| Next changeset 1:e0225f3e8ef6 (2020-09-15) |
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Commit message:
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73" |
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added:
phyloseq_richness.r phyloseq_richness.xml test-data/GP.biom test-data/biom_out.html test-data/count.txt test-data/metadata.txt test-data/observation.txt test-data/test.biom |
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| diff -r 000000000000 -r 0ab4501d805b phyloseq_richness.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_richness.r Mon Sep 14 07:38:57 2020 +0000 |
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| @@ -0,0 +1,83 @@ +library('getopt') +suppressPackageStartupMessages(library('phyloseq')) +Sys.setenv("DISPLAY"=":1") + +options(warn=-1) +option_specification = matrix(c( + 'biomfile','b',2,'character', + 'metafile','m',2,'character', + 'xcolumn','x',2,'numeric', + 'lcolumn','l',2,'numeric', + '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) +} + + +galaxy_biom <- import_biom(options$biomfile) +galaxy_map <- import_qiime_sample_data(options$metafile) +tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species") +tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species") + +number.of.tax.rank<-length(colnames(tax_table(galaxy_biom))) + +if( number.of.tax.rank == 7){ +colnames(tax_table(galaxy_biom)) <- tax_col_norm +}else{ +colnames(tax_table(galaxy_biom)) <- tax_col_extra +} + + +AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map) + + +x.selectedColumn<-colnames(galaxy_map)[options$xcolumn] +l.selectedColumn<-colnames(galaxy_map)[options$lcolumn] + + + + +pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf")) +pngfile_richness <- gsub("[ ]+", "", paste(options$outdir,"/richness.png")) +htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) + + +# Produce PDF file +pdf(pdffile); +plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn) +garbage<-dev.off(); + +#png('richness.png') +bitmap(pngfile_richness,"png16m") +plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn) +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="richness.png"/></a>', + '</td>', + '</tr>', + '</table>', + '<table align="center>', + '<tr>', + '<td valign="middle" style="vertical-align:middle;">', + '<a href="pdffile.pdf"><img src="richness.png"/></a>', + '</td>', + '</tr>', + '</table>', + '</html></body>'); +writeLines(html_output, htmlfile_handle); +close(htmlfile_handle); |
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| diff -r 000000000000 -r 0ab4501d805b phyloseq_richness.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_richness.xml Mon Sep 14 07:38:57 2020 +0000 |
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| @@ -0,0 +1,79 @@ +<tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false"> + <description>Phyloseq Richness Plot</description> + <requirements> + <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> + <requirement type="package" version="1.20.0">r-getopt</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__}/phyloseq_richness.r' + --biomfile='$biom_input' + --metafile='$metadata_input' + --xcolumn="${xaxis_column}" + --lcolumn="${legend_column}" + --outdir="$htmlfile.files_path" + --htmlfile='$htmlfile' + ]]></command> + + <inputs> + <param format="biom1" name="biom_input" type="data" label="BIOM file"/> + <param format="tabular" name="metadata_input" type="data" label="Metadata file"/> + <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/> + <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/> + </inputs> + + <outputs> + <data format="html" name="htmlfile" label="${tool.name}.html"/> + </outputs> + + <tests> + <test> + <param name="biom_input" value="test.biom" ftype="biom1" /> + <param name="metadata_input" value="metadata.txt" /> + <param name="xaxis_column" value="5" /> + <param name="legend_column" value="4" /> + <output name="htmlfile" ftype="html" file="biom_out.html" /> + </test> + </tests> + + + <help> +**What it does** +Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_. + +.. