Mercurial > repos > simon-gladman > phyloseq_filter

changeset 1:9fbb104e16d9 draft

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update
author simon-gladman
date Mon, 12 Nov 2018 22:42:14 -0500
parents 910739de7b80
children 54897b7e0551
files phyloseq_filter.R phyloseq_filter.xml test-data/barplot_after_filtering.png test-data/barplot_after_phyla_filtering.png test-data/barplot_before_filtering.png test-data/barplot_before_phyla_filtering.png test-data/biom_out.biom test-data/biom_out.html test-data/biom_output.biom test-data/biom_output.html test-data/matrix_out.biom test-data/matrix_out.html test-data/out.biom test-data/out_biom.html test-data/pdffile.pdf
diffstat 15 files changed, 59 insertions(+), 73 deletions(-) [+]
line wrap: on
line diff
--- a/phyloseq_filter.R	Wed Sep 05 22:21:43 2018 -0400
+++ b/phyloseq_filter.R	Mon Nov 12 22:42:14 2018 -0500
@@ -2,10 +2,10 @@
 library('ape')
 library('ggplot2')
 suppressPackageStartupMessages(library('phyloseq'))
-library(biomformat)
 library(plyr)
 Sys.setenv("DISPLAY"=":1")
 library(biomformat)
+library(jsonlite)
 suppressPackageStartupMessages(library(metagenomeSeq))
 suppressPackageStartupMessages(library("doParallel"))
 ncores = ceiling(detectCores() * 0.8)
@@ -65,6 +65,12 @@
 pngfile_post_phyla_filtering<- gsub("[ ]+", "", paste(options$outdir,"/barplot_after_phyla_filtering.png"))
 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
 
+### overwrite the write_biom function for proper BIOM format
+### https://github.com/smdabdoub/biomformat/blob/master/R/IO-methods.R#L124
+write_biom <- function(x, biom_file){
+        cat(toJSON(x, always_decimal=TRUE, auto_unbox=TRUE), file=biom_file)
+}
+
 ### This function accepts different two different type of BIOM file format
 readBIOM<-function(inBiom){
 	tryCatch({
@@ -152,7 +158,7 @@
 
     #png('barplot_pre_phyla_filtering.png')
     bitmap(pngfile_pre_phyla_filtering,"png16m")
-    print(sample_data(physeq_pre_phyla_filtering))
+    #print(sample_data(physeq_pre_phyla_filtering))
     barplot_pre_phyla_filtering<-plot_bar(physeq_pre_phyla_filtering, x=colnames(sample_data(physeq_pre_phyla_filtering))[1], fill=kingdom_str) +
                                  geom_bar(stat="identity", position="stack") +
                                  labs(title=paste("Sample Depth Bar Chart",kingdom_str,sep=":"),subtitle="Sample Vs Abundance (Pre Phyla Filtering)",caption="source: Input Biom") +
@@ -181,7 +187,7 @@
 create_HTML<-function(htmlfile){
     htmlfile_handle <- file(htmlfile)
     html_output = c('<html><body>',
-                    '<table align="center>',
+                    '<table align="center">',
                     '<tr>',
                     '<td valign="middle" style="vertical-align:middle;">',
                         '<a href="pdffile.pdf"><img src="barplot_before_filtering.png"/></a>',
@@ -203,7 +209,7 @@
                     '</td>',
                     '</tr>',
                     '</table>',
-                    '</html></body>');
+                    '</body></html>');
      writeLines(html_output, htmlfile_handle);
      close(htmlfile_handle);
 }
@@ -212,7 +218,7 @@
     temp.df<-data.frame(otu_table(physeq_obj))   
     temp.df.counts<-as.data.frame(colSums(temp.df))
     colnames(temp.df.counts)<-"Abundance"
-    print(temp.df.counts)
+    #print(temp.df.counts)
     return(temp.df.counts)
 }
 
@@ -317,12 +323,19 @@
 
     physeq_filter_post_transform = prune_taxa((tax_table(physeq_filter_post_transform)[, kingdom_str] %in% topphyla_post_transform), physeq_filter_post_transform)
 
