Mercurial > repos > iuc > pathview

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pathview.r	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,89 @@
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("pathview")
+    library("optparse")
+})
+
+sessionInfo()
+
+option_list <- list(
+  make_option(c("--pathway_id"), type="character", default=NULL, help="Path to tabular file with gene data"),
+  make_option(c("--pathway_id_fp"), type="character", default=NULL, help="Path to tabular file with pathway ids"),
+  make_option(c("--pathway_id_header"), type="logical", default=FALSE, help="Header for tabular file with pathway ids"),
+  make_option(c("--species"), type="character", default="hsa", help="KEGG code, scientific name or the common name of the species"),
+  make_option(c("--gene_data"), type="character", default=NULL, help="Path to tabular file with gene data"),
+  make_option(c("--gd_header"), type="logical", default=FALSE, help="Header for the gene data file"),
+  make_option(c("--gene_idtype"), type="character", default="entrez", help="ID type used for the gene data"),
+  make_option(c("--cpd_data"), type="character", default=NULL, help="Path to tabular file with compound data"),
+  make_option(c("--cpd_header"), type="logical", default=FALSE, help="Header for the compound data file"),
+  make_option(c("--cpd_idtype"), type="character", default="kegg", help="ID type used for the compound data"),
+  make_option(c("--multi_state"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
+  make_option(c("--match_data"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
+  make_option(c("--kegg_native"), type="logical", default=TRUE, help="Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
+  make_option(c("--same_layer"), type="logical", default=TRUE, help="Plot on same layer?"),
+  make_option(c("--map_null"), type="logical", default=TRUE, help="Map the NULL gene or compound data to pathway?"),
+  make_option(c("--split_group"), type="logical", default=FALSE, help="Split node groups into individual nodes?"),
+  make_option(c("--expand_node"), type="logical", default=FALSE, help="Expand multiple-gene nodes into single-gene nodes?"),
+  make_option(c("--sign_pos"), type="character", default="bottomright", help="Position of pathview signature")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+print(args)
+
+read_table = function(fp, header, rownames=1, colclasses=NA){
+  table = read.table(fp, header=header, sep="\t", row.names=rownames, colClasses=colclasses)
+  # transform to vector if only one column
+  if(dim(table)[2] == 1){
+    names = rownames(table)
+    table = table[,1]
+    names(table) = names
+  }
+  return(table)
+}
+
+get_table = function(fp, header){
+  table = NULL
+  if(!is.null(fp)){
+    table = read_table(fp, header, rownames=1)
+  }
+  return(table)
+}
+
+# load gene_data file
+gene_data = get_table(args$gene_data, args$gd_header)
+
+# load compound data file
+cpd_data = get_table(args$cpd_data, args$cpd_header)
+
+run_pathview = function(pathway_id){
+  pathview(
+    pathway.id=pathway_id,
+    gene.data=gene_data,
+    gene.idtype=args$gene_idtype,
+    cpd.data=cpd_data,
+    cpd.idtype=args$cpd_idtype,
+    species=args$species,
+    multi.state=args$multi_state,
+    match.data=args$match_data,
+    kegg.native=args$kegg_native,
+    same.layer=args$same_layer,
+    split.group=args$split_group,
+    expand.node=args$expand_node,
+    sign.pos=args$sign_pos,
+    map.null=args$map_null)
+}
+
+# get pathway ids
+if(!is.null(args$pathway_id)){
+  run_pathview(args$pathway_id)
+} else {
+  pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character")
+  for(p in pthws){
+    run_pathview(p)
+  }
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pathview.xml	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,405 @@
+<tool id="pathview" name="Pathview" version="@VERSION@+@GALAXY_VERSION@">
+    <description>for pathway based data integration and visualization</description>
+    <macros>
+        <token name="@VERSION@">1.24.0</token>
+        <token name="@GALAXY_VERSION@">galaxy0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">bioconductor-pathview</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ag.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.at.tair.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.bt.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ce.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.cf.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.dm.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.dr.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.eck12.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ecsakai.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.gg.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.mmu.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.pf.plasmo.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.pt.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.sc.sgd.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.ss.eg.db</requirement>
+        <requirement type="package" version="3.8.2">bioconductor-org.xl.eg.db</requirement>
+        <requirement type="package" version="1.6.2">r-optparse</requirement>
+    </requirements>