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-examples.html + +----- + +**Input** + + +- **BIOM file** - this is a BIOM_ file format +- **Metadata file** - this is a metadata file of the experiment design +- **Column used for X-axis** - The horizontal x-axis display on the barplot. +- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to. + +.. _BIOM: http://biom-format.org/ + +----- + +========= +Resources +========= + +**Wrapper Authors** + +QFAB Bioinformatics (support@qfab.org) + + </help> + <citations> + <citation type="doi">10.18129/B9.bioc.phyloseq</citation> + <citation type="doi">doi:10.1186/2047-217X-1-7</citation> + </citations> + ----- + + </help> +</tool> |
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| diff -r 000000000000 -r 0ab4501d805b test-data/GP.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GP.biom Mon Sep 14 07:38:57 2020 +0000 |
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| b'@@ -0,0 +1,1 @@\n+{"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 1.20.1"],"date":["2018-06-01 01:30:56"],"matrix_type":["dense"],"matrix_element_type":["int"],"shape":[19216,26],"rows":[{"id":["549322"],"metadata":{"taxonomy":["549322","Archaea","Crenarchaeota","Thermoprotei"]}},{"id":["522457"],"metadata":{"taxonomy":["522457","Archaea","Crenarchaeota","Thermoprotei"]}},{"id":["951"],"metadata":{"taxonomy":["951","Archaea","Crenarchaeota","Thermoprotei","Sulfolobales","Sulfolobaceae","Sulfolobus","Sulfolobusacidocaldarius"]}},{"id":["244423"],"metadata":{"taxonomy":["244423","Archaea","Crenarchaeota"]}},{"id":["586076"],"metadata":{"taxonomy":["586076","Archaea","Crenarchaeota"]}},{"id":["246140"],"metadata":{"taxonomy":["246140","Archaea","Crenarchaeota"]}},{"id":["143239"],"metadata":{"taxonomy":["143239","Archaea","Crenarchaeota"]}},{"id":["244960"],"metadata":{"taxonomy":["244960","Archaea","Crenarchaeota"]}},{"id":["255340"],"metadata":{"taxonomy":["255340","Archaea","Crenarchaeota"]}},{"id":["144887"],"metadata":{"taxonomy":["144887","Archaea","Crenarchaeota"]}},{"id":["141782"],"metadata":{"taxonomy":["141782","Archaea","Crenarchaeota"]}},{"id":["215972"],"metadata":{"taxonomy":["215972","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["31759"],"metadata":{"taxonomy":["31759","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["30678"],"metadata":{"taxonomy":["30678","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","SAGMA-X"]}},{"id":["138353"],"metadata":{"taxonomy":["138353","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["406058"],"metadata":{"taxonomy":["406058","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["30405"],"metadata":{"taxonomy":["30405","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["1126"],"metadata":{"taxonomy":["1126","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["46043"],"metadata":{"taxonomy":["46043","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["512519"],"metadata":{"taxonomy":["512519","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["554594"],"metadata":{"taxonomy":["554594","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["210741"],"metadata":{"taxonomy":["210741","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["550229"],"metadata":{"taxonomy":["550229","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["105798"],"metadata":{"taxonomy":["105798","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["183473"],"metadata":{"taxonomy":["183473","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["541313"],"metadata":{"taxonomy":["541313","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["540305"],"metadata":{"taxonomy":["540305","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["511243"],"metadata":{"taxonomy":["511243","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["568829"],"metadata":{"taxonomy":["568829","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["185612"],"metadata":{"taxonomy":["185612","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["321018"],"metadata":{"taxonomy":["321018","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae"]}},{"id":["549041"],