changeset 0:0cac08094b86 draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/symmetric_plot commit a68579d7bdde7420b8f04346d3b6e361588acf50"
author qfabrepo
date Mon, 14 Sep 2020 06:04:44 +0000
parents
children 680917d9d415
files symmetric_plot.r symmetric_plot.xml test-data/SymmetricPlot.html test-data/count.txt test-data/metadata.txt test-data/observation.txt
diffstat 6 files changed, 7063 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/symmetric_plot.r	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,182 @@
+library('getopt')
+library('tidyr')
+suppressPackageStartupMessages(library('dplyr'))
+suppressPackageStartupMessages(library('phyloseq'))
+suppressPackageStartupMessages(library('DESeq2'))
+suppressPackageStartupMessages(library('ggplot2'))
+suppressPackageStartupMessages(library('data.table'))
+Sys.setenv("DISPLAY"=":1")
+
+
+options(warn= -1)
+option_specification = matrix(c(
+  'input.data','i',2,'character',
+   'meta.data','m',2,'character',
+   'obs.data','t',2,'character',
+   'record','r',2,'numeric',
+   'taxrank','x',2,'character',
+	'norm','n',2,'logical',
+    'n.column','c',2,'numeric',
+     'g.group','g',2,'character',
+      'outdir','o',2,'character',
+    'htmlfile','h',2,'character'
+),byrow=TRUE,ncol=4);
+
+
+options <- getopt(option_specification);
+options(bitmapType="cairo")
+ 
+
+if (!is.null(options$outdir)) {
+  # Create the directory
+  dir.create(options$outdir,FALSE)
+}
+
+
+input.table<-read.table(options$input.data,header=T,sep="\t",stringsAsFactors = F)
+metadata.table<-read.table(options$meta.data,header=T,sep="\t",stringsAsFactors = F,comment.char="")
+obs.table<-read.table(options$obs.data,header=F,sep="\t",stringsAsFactors = F,comment.char="")
+
+colnames(obs.table)<-c("OTUID","taxonomy")
+
+
+tax_col <- c("OTUID","Kingdom","Phylum","Class","Order","Family","Genus","Species")
+tax_col_extra <- c("OTUID","None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
+
+### remove the leading #sign in column name if the column name begins with number
+colnames(input.table)<-gsub("^X","",colnames(input.table))
+colnames(metadata.table)<-gsub("^X.","",colnames(metadata.table))
+
+
+column.name<-colnames(metadata.table)[options$n.column]
+#in.column<-options$g.column
+in.group<-options$g.group
+nrecord<-options$record
+ranking<-options$taxrank
+
+### create data frame for group
+group.df<-data.frame(group=unlist(strsplit(in.group,",")),stringsAsFactors = F)
+
+### get the number of group
+number.of.group<-dim(group.df)[1]
+
+if(number.of.group != 2){
+  print(paste("Number of group for comparision is",number.of.group,sep=""))
+  quit("yes")
+}
+
+
+
+group1<-metadata.table[which(metadata.table[,column.name] %in% group.df$group[1]),]$SampleID
+group2<-metadata.table[which(metadata.table[,column.name] %in% group.df$group[2]),]$SampleID
+
+sample2group.map <- data.frame(sample=colnames(input.table[,c(group1,group2)]),
+                          groups=c(rep(group.df$group[1],length(group1)),
+                                   rep(group.df$group[2],length(group2))))
+
+
+if(options$norm =="false"){
+### raw count table
+    count.table<-input.table
+    rownames(count.table)<-count.table[,1]
+    count.table<-count.table[,-1]
+
+    suppressMessages(raw.count.deseq.obj<-DESeqDataSetFromMatrix(countData = count.table,colData=metadata.table, as.formula(paste('~',column.name,sep=""))))
+
+    gm_mean = function(x, na.rm=TRUE){
+      exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
+      }
+
+    geoMeans = apply(counts(raw.count.deseq.obj), 1, gm_mean)
+    deseq_obj = estimateSizeFactors(raw.count.deseq.obj, geoMeans = geoMeans)
+    deseq_obj_norm<-counts(deseq_obj,normalized=T)
+} else {
+    deseq_obj_norm<-input.table
+    rownames(deseq_obj_norm)<-deseq_obj_norm[,1]
+    deseq_obj_norm<-deseq_obj_norm[,-1]