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", pathview version" $(R --vanilla --slave -e "library(pathview); cat(sessionInfo()\$otherPkgs\$pathview\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/pathview.r'
+
+#if str($pathway.nb) == 'one'
+    --pathway_id '$pathway.one_id'
+#else
+    --pathway_id_fp '$pathway.tabular'
+    --pathway_id_header $pathway.header
+#end if
+
+    --species '$species'
+
+#if str($gene_data.gd) == 'true'
+    --gene_data '$gene_data.tabular'
+    --gd_header $gene_data.header
+    --gene_idtype '$gene_data.idtype'
+#end if
+
+#if str($cpd_data.cpd) == 'true'
+    --cpd_data '$cpd_data.tabular'
+    --cpd_header $cpd_data.header
+    --cpd_idtype '$cpd_data.idtype'
+#end if
+
+    --multi_state $multi_state
+    --match_data $match_data
+
+    --kegg_native $out.kegg_native.out
+    --same_layer $out.kegg_native.same_layer
+#if str($out.kegg_native.out) == 'TRUE'
+    --map_null $out.kegg_native.map_null
+#else
+    --split_group $out.kegg_native.split_group
+    --expand_node $out.kegg_native.expand_node
+    --sign_pos $out.kegg_native.sign_pos
+#end if
+
+&&
+ls .
+    ]]></command>
+    <inputs>
+        <conditional name="pathway">
+            <param name="nb" type="select" label="Number of pathways to plot">
+                <option value="one" selected="true">One</option>
+                <option value="multiple">Multiple</option>
+            </param>
+            <when value="one">
+                <param name="one_id" type="text" label="KEGG pathway" help="KEGG pathway ID with 5 digits and without the 3 letter KEGG species code.">
+                    <validator type="regex" message="It should be the 5 digits of the KEGG pathway ID.">^(?:\d\d\d\d\d)?$</validator>
+                </param>
+            </when>
+            <when value="multiple">
+                <param name="tabular" type="data" format="tabular" optional="true" label="KEGG pathways" help="A table with one-column with KEGG pathways to plot"/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with column names)?"/>
+            </when>
+        </conditional>
+        <param name="species" type="select" label="Species to use">
+            <option value="aga">Anopheles</option>
+            <option value="ath">Arabidopsis</option>
+            <option value="bta">Bovine</option>
+            <option value="cel">Worm</option>
+            <option value="cfa">Canine</option>
+            <option value="dme">Fly</option>
+            <option value="dre">Zebrafish</option>
+            <option value="eco">E coli strain K12</option>
+            <option value="ecs">E coli strain Sakai</option>
+            <option value="gga">Chicken</option>
+            <option value="hsa" selected="true">Human</option>
+            <option value="mmu">Mouse</option>
+            <option value="mcc">Rhesus</option>
+            <option value="pfa">Malaria</option>
+            <option value="ptr">Chimp</option>
+            <option value="rno">Rat</option>
+            <option value="sce">Yeast</option>
+            <option value="ssc">Pig</option>
+            <option value="xla">Xenopus</option>
+        </param>
+        <conditional name="gene_data">
+            <param name="gd" type="select" label="Provide a gene data file?" help="Gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes.">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param name="tabular" type="data" format="tabular" label="Gene data" help="It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples."/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
+                <param name="idtype" type="select" label="Format for gene data">
+                    <option value="entrez" selected="true">Entrez Gene ID</option>
+                    <option value="symbol">Gene Symbol</option>
+                    <option value="genename">Gene Name</option>
+                    <option value="ensembl">Ensembl Gene ID</option>
+                    <option value="ensemblprot">Ensembl Protein ID</option>
+                    <option value="ensembltrans">Ensembl Trans ID</option>
+                    <option value="unigene">UniGene</option>
+                    <option value="uniprot">UniProt</option>
+                    <option value="refseq">RefSeq</option>
+                    <option value="enzyme">Enzyme</option>
+                    <option value="tair">TAIR</option>
+                    <option value="prosite">Prosite</option>
+                    <option value="orf">ORF</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <conditional name="cpd_data">
+            <param name="cpd" type="select" label="Provide a compound data file?" help="compound data is a broad concept including metabolites, drugs, their  measurements and attributes.">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param name="tabular" type="data" format="tabular" label="Compound data" help="It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples."/>
+                <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
+                <param name="idtype" type="select" label="Format for compound data">
