Ureibacillus s__ OTU_13718 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__ g__ s__ OTU_4593 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminococcus 2 s__ OTU_2343 +k__Bacteria OTU_8708 +k__Bacteria p__SM2F11 c__ o__ f__ g__ s__ OTU_2677 +k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales OTU_9665 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__CYCU-0281 s__ OTU_81 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Chitinophagaceae g__Parafilimonas s__ OTU_6422 +k__Bacteria p__Proteobacteria c__TA18 o__ f__ g__ s__ OTU_1612 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Actinomycetales f__Actinomycetaceae g__Actinomyces s__ OTU_3216 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Aestuariimicrobium s__ OTU_9248 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_5187 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 1 s__ OTU_7882 +k__Bacteria p__Saccharibacteria c__ o__ f__ g__ s__ OTU_1543 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Microbacteriaceae g__Diaminobutyricimonas s__ OTU_11775 +k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__K2-78 s__ OTU_233 +k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Erysipelatoclostridium s__ OTU_4015 +k__Bacteria p__TM6 c__ o__ f__ g__ s__ OTU_8260 +k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales f__Acidimicrobiaceae g__CL500-29 marine group s__ OTU_9548 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Bacteroidaceae g__Bacteroides s__ OTU_5643 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Tessaracoccus s__ OTU_1586 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Corynebacteriales f__Nocardiaceae g__Gordonia s__ OTU_3782 +k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Senegalimassilia s__ OTU_2934 +k__Bacteria p__Armatimonadetes c__ o__ f__ g__ s__ OTU_14570 +k__Bacteria p__Actinobacteria c__Coriobacteriia o__Coriobacteriales f__Coriobacteriaceae g__Atopobium s__ OTU_11781 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Porphyromonadaceae g__Proteiniphilum s__ OTU_3700 +k__Bacteria OTU_6318 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Rhodocyclales f__Rhodocyclaceae g__Uliginosibacterium s__ OTU_2148 +k__Bacteria p__Chloroflexi c__WCHB1-50 o__WCHB1-50 f__WCHB1-50 g__WCHB1-50 s__ OTU_2244 +k__Bacteria p__Bacteroidetes c__BSV13 o__ f__ g__ s__ OTU_7867 +k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__K2-78 s__ OTU_14248 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Myxococcales f__bacteriap25 g__ s__ OTU_12704 +k__Bacteria p__Chloroflexi c__Thermomicrobia o__JG30-KF-CM45 f__ g__ s__ OTU_364 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Christensenellaceae g__Christensenellaceae R-7 group s__ OTU_8245 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_10847 +k__Bacteria p__Acidobacteria c__Holophagae o__Holophagales f__Holophagaceae OTU_1151 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Intrasporangiaceae g__Fodinibacter s__ OTU_1998 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Rhodospirillaceae g__Defluviicoccus s__cluster I OTU_10321 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Burkholderiales f__Comamonadaceae g__Acidovorax s__ OTU_4721 +k__Bacteria p__Verrucomicrobia c__OPB35 soil group o__ f__ g__ s__ OTU_6237 +k__Bacteria p__Saccharibacteria c__Unknown Class o__FW73 OTU_1972 +k__Bacteria p__Elusimicrobia c__Elusimicrobia o__Lineage IIb f__ g__ s__ OTU_11364 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Micrococcales f__Beutenbergiaceae g__Salana s__ OTU_1816 +k__Bacteria p__Actinobacteria c__Actinobacteria o__Propionibacteriales f__Propionibacteriaceae g__Propionimicrobium s__ OTU_14842 +k__Bacteria p__Fusobacteria c__Fusobacteriia o__Fusobacteriales f__Leptotrichiaceae g__uncultured s__ OTU_6533 +k__Bacteria p__Tenericutes c__Mollicutes o__Mollicutes RF9 f__ g__ s__ OTU_8887 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__Litorilinea s__ OTU_12690 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Clostridiaceae 1 g__Proteiniclasticum s__ OTU_3097 +k__Bacteria p__Firmicutes c__Erysipelotrichia o__Erysipelotrichales f__Erysipelotrichaceae g__Faecalitalea s__ OTU_3257 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodospirillales f__Acetobacteraceae