+}
+
+
+#first.50.otu.id<-rownames(counts(raw.count.deseq.obj))[1:50]
+first.50.otu.id<-rownames(deseq_obj_norm)[1:nrecord]
+
+
+#filtered.data<-counts(raw.count.deseq.obj)[first.50.otu.id,c(group1,group2)]
+filtered.data<-deseq_obj_norm[first.50.otu.id,c(group1,group2)]
+filtered.data<-as.data.frame(cbind(OTUID=rownames(filtered.data),filtered.data),stringsAsFactors=F)
+
+nc <- match('OTUID',colnames(filtered.data))
+filtered.data[,-nc]<-sapply(filtered.data[,-nc],as.integer)
+stopifnot(min(range(filtered.data[,-nc]))>=0)
+
+long <- gather(filtered.data,sample,expr,-OTUID)
+suppressMessages((long <- left_join(long, sample2group.map)))
+long$expr[long$groups == group.df$group[1]] <- long$expr*-1
+
+sorted.OTU <- rev(sort(unique(long$OTUID)))
+long$OTUID <- factor(long$OTUID, levels=sorted.OTU)
+long$sample  <- as.factor(long$sample)
+
+
+tax.table.new<-as.data.frame(cbind(obs.table[,1],t(as.data.table(strsplit(obs.table[,2],";")))))
+
+if(length(colnames(tax.table.new)) != length(tax_col_extra))
+{
+colnames(tax.table.new)<-tax_col
+} else {
+colnames(tax.table.new)<-tax_col_extra
+}
+
+long<-cbind(long,tax.table.new[match(long$OTUID,tax.table.new$OTUID),-1])
+
+comparison<-paste(column.name,paste(group.df$group[1],group.df$group[2],sep="-"),sep=" ")
+
+
+p<-ggplot(long,aes(x=reorder(OTUID,expr),y=expr, fill=groups)) +
+  geom_bar(stat='identity') + theme_bw() + 
+  xlab("OTU ID") + 
+  labs(title=comparison) + facet_grid( as.formula(paste(ranking,"~ .",sep="")),scales = "free", space = "free" ) + theme(strip.text.y = element_text(angle = 0)) +
+  coord_flip()
+q<-ggplot_build(p)
+q$layout$panel_ranges[[1]]$x.labels <- gsub("-","",q$layout$panel_ranges[[1]]$x.labels)
+#Reassemble the plot using ggplot_gtable()
+q<-ggplot_gtable(q)
+
+
+
+
+pdffile <- gsub("[ ]+", "", paste(options$outdir,"/symmetric.pdf"))
+pngfile_symmetric <- gsub("[ ]+", "", paste(options$outdir,"/symmetric.png"))
+htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
+
+
+# Produce PDF file
+pdf(pdffile);
+plot(q)
+garbage<-dev.off();
+
+#png('richness.png')
+bitmap(pngfile_symmetric,"png16m",height=10,width=10,res=100)
+plot(q)
+garbage<-dev.off()
+
+# Produce the HTML file
+ htmlfile_handle <- file(htmlfile)
+ html_output = c('<html><body>',
+ 	        	 '<table align="center">',
+ 		         '<tr>',
+ 		         '<td valign="middle" style="vertical-align:middle;">',
+                 '<a href="pdffile.pdf"><img src="symmetric.png"/></a>',
+ 		         '</td>',
+ 		         '</tr>',
+ 		         '</table>',
+ 	        '<table align="center>',
+ 		'<tr>',
+ 		'<td valign="middle" style="vertical-align:middle;">',
+                 '<a href="pdffile.pdf"><img src="symmetric.png"/></a>',
+ 		'</td>',
+ 		'</tr>',
+ 		'</table>',
+                 '</html></body>');
+ writeLines(html_output, htmlfile_handle);
+ close(htmlfile_handle);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/symmetric_plot.xml	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,135 @@
+<tool id="symmetricPlot" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
+  <description>Symmetric Plot</description>
+  <requirements>
+          <requirement type="package" version="3.4.1">r-base</requirement>
+          <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
+		  <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
+		  <requirement type="package" version="1.20.0">r-getopt</requirement>
+		  <requirement type="package" version="0.6.3">r-tidyr</requirement>
+		  <requirement type="package" version="9.18">ghostscript</requirement>
+<tool id="symmetricPlot2" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
+  <description>Symmetric Plot</description>
+  <requirements>
+	  <requirement type="package" version="3.4.1">r-base</requirement>
+          <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