"metadata":{"taxonomy":["549041","Archaea","Crenarchaeota","Thaumarchaeota","Cenarchaeales","Cenarchaeaceae","Cenarchaeu'..b',0,0,0,0,0,0,0],[0,3,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1],[14,18,6,2,2,0,0,0,8,0,3,2,26,4,1,0,5,5,20,3,68,10,1,8414,7078,7436],[0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,17,12,6],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,2],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,5,8],[0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,6,4,2],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,11,8,6],[0,0,0,0,0,0,0,0,0,0,0,0,1,0,4,0,0,0,0,1,1,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,3,1,0,0,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,3,6,0,0,0,0,0],[0,3,0,0,0,1,0,0,0,0,0,0,3,6,12,0,0,0,0,1,3,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],[1,10,0,0,0,0,0,0,0,0,0,1,14,37,58,0,0,0,0,3,4,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0],[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,7,0,0,0,0,0],[1,0,0,11,56,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0],[0,0,0,0,3,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No newline at end of file\n' |
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| diff -r 000000000000 -r 0ab4501d805b test-data/biom_out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom_out.html Mon Sep 14 07:38:57 2020 +0000 |
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| @@ -0,0 +1,9 @@ +<html><body> +<table align="center"> +<tr> +<td valign="middle" style="vertical-align:middle;"> +<a href="pdffile.pdf"><img src="richness.png"/></a> +</td> +</tr> +</table> +</html></body> |
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| diff -r 000000000000 -r 0ab4501d805b test-data/count.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count.txt Mon Sep 14 07:38:57 2020 +0000 |
| b |
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t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+724250\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+1085592\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+534772\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+333049\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+298785\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+1080675\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+272488\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+550699\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+182712\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+343331\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+1044577\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+511768\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r 0ab4501d805b test-data/metadata.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.txt Mon Sep 14 07:38:57 2020 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 0ab4501d805b test-data/observation.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/observation.txt Mon Sep 14 07:38:57 2020 +0000 |
| [ |
| b'@@ -0,0 +1,3359 @@\n+OTUID\ttaxonomy\n+775126\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+228502\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__\n+314713\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__\n+314425\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__\n+316122\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+432015\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+4374047\tk__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__\n+344726\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+1078157\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__\n+974097\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__\n+323154\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+266555\tk__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__\n+4316029\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__; s__\n+317867\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+190425\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+323592\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+258628\