g__uncultured s__ OTU_3161 +k__Bacteria p__Actinobacteria c__Thermoleophilia o__Solirubrobacterales f__480-2 g__ s__ OTU_11903 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__Ruminiclostridium 5 s__ OTU_7508 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__ g__ s__ OTU_10969 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__Oligoflexales f__Oligoflexaceae g__ s__ OTU_1801 +k__Bacteria p__Proteobacteria c__Betaproteobacteria o__Neisseriales f__Neisseriaceae g__Rivicola s__ OTU_3488 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria o__GR-WP33-30 f__ g__ s__ OTU_933 +k__Bacteria p__Lentisphaerae c__PBS-III-20 o__ f__ g__ s__ OTU_3824 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales f__AKIW1012 g__ s__ OTU_777 +k__Bacteria p__TM6 c__ o__ f__ g__ s__ OTU_3169 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae g__[Eubacterium] coprostanoligenes group s__ OTU_12385 +k__Bacteria p__Armatimonadetes c__ o__ f__ g__ s__ OTU_1496 +k__Bacteria p__Actinobacteria c__Acidimicrobiia o__Acidimicrobiales f__Microthricaceae g__ s__ OTU_11294 +k__Bacteria p__Bacteroidetes c__Sphingobacteriia o__Sphingobacteriales f__Saprospiraceae g__Lewinella s__ OTU_1968 +k__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rickettsiales OTU_8832 +k__Bacteria p__Proteobacteria c__Deltaproteobacteria OTU_8652 +k__Bacteria p__Chlorobi c__Chlorobia o__Chlorobiales f__OPB56 g__ s__ OTU_13621 +k__Bacteria p__Microgenomates c__ o__ f__ g__ s__ OTU_3043 +k__Bacteria p__Firmicutes c__Clostridia o__Clostridiales f__Ruminococcaceae OTU_10760 +k__Bacteria p__Bacteroidetes c__Bacteroidia o__Bacteroidales f__Bacteroidaceae g__Bacteroides s__ OTU_14173 +k__Bacteria p__Cyanobacteria c__Chloroplast o__ f__ g__ s__ OTU_10746 +k__Bacteria p__Chloroflexi c__Caldilineae o__Caldilineales f__Caldilineaceae g__uncultured s__ OTU_284 +k__Bacteria p__Saccharibacteria c__ o__ f__ g__ s__ OTU_5049 +k__Bacteria p__Chloroflexi c__Anaerolineae o__Anaerolineales f__Anaerolineaceae g__uncultured s__ OTU_2397 +k__Bacteria p__Planctomycetes c__Planctomycetacia o__Planctomycetales f__Planctomycetaceae g__uncultured s__ OTU_2913 +k__Bacteria p__Bacteroidetes OTU_9512
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.tsv Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,68 @@ +SampleID Plant Date Year Period +16SAMP-747 16SAMP-747 Aalborg East 2010-02-04 2010 Winter +16S-AMP-1168 16S-AMP-1168 Aalborg West 2013-05-06 2013 Spring +16SAMP-4603 16SAMP-4603 Aalborg East 2014-08-19 2014 Summer +16S-AMP-1149 16S-AMP-1149 Aalborg East 2013-10-28 2013 Fall +16SAMP-537 16SAMP-537 Aalborg West 2010-08-19 2010 Summer +16S-AMP-1114 16S-AMP-1114 Aalborg West 2013-02-04 2013 Winter +16SAMP-3893 16SAMP-3893 Aalborg East 2014-02-06 2014 Winter +16SAMP-703 16SAMP-703 Aalborg East 2006-02-04 2006 Winter +16SAMP-638 16SAMP-638 Aalborg East 2012-10-28 2012 Fall +16SAMP-2611 16SAMP-2611 Aalborg East 2011-02-04 2011 Winter +16S-AMP-1100 16S-AMP-1100 Aalborg West 2012-08-19 2012 Summer +16SAMP-608 16SAMP-608 Aalborg East 2011-10-28 2011 Fall +16SAMP-636 16SAMP-636 Aalborg East 2012-05-06 2012 Spring +16SAMP-13288 16SAMP-13288 Aalborg West 2015-02-09 2015 Winter +16SAMP-719 16SAMP-719 Aalborg East 2007-08-19 2007 Summer +16S-AMP-1098 16S-AMP-1098 Aalborg West 2012-02-04 2012 Winter +16SAMP-536 16SAMP-536 Aalborg West 2010-05-06 2010 Spring +16S-AMP-1169 16S-AMP-1169 Aalborg West 2013-08-19 2013 Summer +16SAMP-635 16SAMP-635 Aalborg East 2012-02-04 2012 Winter +16SAMP-637 16SAMP-637 Aalborg East 2012-08-19 2012 Summer +16SAMP-717 16SAMP-717 Aalborg East 2007-02-04 2007 Winter +16S-AMP-1148 16S-AMP-1148 Aalborg East 2013-08-19 2013 Summer +16SAMP-735 16SAMP-735 Aalborg West 2008-05-06 2008 Spring +16SAMP-729 16SAMP-729 Aalborg East 2008-08-19 2008 Summer +16SAMP-738 16SAMP-738 Aalborg East 2009-02-04 2009 Winter +16SAMP-2613 16SAMP-2613 Aalborg West 2011-08-19 2011 Summer +16SAMP-10925 16SAMP-10925 Aalborg East 2015-10-27 2015 Fall +16SAMP-3913 16SAMP-3913 Aalborg East 2014-07-03 2014 Summer +16SAMP-716 16SAMP-716 Aalborg West 2006-02-04 2006 Winter +16SAMP-726 16SAMP-726 Aalborg West 2007-08-19 2007 Summer +16SAMP-728 16SAMP-728 Aalborg East 2008-05-06 2008 Spring +16SAMP-625 16SAMP-625 Aalborg West 2011-02-04 2011 Winter +16SAMP-736 16SAMP-736 Aalborg West 2008-08-19 2008 Summer +16SAMP-13281 16SAMP-13281 Aalborg East 2015-02-10 2015 Winter +16SAMP-626 16SAMP-626 Aalborg West 2011-10-28 2011 Fall +16SAMP-704 16SAMP-704 Aalborg East 2006-05-06 2006 Spring +16SAMP-2612 16SAMP-2612 Aalborg East 2011-08-19 2011 Summer +16SAMP-746 16SAMP-746 Aalborg West 2009-05-06 2009 Spring +16SAMP-522 16SAMP-522 Aalborg East 2010-10-28 2010 Fall +16SAMP-516 16SAMP-516 Aalborg West 2009-10-28 2009 Fall +16S-AMP-1170 16S-AMP-1170 Aalborg West 2013-10-28 2013 Fall +16S-AMP-1099 16S-AMP-1099 Aalborg West 2012-05-06 2012 Spring +16SAMP-10932 16SAMP-10932 Aalborg West 2015-10-27 2015 Fall +16SAMP-740 16SAMP-740 Aalborg East 2009-10-28 2009 Fall +16SAMP-739 16SAMP-739 Aalborg East 2009-05-06 2009 Spring +16SAMP-4597 16SAMP-4597 Aalborg West 2014-05-05 2014 Spring +16SAMP-535 16SAMP-535 Aalborg West 2010-02-04 2010 Winter +16SAMP-3941 16SAMP-3941 Aalborg West 2014-08-18 2014 Summer +16SAMP-3953 16SAMP-3953 Aalborg West 2014-11-12 2014 Fall +16SAMP-720 16SAMP-720 Aalborg East 2007-10-28 2007 Fall +16SAMP-705 16SAMP-705 Aalborg East 2006-08-19 2006 Summer +16SAMP-10907 16SAMP-10907 Aalborg East 2015-08-24 2015 Summer +16SAMP-538 16SAMP-538 Aalborg West 2010-10-28 2010 Fall +16SAMP-10911 16SAMP-10911 Aalborg West 2015-08-24 2015 Summer +16SAMP-737 16SAMP-737 Aalborg West 2008-10-28 2008 Fall +16SAMP-4591 16SAMP-4591 Aalborg West 2014-02-04 2014 Winter +16SAMP-745 16SAMP-745 Aalborg West 2009-02-04 2009 Winter +16SAMP-706 16SAMP-706 Aalborg East 2006-10-28 2006 Fall +16SAMP-3946 16SAMP-3946 Aalborg East 2014-11-13 2014 Fall +16S-AMP-1101 16S-AMP-1101 Aalborg West 2012-10-28 2012 Fall +16SAMP-10896 16SAMP-10896 Aalborg West 2015-05-04 2015 Spring +16SAMP-10891 16SAMP-10891 Aalborg East 2015-05-04 2015 Spring +16SAMP-748 16SAMP-748 Aalborg East 2010-05-06 2010 Spring +16SAMP-725 16SAMP-725 Aalborg West 2007-02-04 2007 Winter +16SAMP-730 16SAMP-730 Aalborg East 2008-10-28 2008 Fall +16S-AMP-1107 16S-AMP-1107 Aalborg East 2013-05-06 2013 Spring +16SAMP-727 16SAMP-727 Aalborg East 2008-02-04 2008 Winter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate.R Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,10 @@ +library(ampvis2) + +# subset taxa using 200 random OTUs +aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200)) + +ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk") +amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F) +amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu") +write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F) +write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate.sh Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,5 @@ + +Rscript generate.R + +sed -i -e 's/"//g' AalborgWWTPs.tax +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rich-dense.biom Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,55 @@ +{ + "id":null, + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "QIIME revision 1.4.0-dev", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "dense", + "matrix_element_type": "int", + "shape": [5,6], + "data": [[0,0,1,0,0,0], + [5,1,0,2,3,1], + [0,0,1,4,2,0], + [2,1,1,0,0,1], + [0,1,1,0,0,0]] +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rich-sparse.biom Mon Apr 04 10:21:36 2022 +0000 @@ -0,0 +1,66 @@ +{ + "id":"w00asdt", + "format": "1.0.0", + "format_url": "http://biom-format.org", + "type": "OTU table", + "generated_by": "QIIME revision XYZ", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}}, + {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}}, + {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample4", "metadata":{ + "BarcodeSequence":"CTCTCGGCCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample5", "metadata":{ + "BarcodeSequence":"CTCTCTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}}, + {"id":"Sample6", "metadata":{ + "BarcodeSequence":"CTAACTACCAAT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"skin", + "Description":"human skin"}} + ], + "matrix_type": "sparse", + "matrix_element_type": "int", + "shape": [5, 6], + "data":[[0,2,1], + [1,0,5], + [1,1,1], + [1,3,2], + [1,4,3], + [1,5,1], + [2,2,1], + [2,3,4], + [2,5,2], + [3,0,2], + [3,1,1], + [3,2,1], + [3,5,1], + [4,1,1], + [4,2,1] + ] + }