+                    <option value="kegg" selected="true">KEGG (include compound, glycan and drug accessions)</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <param name="multi_state" type="boolean" checked="true" label="Should multiple states of gene or compond data be intergrated and plotted in the same graph?" help="Gene or compound nodes will be sliced into multiple pieces corresponding to the number of states in the data" />
+        <param name="match_data" type="boolean" checked="true" label="Are the gene and compound data paired?" help="When let sample sizes of gene and compound be m and n, when m>n, extra columns of NA's (mapped to no color) will be added to make the sample size the same" />
+        <section name="out" title="Output Options" expanded="true">
+            <conditional name="kegg_native">
+                <param name="out" type="select" label="Output for pathway">
+                    <option value="TRUE" selected="true">KEGG native</option>
+                    <option value="FALSE">Graphviz</option>
+                </param>
+                <when value="TRUE">
+                    <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, node colors will be plotted in the same layer as the pathway graph." />
+                    <param name="map_null" type="boolean" checked="true" label="Map the NULL gene or compound data to pathway?" help="When NULL data are mapped, the gene or compound nodes in the pathway will berendered as actually mapped nodes, except with NA-valued color. When NULL data are not mapped, the nodes are rendered as unmapped nodes." />
+                </when>
+                <when value="FALSE">
+                    <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, edge/node type legend will be plotted in the same page." />
+                    <param name="split_group" type="boolean" checked="false" label="Split node groups into individual nodes?" help="Each split member nodes inherits all edges from the node group. This option also effects most metabolic pathways even without group nodes defined orginally. For these pathways, genes involved in the same reaction are grouped automatically when converting reactions to edges unless split.group is true." />
+                    <param name="expand_node" type="boolean" checked="false" label="Expand multiple-gene nodes into single-gene nodes?" help="Each expanded single-gene nodes inherits all edges from the original multiple-gene node. This option is not effective for most metabolic pathways where it conflits with converting reactions to edges." />
+                    <param name="sign_pos" type="select" label="Position of pathview signature">
+                        <option value="bottomright" selected="true">Bottom right</option>
+                        <option value="bottomleft">Bottom left</option>
+                        <option value="topleft">Top left</option>
+                        <option value="topright">Top right</option>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="one_kegg_native" format="png" from_work_dir="*.pathview.png" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id})">
+            <filter>pathway['nb'] == 'one'</filter>
+            <filter>out['kegg_native']['out'] == 'TRUE'</filter>
+        </data>
+        <data name="one_graphviz" format="pdf" from_work_dir="*.pathview.pdf" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id}), Graphviz format">
+            <filter>pathway['nb'] == 'one'</filter>
+            <filter>out['kegg_native']['out'] == 'FALSE'</filter>
+        </data>
+        <collection name="multiple_kegg_native" type="list" label="${tool.name} on ${on_string}: KEGG Pathways">
+            <filter>pathway['nb'] == 'multiple'</filter>
+            <filter>out['kegg_native']['out'] == 'TRUE'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.png" directory="." ext="png"/>
+        </collection>
+        <collection name="multiple_graphviz" type="list" label="${tool.name} on ${on_string}: KEGG Pathways, Graphviz format">
+            <filter>pathway['nb'] == 'multiple'</filter>
+            <filter>out['kegg_native']['out'] == 'FALSE'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.pdf" directory="." ext="pdf"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="one" />
+                <param name="one_id" value="00010"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="TRUE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="map_null" value="true"/>
+                </conditional>
+            </section>
+            <output name="one_kegg_native" ftype="png" file="dme00010.png" compare="sim_size" delta="30000"/>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="one" />
+                <param name="one_id" value="00010"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="FALSE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="split_group" value="false" />
+                    <param name="expand_node" value="false"/>
+                    <param name="sign_pos" value="bottomright"/>
+                </conditional>
+            </section>
+            <output name="one_graphviz" ftype="pdf" file="dme00010.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="multiple" />
+                <param name="tabular" value="pathways.tabular"/>
+                <param name="header" value="false"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="TRUE" />