+	### remove samples with zero value
+    otu_table(physeq_filter_post_transform)<-otu_table(physeq_filter_post_transform)[,colSums(otu_table(physeq_filter_post_transform)) > 0]
 
     create_PDF(pdffile,before_filtering_dataframe_sampleCounts,after_filtering_dataframe_sampleCounts,physeq_filter_pre_transform,physeq_filter_post_transform,kingdom_str,htmlfile,pngfile_before_filtering,pngfile_after_filtering,pngfile_pre_phyla_filtering,pngfile_post_phyla_filtering)
 
     ### convert phyloseq object to metagenomeSeq - preparing for BIOM output
-    metagenomeSeq_obj <- phyloseq_to_metagenomeSeq(physeq_filter_post_transform)
-    metagenomeSeq_biom <- MRexperiment2biom(metagenomeSeq_obj)
+    #metagenomeSeq_obj <- phyloseq_to_metagenomeSeq(physeq_filter_post_transform)
+    #metagenomeSeq_biom <- MRexperiment2biom(metagenomeSeq_obj)
+	
+	biom_obj=make_biom(otu_table(physeq_filter_post_transform),sample_metadata=sample_data(physeq_filter_post_transform),observation_metadata=tax_table(physeq_filter_post_transform),matrix_element_type="float")
+    biom_obj_2_metagenomeSeq_obj<-biom2MRexperiment(biom_obj)
+    metagenomeSeq_biom <- MRexperiment2biom(biom_obj_2_metagenomeSeq_obj)
+
 
     ## write biom file
     write_biom(metagenomeSeq_biom, biom_file=options$outbiom)
--- a/phyloseq_filter.xml	Wed Sep 05 22:21:43 2018 -0400
+++ b/phyloseq_filter.xml	Mon Nov 12 22:42:14 2018 -0500
@@ -70,11 +70,11 @@
                 <param name="input" value="GP.biom" ftype="biom1"/>
             </conditional>
             <output name="htmlfile" ftype="html" file="biom_out.html" />
-            <output name="outputbiom" >
-                <assert_contents>
+            <output name="outputbiom" file="out.biom" lines_diff="2" ftype="biom1"/>
+                <!-- <assert_contents>
                     <has_text text="Biological Observation Matrix"/>
                 </assert_contents>
-            </output>
+            </output> -->
         </test>
         <test>  <!-- Test #2: Test TABULAR format inputs -->
             <conditional name="file_source">
@@ -94,22 +94,20 @@
 
     <help>
 **What it does**
-Filter BIOM file using R package called phyloseq_.
+Filter out low abundance OTUs and/or data corresponding to the least represented taxonomic grouping using R package called R_package_called_phyloseq_, and specifically according to the pre-processing step outlined in the Phyloseq_Ordination_Plot_Tutorial_.
 
-.. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html
+.. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html
+.. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html
 
 -----
 
 **Input**
 
-- **Choose an input file type** - BIOM File or TABULAR file
-- **OTU TABLE** - this is a OTU matrix
-- **Taxonomy TABLE** - this is a TAX matrix
-- **Metadata TABLE** - this is a metadata file of the experiment design
-- **Select a taxonomic rank for the analysis** - select a taxonomy for filtering
-- **Specify value of Y (where 1.0=100%)** - Filter out OTUs from the analysis that do not appear more than X times in more than Y% of the samples
-- **Specify value of X** - Remove OTUs that do not appear more than X times (e.g., 5 times)
-- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - taxonomic rank units (e.g. Phyla, Class etc) to keep
+- **Choose an input file type** - either 1 BIOM file or 3 TABULAR files (i.e. OTU, Taxonomy and Metadata tables)
+- **Select a taxonomic rank for the analysis** - if filtering out low abundance taxa, this is the level of the taxonomy that you want to filter on (e.g. phyla, species)
+- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - the number of the most abundant taxonomic rank units specified above to keep (e.g. remove all the most abundant 5 phyla or species)
+- **Specify value of X** - if filtering out low abundance OTUs, use this to specify a value of X (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
+- **Specify value of Y (where 1.0=100%)** - if filtering out low abundance OTUs use this to specify a value of Y (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
 