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+277152\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+271499\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+338644\tk__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Adlercreutzia; s__\n+338640\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__\n+313804\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+344723\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+188785\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+182836\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+350381\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+338004\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+646532\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+131618\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+351343\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus\n+309703\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__\n+339092\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__[Ruminococcus]; s__gnavus\n+468933\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__\n+277588\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+4372373\tk__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea\n+4432700\tk__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea\n+4429481\tk__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea\n+4323499\tk__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinerea\n+140239\tk__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria; s__cinere'..b'iraceae; g__; s__\n+307193\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__\n+183927\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+329268\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+313274\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+258750\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+272646\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+269427\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+3697034\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Enterococcaceae; g__Enterococcus; s__\n+2632775\tk__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Aeromonadales; f__Aeromonadaceae; g__; s__\n+349874\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+232276\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__\n+341448\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+273479\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+553352\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__Lactobacillus; s__\n+172503\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+290844\tk__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__\n+788402\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Coprococcus; s__\n+752420\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+706077\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+189184\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+204126\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__\n+204125\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+1918929\tk__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__\n+1058958\tk__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__\n+266697\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+273308\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+356148\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+314903\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+267671\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+275619\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+272256\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+274237\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+188092\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+180535\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+273631\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__\n+288344\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+212201\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+1961361\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+665761\tk__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__\n+131558\tk__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__\n+247570\tk__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__\n' |