+	  <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
+          <requirement type="package" version="1.20.0">r-getopt</requirement>
+	  <requirement type="package" version="0.6.3">r-tidyr</requirement>
+          <requirement type="package" version="9.18">ghostscript</requirement>
+  </requirements>
+  <version_command><![CDATA[
+	   echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+   ]]></version_command>
+  <command detect_errors="exit_code"><![CDATA[
+	  Rscript '${__tool_directory__}/symmetric_plot.r' 
+	  	--input.data='$input_table' 
+		--meta.data='$meta_table' 
+		--obs.data='$obs_table' 
+		--taxrank='$taxonomy_rank' 
+		--record='$nTop' 
+		--norm="${norm_bool}" 
+		--n.column="${selectedCol}" 
+		--g.group="${group}" 
+		--outdir="$htmlfile.files_path" 
+		--htmlfile='$htmlfile' 
+  ]]></command>
+ 
+  <inputs>
+    <param format="tabular" name="input_table" type="data" label="Count table file"/>
+    <param format="tabular" name="meta_table" type="data" label="Metadata file"/>
+    <param format="tabular" name="obs_table" type="data" label="OTU Taxonomy file"/>
+
+    <param name="nTop" type="select" display="radio" label="Select number of records to display">
+      <option value="20" selected="true">20</option>
+      <option value="30">30</option>
+      <option value="40">40</option>
+      <option value="50">50</option>
+      <option value="100">100</option>
+    </param>
+
+    <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank">
+      <option value="Kingdom" selected="true">Kingdom</option>
+      <option value="Phylum">Phylum</option>
+      <option value="Class">Class</option>
+      <option value="Order">Order</option>
+      <option value="Family">Family</option>
+      <option value="Genus">Genus</option>
+      <option value="Species">Species</option>
+    </param>
+
+
+    <param name="norm_bool" type="boolean" truevalue="true" falsevalue="false" checked="false" label="is the data normalised?"/> 
+    <param name="selectedCol" type="data_column" data_ref="meta_table" use_header_names="TRUE" label="Variable to compare"/>
+    <param name="group" type="text" label="Fill in two comparable group separated by comma"/>
+
+  </inputs>
+ 
+  <outputs>
+    <data format="html" name="htmlfile" label="${tool.name} SymmetricPlot.html"/>   
+  </outputs>
+
+  <tests>
+  	<test>
+		<param name="input_table" value="count.txt"/>
+		<param name="meta_table" value="metadata.txt"/>
+		<param name="obs_table" value="observation.txt"/>
+		<param name="nTop" value="30"/>
+		<param name="taxonomy_rank" value="Phylum"/>
+		<param name="selectedCol" value="3"/>
+		<param name="group" value="Early,Late"/>
+		<output name="htmlfile" ftype="html" file="SymmetricPlot.html"/></test>
+   </tests>
+  <help>
+.. class:: infomark
+
+**TIP:** The input data should be in tabular format.
+
+.. class:: infomark
+
+**TIP:** The first column should contain OTU ID.
+
+.. class:: infomark
+
+**TIP:** This program takes in two files:1)raw count/normalised table, 2) a metadata file
+   
+.. class:: infomark
+  
+**What it does**
+ 
+ This program uses an R package called DESeq2_ and ggplot2_ to create a symmetric bar plot.
+
+.. _DESeq2 : https://bioconductor.org/packages/release/bioc/html/DESeq2.html
+.. _ggplot2: https://ggplot2.tidyverse.org/
+
+=======
+ This program uses an R package called DESeq2 and ggplot2 to create a symmetric bar plot.
+  
+-----
+
+**Syntax**
+
+This tool creates a symmetric plot based on input table. The input table,if it is a raw count table, will be normalised by DESeq "counts" function with flag "normalised=T".
+   
+- **A normalised dataset** - set to "Yes" only if the input table is a normalised dataset
+- **Group of choice** - The group of choice will appear in the title of the plot(e.g., Tissue, protein and etc).