+                    <param name="same_layer" value="true"/>
+                    <param name="map_null" value="true"/>
+                </conditional>
+            </section>
+            <output_collection name="multiple_kegg_native" count="2">
+                <element name="dme00010" ftype="png" file="dme00010.png" compare="sim_size" delta="30000"/>
+                <element name="dme00480" ftype="png" file="dme00480.png" compare="sim_size" delta="40000"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="pathway">
+                <param name="nb" value="multiple" />
+                <param name="tabular" value="pathways.tabular"/>
+                <param name="header" value="false"/>
+            </conditional>
+            <param name="species" value="dme"/>
+            <conditional name="gene_data">
+                <param name="gd" value="true"/>
+                <param name="tabular" value="gene_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="ensembl"/>
+            </conditional>
+            <conditional name="cpd_data">
+                <param name="cpd" value="false"/>
+                <param name="tabular" value="cpd_data.tabular"/>
+                <param name="header" value="false"/>
+                <param name="idtype" value="kegg"/>
+            </conditional>
+            <param name="multi_state" value="true" />
+            <param name="match_data" value="true"/>
+            <section name="out">
+                <conditional name="kegg_native">
+                    <param name="out" value="FALSE" />
+                    <param name="same_layer" value="false"/>
+                    <param name="split_group" value="false" />
+                    <param name="expand_node" value="false"/>
+                    <param name="sign_pos" value="bottomright"/>
+                </conditional>
+            </section>
+            <output_collection name="multiple_graphviz" count="2">
+                <element name="dme00010" ftype="pdf" file="dme00010_cpd.pdf" compare="sim_size"/>
+                <element name="dme00480" ftype="pdf" file="dme00480_cpd.pdf" compare="sim_size"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Pathview is a stand-alone software package for pathway based data integration and visualization.
+
+This package can be divided into four functional modules: the Downloader, Parser, Mapper andViewer.
+Mostly importantly, pathview maps and renders user data on relevant pathway graphs.
+
+Notice that KEGG requires subscription for FTP access since May 2011.
+However,Pathview downloads individual pathway graphs and data files through API or HTTP access, which is freely available (for academic and non-commerical uses).
+Pathview uses KEGGgraph (Zhang and Wiemann, 2009) when parsing KEGG xml data files.
+
+
+Options map closely to the excellent pathview manual_.
+
+-----
+
+**Inputs**
+
+Pathview provides strong support for data integration. It works with:
+
+- essentially all types of biological data mappable to pathways (gene expression, protein expression, genetic association, metabolite, genomic data, literature, etc)
+- over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs
+- pathways for about 4800 species as well as KEGG orthology
+- various data attributes and formats, i.e.  continuous/discrete data, matrices/vectors, single/multiple samples etc.
+
+Pathview can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways.
+
+*Pathway ids*
+
+Either just the name or a table with one column with the different pathway ids to represent.
+
+
+*Gene data*
+
+The first input of Pathview is a gene data table. Here gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes.
+
+It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples.
+The first line can include the sample names.
+
+Here gene id is a generic concepts, including multiple types of gene, transcript and protein uniquely mappable to KEGG gene IDs. KEGG ortholog IDs are also treated as gene IDs as to handle metagenomic data.
+
+Example:
+
+    =========== =================
+    FBgn0039155	-4.14844993705661
+    FBgn0003360	-2.99977727873544
+    FBgn0026562	-2.38016404989418
+    FBgn0025111	2.69993883050214
+    FBgn0029167	-2.10506155636758
+    =========== =================
+
+*Compound data*
+
+We also frequently want to look at metabolic pathways too. Besides gene nodes, these pathways also have compound nodes.
+Therefore, we may integrate or visualize both gene data and compound data with metabolic pathways.
+
+Here compound data is a broad concept including metabolites, drugs, their  measurements and attributes.
+
+The format is similar to the gene data table, except named with IDs mappable to KEGG compound IDs.
+Over 20 types of IDs included in CHEMBL database can be used here.
+
+-----
+
+**Outputs**
+
+Pathview generates both native KEGG view and Graphviz view for pathways.
+
+KEGG view keeps all the meta-data on pathways, spacial and temporal information, tissue/cell types, inputs, outputs and connections. This is important for human reading and interpretation of pathway biology.
+
+.. image:: $PATH_TO_IMAGES/dme00010_native.png
+   :width: 60 %
+
+Graphviz view provides better control of node and edge attributes, better view of pathway topology, better understanding of the pathway analysis statistics.