| b |
| diff -r 000000000000 -r 0ab4501d805b test-data/test.biom --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.biom Mon Sep 14 07:38:57 2020 +0000 |
| [ |
| b'@@ -0,0 +1,1 @@\n+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-09-08T01:49:15.647451","type": "OTU table","matrix_element_type": "float","shape": [5339, 18],"data": [[0,0,1313.0],[0,1,354.0],[0,2,519.0],[0,3,707.0],[0,4,359.0],[0,5,300.0],[0,6,793.0],[0,7,832.0],[0,8,1719.0],[0,9,379.0],[0,10,236.0],[0,11,430.0],[0,12,315.0],[0,13,525.0],[0,14,355.0],[0,15,651.0],[0,16,176.0],[0,17,274.0],[1,0,297.0],[1,1,107.0],[1,2,69.0],[1,3,104.0],[1,4,30.0],[1,5,80.0],[1,6,199.0],[1,7,169.0],[1,8,100.0],[1,9,64.0],[1,10,54.0],[1,11,67.0],[1,12,63.0],[1,13,126.0],[1,14,62.0],[1,15,59.0],[1,16,58.0],[1,17,35.0],[2,0,806.0],[2,1,44.0],[2,2,176.0],[2,3,201.0],[2,4,71.0],[2,5,159.0],[2,6,415.0],[2,7,448.0],[2,8,437.0],[2,9,164.0],[2,10,114.0],[2,11,142.0],[2,12,85.0],[2,13,198.0],[2,14,109.0],[2,15,313.0],[2,16,99.0],[2,17,170.0],[3,0,13.0],[3,1,3.0],[3,2,6.0],[3,3,8.0],[3,4,3.0],[3,5,6.0],[3,6,7.0],[3,7,17.0],[3,8,14.0],[3,9,3.0],[3,10,2.0],[3,11,6.0],[3,12,4.0],[3,13,12.0],[3,14,1.0],[3,15,14.0],[3,16,5.0],[3,17,3.0],[4,0,872.0],[4,1,424.0],[4,2,415.0],[4,3,551.0],[4,4,220.0],[4,5,273.0],[4,6,584.0],[4,7,702.0],[4,8,1143.0],[4,9,313.0],[4,10,235.0],[4,11,472.0],[4,12,151.0],[4,13,487.0],[4,14,332.0],[4,15,442.0],[4,16,192.0],[4,17,264.0],[5,0,515.0],[5,1,55.0],[5,2,9.0],[5,3,13.0],[5,4,10.0],[5,5,57.0],[5,6,263.0],[5,7,209.0],[5,8,38.0],[5,9,84.0],[5,10,61.0],[5,11,9.0],[5,12,28.0],[5,13,105.0],[5,14,5.0],[5,15,16.0],[5,16,36.0],[5,17,19.0],[6,0,121.0],[6,1,26.0],[6,2,35.0],[6,3,39.0],[6,4,5.0],[6,5,36.0],[6,6,53.0],[6,7,68.0],[6,8,73.0],[6,9,28.0],[6,10,27.0],[6,11,29.0],[6,12,20.0],[6,13,64.0],[6,14,16.0],[6,15,42.0],[6,16,22.0],[6,17,19.0],[7,0,2.0],[7,5,1.0],[7,6,2.0],[7,7,1.0],[7,13,3.0],[7,16,2.0],[8,0,1344.0],[8,1,517.0],[8,2,597.0],[8,3,931.0],[8,4,363.0],[8,5,368.0],[8,6,772.0],[8,7,805.0],[8,8,3225.0],[8,9,397.0],[8,10,284.0],[8,11,457.0],[8,12,246.0],[8,13,563.0],[8,14,235.0],[8,15,890.0],[8,16,194.0],[8,17,283.0],[9,0,21.0],[9,1,116.0],[9,5,5.0],[9,6,29.0],[9,7,8.0],[9,8,2.0],[9,9,5.0],[9,10,1.0],[9,12,4.0],[9,13,14.0],[9,16,2.0],[9,17,1.0],[10,0,5.0],[10,3,1.0],[10,5,1.0],[10,6,1.0],[10,7,2.0],[10,8,2.0],[10,11,1.0],[10,12,3.0],[10,14,1.0],[10,15,2.0],[10,16,1.0],[10,17,1.0],[11,1,5.0],[11,2,2.0],[11,3,13.0],[11,4,30.0],[11,5,3.0],[11,6,8.0],[11,7,11.0],[11,8,76.0],[11,9,3.0],[11,10,8.0],[11,11,25.0],[11,12,1.0],[11,13,7.0],[11,14,29.0],[11,15,6.0],[11,16,4.0],[11,17,10.0],[12,0,573.0],[12,1,176.0],[12,2,545.0],[12,3,531.0],[12,4,139.0],[12,5,146.0],[12,6,532.0],[12,7,484.0],[12,8,382.0],[12,9,208.0],[12,10,202.0],[12,11,649.0],[12,12,219.0],[12,13,380.0],[12,14,580.0],[12,15,471.0],[12,16,127.0],[12,17,151.0],[13,0,1173.0],[13,1,467.0],[13,2,6.0],[13,3,12.0],[13,4,36.0],[13,5,354.0],[13,6,866.0],[13,7,648.0],[13,8,113.0],[13,9,320.0],[13,10,269.0],[13,11,2.0],[13,12,174.0],[13,13,463.0],[13,14,1.0],[13,15,22.0],[13,16,222.0],[13,17,19.0],[14,0,319.0],[14,1,81.0],[14,2,1.0],[14,3,1.0],[14,5,112.0],[14,6,283.0],[14,7,180.0],[14,8,17.0],[14,9,107.0],[14,10,37.0],[14,11,1.0],[14,12,51.0],[14,13,120.0],[14,14,6.0],[14,15,25.0],[14,16,36.0],[14,17,36.0],[15,0,301.0],[15,1,168.0],[15,2,309.0],[15,3,263.0],[15,4,109.0],[15,5,180.0],[15,6,228.0],[15,7,318.0],[15,8,688.0],[15,9,145.0],[15,10,103.0],[15,11,229.0],[15,12,81.0],[15,13,262.0],[15,14,213.0],[15,15,335.0],[15,16,80.0],[15,17,231.0],[16,1,21.0],[16,2,13.0],[16,3,14.0],[16,4,93.0],[16,7,1.0],[16,8,173.0],[16,10,1.0],[16,11,67.0],[16,14,66.0],[16,15,5.0],[16,17,8.0],[17,4,2.0],[17,8,1.0],[17,11,1.0],[17,14,1.0],[18,0,15.0],[18,1,54.0],[18,2,13.0],[18,3,40.0],[18,4,147.0],[18,5,4.0],[18,6,19.0],[18,7,25.0],[18,8,285.0],[18,9,8.0],[18,10,17.0],[18,11,57.0],[18,12,1.0],[18,13,3.0],[18,14,25.0],[18,15,13.0],[18,16,1.0],[18,17,35.0],[19,0,1112.0],[19,1,437.0],[19,2,292