+- **Select a group** - This is a list of group to use in comparison(e.g., Tissue A vs Tissue B). This should be the same as "Group of choice".
+- **Select only two groups to compare** - select only two groups of interest for comparison.
+
+-----
+
+=========
+Resources
+=========
+
+=======
+**Wrapper Author**
+
+QFAB Bioinformatics (support@qfab.org)
+
+  </help>
+  <citations>
+  	<citation type="doi">10.18129/B9.bioc.DESeq2</citation>
+	<citation type="doi">10.1007/978-3-319-24277-4</citation>
+  </citations>
+=======
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SymmetricPlot.html	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,9 @@
+<html><body>
+<table align="center">
+<tr>
+<td valign="middle" style="vertical-align:middle;">
+<a href="pdffile.pdf"><img src="symmetric.png"/></a>
+</td>
+</tr>
+</table>
+</html></body>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count.txt	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,3359 @@
+OTUID	F3D147	F3D0	F3D7	F3D6	F3D1	F3D144	F3D148	F3D149	F3D2	F3D141	F3D146	F3D9	F3D142	F3D145	F3D8	F3D3	F3D143	F3D5
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+182733	13	3	6	8	3	6	7	17	14	3	2	6	4.15703690412737	12	1	14	5	3
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+789537	515	55	9	13	10	57	263	209	38	84	61	9	29.0992583288916	105	5	16	36	19
+835517	2	0	0	0	0	1	2	1	0	0	0	0	0	3	0	0	2	0
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+511768	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.txt	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,19 @@
+#SampleID	dpw	time	Food	Replicate_Group
+F3D0	0	Early	None	Group1
+F3D1	1	Early	None	Group1
+F3D2	2	Early	None	Group1
+F3D3	3	Early	Cheddar	Group2
+F3D5	5	Early	Cheddar	Group2
+F3D6	6	Early	Cheddar	Group2
+F3D7	7	Early	Swiss	Group3
+F3D8	8	Early	Swiss	Group3
+F3D9	9	Early	Swiss	Group3
+F3D141	141	Late	Cheddar	Group4
+F3D142	142	Late	Cheddar	Group4
+F3D143	143	Late	Cheddar	Group4
+F3D144	144	Late	None	Group5
+F3D145	145	Late	None	Group5
+F3D146	146	Late	None	Group5
+F3D147	147	Late	Swiss	Group6
+F3D148	148	Late	Swiss	Group6
+F3D149	149	Late	Swiss	Group6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/observation.txt	Mon Sep 14 06:04:44 2020 +0000
@@ -0,0 +1,3359 @@
+OTUID	taxonomy
+775126	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+228502	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+314713	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+314425	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+316122	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+432015	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+4374047	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+344726	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+1078157	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+974097	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+323154	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+266555	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+4316029	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__; s__
+317867	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+190425	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+323592	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+258628	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+277152	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+271499	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+338644	k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__
+338640	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+313804	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+344723	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+188785	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+182836	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+350381	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+338004	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+646532	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+131618	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+351343	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus
+309703	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__
+339092	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus
+468933	k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__
+277588	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+4372373	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4432700	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4429481	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+4323499	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+140239	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+38755	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+104315	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+832727	k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea
+694039	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
+4345528	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__vaginalis
+265211	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+249167	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+194673	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+843590	k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Actinomycetaceae; g__Actinomyces; s__
+267335	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus
+323775	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+270215	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+270219	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+348088	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+216429	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+275470	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+332865	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+312515	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+258340	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+191387	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+193723	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+271784	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+266556	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+162485	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
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+178548	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__
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+315669	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+271077	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+297258	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__
+761977	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+197989	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+689204	k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Enterococcaceae; g__Enterococcus; s__
+272328	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+332132	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+214116	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+767392	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
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+133686	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__
+637525	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+802273	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+785748	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+792826	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__
+153978	k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__
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+188345	k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__
+307548	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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+198107	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+195475	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+188495	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+785736	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+619863	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+697920	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+606054	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+606678	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+798357	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+676185	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+666572	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+679698	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+655467	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+715765	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+796526	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+704212	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+623444	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+714562	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+606737	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
+702318	k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__
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