 -----
 
Binary file test-data/barplot_after_filtering.png has changed
Binary file test-data/barplot_after_phyla_filtering.png has changed
Binary file test-data/barplot_before_filtering.png has changed
Binary file test-data/barplot_before_phyla_filtering.png has changed
--- a/test-data/biom_out.biom	Wed Sep 05 22:21:43 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"id":{},"format":["Biological Observation Matrix 1.0.0-dev"],"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],"type":["OTU table"],"generated_by":["metagenomeSeq 1.20.0"],"date":["2018-09-05 13:01:33"],"matrix_type":["dense"],"matrix_element_type":["int"],"shape":[204,26],"rows":[{"id":["12812"],"metadata":{"taxonomy":["12812","Bacteria","Actinobacteria","Actinobacteria","koll13"]}},{"id":["546222"],"metadata":{"taxonomy":["546222","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":["313857"],"metadata":{"taxonomy":["313857","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["252398"],"metadata":{"taxonomy":["252398","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["331093"],"metadata":{"taxonomy":["331093","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["317658"],"metadata":{"taxonomy":["317658","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["329744"],"metadata":{"taxonomy":["329744","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":["242450"],"metadata":{"taxonomy":["242450","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":["556066"],"metadata":{"taxonomy":["556066","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Microbacteriaceae","Agromyces"]}},{"id":["543491"],"metadata":{"taxonomy":["543491","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia"]}},{"id":["58301"],"metadata":{"taxonomy":["58301","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiaaeria"]}},{"id":["471141"],"metadata":{"taxonomy":["471141","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiamucilaginosa"]}},{"id":["13034"],"metadata":{"taxonomy":["13034","Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Mycobacteriaceae","Mycobacterium"]}},{"id":["469868"],"metadata":{"taxonomy":["469868","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumdentium"]}},{"id":["326977"],"metadata":{"taxonomy":["326977","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumadolescentis"]}},{"id":["469873"],"metadata":{"taxonomy":["469873","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumpseudocatenulatum"]}},{"id":["471180"],"metadata":{"taxonomy":["471180","Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium"]}},{"id":["60254"],"metadata":{"taxonomy":["60254","Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":["589787"],"metadata":{"taxonomy":["589787","Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":["535929"],"metadata":{"taxonomy":["535929","Bacteria","Cyanobacteria","Chloroplast","Cryptophyta"]}},{"id":["308887"],"metadata":{"taxonomy":["308887","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["278521"],"metadata":{"taxonomy":["278521","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["561077"],"metadata":{"taxonomy":["561077","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["542011"],"metadata":{"taxonomy":["542011","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["332808"],"metadata":{"taxonomy":["332808","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["317182"],"metadata":{"taxonomy":["317182","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["549656"],"metadata":{"taxonomy":["549656","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["327536"],"metadata":{"taxonomy":["327536","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["340216"],"metadata":{"taxonomy":["340216","Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":["279599"],"metadata":{"taxonomy":["279599","Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae","Dolichospermum"]}},{"id":["235567"],"metadata":{"taxonomy":["235567","Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae"]}},{"id