.0],[19,3,391.0],[19,4,66.0],[19,5,343.0],[19,6,906.0],[19,7,913.0],[19,8,460.0],[19,9,510'..b'"NewOTU.Ref-2369", "metadata": {}},{"id": "NewOTU.Ref-2370", "metadata": {}},{"id": "NewOTU.Ref-2371", "metadata": {}},{"id": "NewOTU.Ref-2372", "metadata": {}},{"id": "NewOTU.Ref-2373", "metadata": {}},{"id": "NewOTU.Ref-2374", "metadata": {}},{"id": "NewOTU.Ref-2375", "metadata": {}},{"id": "NewOTU.Ref-2376", "metadata": {}},{"id": "NewOTU.Ref-2377", "metadata": {}},{"id": "NewOTU.Ref-2378", "metadata": {}},{"id": "NewOTU.Ref-2379", "metadata": {}},{"id": "NewOTU.Ref-2380", "metadata": {}},{"id": "NewOTU.Ref-2381", "metadata": {}},{"id": "NewOTU.Ref-2382", "metadata": {}},{"id": "NewOTU.Ref-2383", "metadata": {}},{"id": "NewOTU.Ref-2384", "metadata": {}},{"id": "NewOTU.Ref-2385", "metadata": {}},{"id": "NewOTU.Ref-2386", "metadata": {}},{"id": "NewOTU.Ref-2387", "metadata": {}},{"id": "NewOTU.Ref-2388", "metadata": {}},{"id": "NewOTU.Ref-2389", "metadata": {}},{"id": "NewOTU.Ref-2390", "metadata": {}},{"id": "NewOTU.Ref-2391", "metadata": {}},{"id": "NewOTU.Ref-2392", "metadata": {}},{"id": "NewOTU.Ref-2393", "metadata": {}},{"id": "NewOTU.Ref-2394", "metadata": {}},{"id": "NewOTU.Ref-2395", "metadata": {}},{"id": "NewOTU.Ref-2396", "metadata": {}},{"id": "NewOTU.Ref-2397", "metadata": {}},{"id": "NewOTU.Ref-2398", "metadata": {}},{"id": "NewOTU.Ref-2399", "metadata": {}},{"id": "NewOTU.Ref-2400", "metadata": {}},{"id": "NewOTU.Ref-2401", "metadata": {}},{"id": "NewOTU.Ref-2402", "metadata": {}},{"id": "NewOTU.Ref-2403", "metadata": {}},{"id": "NewOTU.Ref-2404", "metadata": {}},{"id": "NewOTU.Ref-2405", "metadata": {}},{"id": "NewOTU.Ref-2406", "metadata": {}},{"id": "NewOTU.Ref-2407", "metadata": {}},{"id": "NewOTU.Ref-2408", "metadata": {}},{"id": "NewOTU.Ref-2409", "metadata": {}},{"id": "NewOTU.Ref-2410", "metadata": {}},{"id": "NewOTU.Ref-2411", "metadata": {}},{"id": "NewOTU.Ref-2412", "metadata": {}},{"id": "NewOTU.Ref-2413", "metadata": {}},{"id": "NewOTU.Ref-2414", "metadata": {}},{"id": "NewOTU.Ref-2415", "metadata": {}},{"id": "NewOTU.Ref-2416", "metadata": {}},{"id": "NewOTU.Ref-2417", "metadata": {}}],"columns": [{"id": "F3D147", "metadata": {"Food": "Swiss", "dpw": "147", "Replicate_Group": "Group6", "time": "Late"}},{"id": "F3D0", "metadata": {"Food": "None", "dpw": "0", "Replicate_Group": "Group1", "time": "Early"}},{"id": "F3D7", "metadata": {"Food": "Swiss", "dpw": "7", "Replicate_Group": "Group3", "time": "Early"}},{"id": "F3D6", "metadata": {"Food": "Cheddar", "dpw": "6", "Replicate_Group": "Group2", "time": "Early"}},{"id": "F3D1", "metadata": {"Food": "None", "dpw": "1", "Replicate_Group": "Group1", "time": "Early"}},{"id": "F3D144", "metadata": {"Food": "None", "dpw": "144", "Replicate_Group": "Group5", "time": "Late"}},{"id": "F3D148", "metadata": {"Food": "Swiss", "dpw": "148", "Replicate_Group": "Group6", "time": "Late"}},{"id": "F3D149", "metadata": {"Food": "Swiss", "dpw": "149", "Replicate_Group": "Group6", "time": "Late"}},{"id": "F3D2", "metadata": {"Food": "None", "dpw": "2", "Replicate_Group": "Group1", "time": "Early"}},{"id": "F3D141", "metadata": {"Food": "Cheddar", "dpw": "141", "Replicate_Group": "Group4", "time": "Late"}},{"id": "F3D146", "metadata": {"Food": "None", "dpw": "146", "Replicate_Group": "Group5", "time": "Late"}},{"id": "F3D9", "metadata": {"Food": "Swiss", "dpw": "9", "Replicate_Group": "Group3", "time": "Early"}},{"id": "F3D142", "metadata": {"Food": "Cheddar", "dpw": "142", "Replicate_Group": "Group4", "time": "Late"}},{"id": "F3D145", "metadata": {"Food": "None", "dpw": "145", "Replicate_Group": "Group5", "time": "Late"}},{"id": "F3D8", "metadata": {"Food": "Swiss", "dpw": "8", "Replicate_Group": "Group3", "time": "Early"}},{"id": "F3D3", "metadata": {"Food": "Cheddar", "dpw": "3", "Replicate_Group": "Group2", "time": "Early"}},{"id": "F3D143", "metadata": {"Food": "Cheddar", "dpw": "143", "Replicate_Group": "Group4", "time": "Late"}},{"id": "F3D5", "metadata": {"Food": "Cheddar", "dpw": "5", "Replicate_Group": "Group2", "time": "Early"}}]}\n\\ No newline at end of file\n' |