+
+.. image:: $PATH_TO_IMAGES/dme00010_graphviz.png
+   :width: 60 %
+
+.. _manual: https://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf
+.. _KEGG: http://www.genome.jp/kegg
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt285</citation>
+    </citations>
+</tool>
\ No newline at end of file
Binary file static/images/dme00010_graphviz.png has changed
Binary file static/images/dme00010_native.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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Binary file test-data/dme00010.pdf has changed
Binary file test-data/dme00010.png has changed
Binary file test-data/dme00010_cpd.pdf has changed
Binary file test-data/dme00480.png has changed
Binary file test-data/dme00480_cpd.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_data.tabular	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,17559 @@
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+FBgn0267136	0.0407271634626921
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+FBgn0038529	0.0046453075757512
+FBgn0053534	NA
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+FBgn0051162	NA
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+FBgn0038959	0.0259048852758553
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+FBgn0263554	NA
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+FBgn0039048	0.18098462513967
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+FBgn0051515	NA
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+FBgn0265382	-0.0104715474396846
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+FBgn0259193	0.00100140154930125
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+FBgn0039081	0.00264552225403609
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+FBgn0039104	-0.0347991677813404
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+FBgn0047351	-0.0115548488015654
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+FBgn0264844	NA
+FBgn0039106	0.0953149432890024
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+FBgn0267760	-0.133002045134226
+FBgn0262974	0.0347770582413837
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+FBgn0004185	NA
+FBgn0039124	0.305971728439728
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+FBgn0264741	NA
+FBgn0264740	0.00103976281263618
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+FBgn0267761	0.0682013578560441
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+FBgn0039147	-0.0553045538598915
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+FBgn0039151	0.103392171798511
+FBgn0039154	-0.166033213142093
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+FBgn0002863	NA
+FBgn0264901	-0.0773911390618347
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+FBgn0051130	-0.0360044129953397
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+FBgn0267222	-0.061236396159064
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+FBgn0039193	-0.0332421219468146
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+FBgn0039197	0.0046453075757512
+FBgn0039198	0.00100140154930127
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+FBgn0000036	0.0301300793249436
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+FBgn0263409	NA
+FBgn0267209	0.0414203162619417
+FBgn0051128	-0.0239020821772528
+FBgn0000039	0.0824837173088787
+FBgn0262389	NA
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+FBgn0039202	0.00997262703764162
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+FBgn0011845	0.0166940180059705
+FBgn0004188	-0.0239404434405877
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+FBgn0267763	-0.151601258774789
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+FBgn0262858	0.0319971368003285
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+FBgn0003719	0.0588669239016608
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+FBgn0039232	0.0228363629085489
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+FBgn0004897	0.0465732801304427
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+FBgn0054027	0.0731465635042654
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+FBgn0260229	NA
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+FBgn0267767	0.0179565700386897
+FBgn0039283	0.0311384252298648
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+FBgn0039298	0.00103976281263618
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+FBgn0266741	-0.0343147497277118
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+FBgn0039312	-0.0282445790869461
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+FBgn0039346	-0.127166150296052
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+FBgn0267577	NA
+FBgn0262388	NA
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+FBgn0266735	0.0116907700445181
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+FBgn0263622	NA
+FBgn0263623	-0.013212713682036
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+FBgn0263453	0.00660707788742401
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+FBgn0267366	0.185119818075866
+FBgn0082923	0.0234974310374596
+FBgn0039565	NA
+FBgn0259990	NA
+FBgn0051253	NA
+FBgn0051054	0.010624404787608
+FBgn0267108	NA
+FBgn0051131	NA
+FBgn0039568	-0.0260546553889348
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+FBgn0004171	-0.00561083975068821