":["557211"],"metadata":{"taxonomy":["557211","Bacteria","Cyanobacteria","Synechococcophycideae","Synechococcales","Synechococcaceae","Prochlorococcus"]}},{"id":["263681"],"metadata":{"taxonomy":["263681","Bacteria","Cyanobacteria","4C0d-2","YS2"]}},{"id":["162077"],"metadata":{"taxonomy":["162077","Bacteria","Proteobacteria","Epsilonproteobacteria","Campylobacterales","Campylobacteraceae","Campylobacter","Campylobacterconcisus"]}},{"id":["361480"],"metadata":{"taxonomy":["361480","Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Alcaligenaceae"]}},{"id":["228077"],"metadata":{"taxonomy":["228077","Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":["540352"],"metadata":{"taxonomy":["540352","Bacteria","Proteobacteria","Betaproteobacteria","Neisseriales","Neisseriaceae"]}},{"id":["360229"],"metadata":{"taxonomy":["360229","Bacteria","Proteobacteria","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\ No newline at end of file
--- a/test-data/biom_out.html	Wed Sep 05 22:21:43 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/test-data/biom_output.biom	Wed Sep 05 22:21:43 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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\ No newline at end of file
--- a/test-data/biom_output.html	Wed Sep 05 22:21:43 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
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--- a/test-data/matrix_out.biom	Wed Sep 05 22:21:43 2018 -0400
+++ b/test-data/matrix_out.biom	Mon Nov 12 22:42:14 2018 -0500
@@ -1,1 +1,1 @@
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\ No newline at end of file
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South Carolina Pine soil, pH 4.9"}},{"id":"CC1","metadata":{"X.SampleID":"CC1","Primer":"ILBC_02","Final_Barcode":"AACTCG","Barcode_truncated_plus_T":"CGAGTT","Barcode_full_length":"CATCGACGAGT","SampleType":"Soil","Description":"Cedar Creek Minnesota, grassland, pH 6.1"}},{"id":"SV1","metadata":{"X.SampleID":"SV1","Primer":"ILBC_03","Final_Barcode":"AACTGT","Barcode_truncated_plus_T":"ACAGTT","Barcode_full_length":"GTACGCACAGT","SampleType":"Soil","Description":"Sevilleta new Mexico, desert scrub, pH 8.3"}},{"id":"M31Fcsw","metadata":{"X.SampleID":"M31Fcsw","Primer":"ILBC_04","Final_Barcode":"AAGAGA","Barcode_truncated_plus_T":"TCTCTT","Barcode_full_length":"TCGACATCTCT","SampleType":"Feces","Description":"M3, Day 1, fecal swab, whole body study"}},{"id":"M11Fcsw","metadata":{"X.SampleID":"M11Fcsw","Primer":"ILBC_05","Final_Barcode":"AAGCTG","Barcode_truncated_plus_T":"CAGCTT","Barcode_full_length":"CGACTGCAGCT","SampleType":"Feces","Description":"M1, Day 1, fecal swab, whole body study "}},{"id":"M31Plmr","metadata":{"X.SampleID":"M31Plmr","Primer":"ILBC_07","Final_Barcode":"AATCGT","Barcode_truncated_plus_T":"ACGATT","Barcode_full_length":"CGAGTCACGAT","SampleType":"Skin","Description":"M3, Day 1, right palm, whole body study"}},{"id":"M11Plmr","metadata":{"X.SampleID":"M11Plmr","Primer":"ILBC_08","Final_Barcode":"ACACAC","Barcode_truncated_plus_T":"GTGTGT","Barcode_full_length":"GCCATAGTGTG","SampleType":"Skin","Description":"M1, Day 1, right palm, whole body study "}},{"id":"F21Plmr","metadata":{"X.SampleID":"F21Plmr","Primer":"ILBC_09","Final_Barcode":"ACACAT","Barcode_truncated_plus_T":"ATGTGT","Barcode_full_length":"GTAGACATGTG","SampleType":"Skin","Description":"F1, Day 1,  right palm, whole body study "}},{"id":"M31Tong","metadata":{"X.SampleID":"M31Tong","Primer":"ILBC_10","Final_Barcode":"ACACGA","Barcode_truncated_plus_T":"TCGTGT","Barcode_full_length":"TGTGGCTCGTG","SampleType":"Tongue","Description":"M3, Day 1, tongue, whole body study "}},{"id":"M11Tong","metadata":{"X.SampleID":"M11Tong","Primer":"ILBC_11","Final_Barcode":"ACACGG","Barcode_truncated_plus_T":"CCGTGT","Barcode_full_length":"TAGACACCGTG","SampleType":"Tongue","Description":"M1, Day 1, tongue, whole body study "}},{"id":"LMEpi24M","metadata":{"X.SampleID":"LMEpi24M","Primer":"ILBC_13","Final_Barcode":"ACACTG","Barcode_truncated_plus_T":"CAGTGT","Barcode_full_length":"CATGAACAGTG","SampleType":"Freshwater","Description":"Lake Mendota Minnesota, 24 meter epilimnion "}},{"id":"SLEpi20M","metadata":{"X.SampleID":"SLEpi20M","Primer":"ILBC_15","Final_Barcode":"ACAGAG","Barcode_truncated_plus_T":"CTCTGT","Barcode_full_length":"AGCCGACTCTG","SampleType":"Freshwater","Description":"Sparkling Lake Wisconsin, 20 meter eplimnion"}},{"id":"AQC1cm","metadata":{"X.SampleID":"AQC1cm","Primer":"ILBC_16","Final_Barcode":"ACAGCA","Barcode_truncated_plus_T":"TGCTGT","Barcode_full_length":"GACCACTGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 0-1cm depth"}},{"id":"AQC4cm","metadata":{"X.SampleID":"AQC4cm","Primer":"ILBC_17","Final_Barcode":"ACAGCT","Barcode_truncated_plus_T":"AGCTGT","Barcode_full_length":"CAAGCTAGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 3-4 cm depth"}},{"id":"AQC7cm","metadata":{"X.SampleID":"AQC7cm","Primer":"ILBC_18","Final_Barcode":"ACAGTG","Barcode_truncated_plus_T":"CACTGT","Barcode_full_length":"ATGAAGCACTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 6-7 cm depth"}},{"id":"NP2","metadata":{"X.SampleID":"NP2","Primer":"ILBC_19","Final_Barcode":"ACAGTT","Barcode_truncated_plus_T":"AACTGT","Barcode_full_length":"TCGCGCAACTG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 1"}},{"id":"NP3","metadata":{"X.SampleID":"NP3","Primer":"ILBC_20","Final_Barcode":"ACATCA","Barcode_truncated_plus_T":"TGATGT","Barcode_full_length":"GCTAAGTGATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 2"}},{"id":"NP5","metadata":{"X.SampleID":"NP5","Primer":"ILBC_21","Final_Barcode":"ACATGA","Barcode_truncated_plus_T":"TCATGT","Barcode_full_length":"GAACGATCATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 3"}},{"id":"TRRsed1","metadata":{"X.SampleID":"TRRsed1","Primer":"ILBC_22","Final_Barcode":"ACATGT","Barcode_truncated_plus_T":"ACATGT","Barcode_full_length":"CACGTGACATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 1"}},{"id":"TRRsed2","metadata":{"X.SampleID":"TRRsed2","Primer":"ILBC_23","Final_Barcode":"ACATTC","Barcode_truncated_plus_T":"GAATGT","Barcode_full_length":"TGCGCTGAATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 2"}},{"id":"TRRsed3","metadata":{"X.SampleID":"TRRsed3","Primer":"ILBC_24","Final_Barcode":"ACCACA","Barcode_truncated_plus_T":"TGTGGT","Barcode_full_length":"GATGTATGTGG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 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\ No newline at end of file
--- a/test-data/matrix_out.html	Wed Sep 05 22:21:43 2018 -0400
+++ b/test-data/matrix_out.html	Mon Nov 12 22:42:14 2018 -0500
@@ -1,5 +1,5 @@
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@@ -21,4 +21,4 @@
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+</body></html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.biom	Mon Nov 12 22:42:14 2018 -0500
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South Carolina Pine soil, pH 4.9"}},{"id":"CC1","metadata":{"X.SampleID":"CC1","Primer":"ILBC_02","Final_Barcode":"AACTCG","Barcode_truncated_plus_T":"CGAGTT","Barcode_full_length":"CATCGACGAGT","SampleType":"Soil","Description":"Cedar Creek Minnesota, grassland, pH 6.1"}},{"id":"SV1","metadata":{"X.SampleID":"SV1","Primer":"ILBC_03","Final_Barcode":"AACTGT","Barcode_truncated_plus_T":"ACAGTT","Barcode_full_length":"GTACGCACAGT","SampleType":"Soil","Description":"Sevilleta new Mexico, desert scrub, pH 8.3"}},{"id":"M31Fcsw","metadata":{"X.SampleID":"M31Fcsw","Primer":"ILBC_04","Final_Barcode":"AAGAGA","Barcode_truncated_plus_T":"TCTCTT","Barcode_full_length":"TCGACATCTCT","SampleType":"Feces","Description":"M3, Day 1, fecal swab, whole body study"}},{"id":"M11Fcsw","metadata":{"X.SampleID":"M11Fcsw","Primer":"ILBC_05","Final_Barcode":"AAGCTG","Barcode_truncated_plus_T":"CAGCTT","Barcode_full_length":"CGACTGCAGCT","SampleType":"Feces","Description":"M1, Day 1, fecal swab, whole body study "}},{"id":"M31Plmr","metadata":{"X.SampleID":"M31Plmr","Primer":"ILBC_07","Final_Barcode":"AATCGT","Barcode_truncated_plus_T":"ACGATT","Barcode_full_length":"CGAGTCACGAT","SampleType":"Skin","Description":"M3, Day 1, right palm, whole body study"}},{"id":"M11Plmr","metadata":{"X.SampleID":"M11Plmr","Primer":"ILBC_08","Final_Barcode":"ACACAC","Barcode_truncated_plus_T":"GTGTGT","Barcode_full_length":"GCCATAGTGTG","SampleType":"Skin","Description":"M1, Day 1, right palm, whole body study "}},{"id":"F21Plmr","metadata":{"X.SampleID":"F21Plmr","Primer":"ILBC_09","Final_Barcode":"ACACAT","Barcode_truncated_plus_T":"ATGTGT","Barcode_full_length":"GTAGACATGTG","SampleType":"Skin","Description":"F1, Day 1,  right palm, whole body study "}},{"id":"M31Tong","metadata":{"X.SampleID":"M31Tong","Primer":"ILBC_10","Final_Barcode":"ACACGA","Barcode_truncated_plus_T":"TCGTGT","Barcode_full_length":"TGTGGCTCGTG","SampleType":"Tongue","Description":"M3, Day 1, tongue, whole body study "}},{"id":"M11Tong","metadata":{"X.SampleID":"M11Tong","Primer":"ILBC_11","Final_Barcode":"ACACGG","Barcode_truncated_plus_T":"CCGTGT","Barcode_full_length":"TAGACACCGTG","SampleType":"Tongue","Description":"M1, Day 1, tongue, whole body study "}},{"id":"LMEpi24M","metadata":{"X.SampleID":"LMEpi24M","Primer":"ILBC_13","Final_Barcode":"ACACTG","Barcode_truncated_plus_T":"CAGTGT","Barcode_full_length":"CATGAACAGTG","SampleType":"Freshwater","Description":"Lake Mendota Minnesota, 24 meter epilimnion "}},{"id":"SLEpi20M","metadata":{"X.SampleID":"SLEpi20M","Primer":"ILBC_15","Final_Barcode":"ACAGAG","Barcode_truncated_plus_T":"CTCTGT","Barcode_full_length":"AGCCGACTCTG","SampleType":"Freshwater","Description":"Sparkling Lake Wisconsin, 20 meter eplimnion"}},{"id":"AQC1cm","metadata":{"X.SampleID":"AQC1cm","Primer":"ILBC_16","Final_Barcode":"ACAGCA","Barcode_truncated_plus_T":"TGCTGT","Barcode_full_length":"GACCACTGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 0-1cm depth"}},{"id":"AQC4cm","metadata":{"X.SampleID":"AQC4cm","Primer":"ILBC_17","Final_Barcode":"ACAGCT","Barcode_truncated_plus_T":"AGCTGT","Barcode_full_length":"CAAGCTAGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 3-4 cm depth"}},{"id":"AQC7cm","metadata":{"X.SampleID":"AQC7cm","Primer":"ILBC_18","Final_Barcode":"ACAGTG","Barcode_truncated_plus_T":"CACTGT","Barcode_full_length":"ATGAAGCACTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 6-7 cm depth"}},{"id":"NP2","metadata":{"X.SampleID":"NP2","Primer":"ILBC_19","Final_Barcode":"ACAGTT","Barcode_truncated_plus_T":"AACTGT","Barcode_full_length":"TCGCGCAACTG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 1"}},{"id":"NP3","metadata":{"X.SampleID":"NP3","Primer":"ILBC_20","Final_Barcode":"ACATCA","Barcode_truncated_plus_T":"TGATGT","Barcode_full_length":"GCTAAGTGATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 2"}},{"id":"NP5","metadata":{"X.SampleID":"NP5","Primer":"ILBC_21","Final_Barcode":"ACATGA","Barcode_truncated_plus_T":"TCATGT","Barcode_full_length":"GAACGATCATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 3"}},{"id":"TRRsed1","metadata":{"X.SampleID":"TRRsed1","Primer":"ILBC_22","Final_Barcode":"ACATGT","Barcode_truncated_plus_T":"ACATGT","Barcode_full_length":"CACGTGACATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 1"}},{"id":"TRRsed2","metadata":{"X.SampleID":"TRRsed2","Primer":"ILBC_23","Final_Barcode":"ACATTC","Barcode_truncated_plus_T":"GAATGT","Barcode_full_length":"TGCGCTGAATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 2"}},{"id":"TRRsed3","metadata":{"X.SampleID":"TRRsed3","Primer":"ILBC_24","Final_Barcode":"ACCACA","Barcode_truncated_plus_T":"TGTGGT","Barcode_full_length":"GATGTATGTGG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 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\ No newline at end of file
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+++ b/test-data/out_biom.html	Mon Nov 12 22:42:14 2018 -0500
@@ -0,0 +1,24 @@
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Binary file test-data/pdffile.pdf has changed