+FBgn0039576	0.00103976281263618
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+FBgn0039577	NA
+FBgn0267773	0.0450191576222557
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+FBgn0039582	0.109623920201262
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+FBgn0263579	-0.013212713682036
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+FBgn0039625	NA
+FBgn0039628	-0.0384155063708854
+FBgn0039629	0.0216164288577848
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+FBgn0039645	-0.0520276782380036
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+FBgn0262448	NA
+FBgn0262404	NA
+FBgn0039656	-0.209506150438705
+FBgn0051427	-0.139576535978552
+FBgn0267104	0.0579173645816067
+FBgn0267128	0.102388281807765
+FBgn0267107	0.187214576775736
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+FBgn0040623	NA
+FBgn0039666	0.0626294668825027
+FBgn0039669	0.0165556269155051
+FBgn0263588	-0.0132510749453709
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+FBgn0039683	-0.109602510082851
+FBgn0267129	-0.013212713682036
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+FBgn0039685	0.118710411806916
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+FBgn0039723	-0.0617545205695294
+FBgn0051202	0.0183414304150306
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+FBgn0260760	NA
+FBgn0004622	0.101977745072263
+FBgn0039728	-0.24672868034839
+FBgn0085327	0.0200884654517208
+FBgn0039739	0.0116907700445181
+FBgn0267780	0.0190926555348738
+FBgn0264837	NA
+FBgn0041102	0.0344041030623057
+FBgn0001281	-0.0308060990452605
+FBgn0003510	-0.013212713682036
+FBgn0003511	NA
+FBgn0264838	-0.0569977864957178
+FBgn0039744	0.103475484724818
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+FBgn0267781	-0.126572203549967
+FBgn0266442	-0.0163581534031206
+FBgn0266443	0.0941883438575417
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+FBgn0039758	-0.0126320894472401
+FBgn0051383	NA
+FBgn0051023	NA
+FBgn0085328	-0.0444219253731768
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+FBgn0267782	-0.0124221130722458
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+FBgn0267783	0.288564753971982
+FBgn0267130	0.0414203162619417
+FBgn0027544	NA
+FBgn0261704	NA
+FBgn0039768	-0.0513201449661608
+FBgn0039769	0.00952509822164646
+FBgn0039770	-0.0124465689520283
+FBgn0039771	-0.0227136623572088
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+FBgn0051371	-0.064511008916901
+FBgn0051014	-0.007733219917331
+FBgn0039782	-0.00257380867137143
+FBgn0263527	NA
+FBgn0054041	0.0591284298604563
+FBgn0039783	0.0026495021604168
+FBgn0051524	0.0417037837151231
+FBgn0039784	0.16468579767345
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+FBgn0051017	0.0271596180674347
+FBgn0051016	0.104880253984398
+FBgn0267131	0.00833888610585811
+FBgn0266259	NA
+FBgn0264985	0.0259048852758553
+FBgn0039792	-0.00564960262119361
+FBgn0051013	0.0368147450517201
+FBgn0051015	-0.0275753020346908
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+FBgn0039796	0.0352042867026678
+FBgn0000274	0.0259432465391903
+FBgn0267654	-0.0104715474396846
+FBgn0267784	NA
+FBgn0051010	-0.0343147497277118
+FBgn0262883	7.25765988310375e-06
+FBgn0262444	0.0116524087811832
+FBgn0003720	0.0170989679487544
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+FBgn0267786	-0.013212713682036
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+FBgn0053920	0.01236873856937
+FBgn0263562	NA
+FBgn0039816	0.080203231628958
+FBgn0039817	0.0437479894478369
+FBgn0039818	0.213619476271765
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+FBgn0263412	0.0197371086043364
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+FBgn0263544	NA
+FBgn0039832	0.15077621349394
+FBgn0039838	-0.0317890942807231
+FBgn0040628	0.0659145857505564
+FBgn0040629	-0.0570489398673334
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+FBgn0017448	0.151701110065153
+FBgn0265203	0.0116524087811832
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+FBgn0035103	0.27489371983196
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+FBgn0083992	-0.00806630212479075
+FBgn0063924	NA
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+FBgn0035138	-0.0761705302397463
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+FBgn0266927	0.0219591499824967
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+FBgn0267664	0.062549111911956
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+FBgn0052482	-0.0551812833709636
+FBgn0052480	-0.0573776871893459
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+FBgn0086063	-0.013212713682036
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+FBgn0086065	0.0295402566575646
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+FBgn0004429	-0.00799050515028647
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+FBgn0053966	NA
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+FBgn0035192	0.023359521717318
+FBgn0035193	0.102776332173098
+FBgn0052318	0.00100140154930126
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+FBgn0035197	NA
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+FBgn0003295	-0.0903311994521602
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+FBgn0052328	NA
+FBgn0052329	NA
+FBgn0011851	NA
+FBgn0011852	NA
+FBgn0011853	NA
+FBgn0052324	NA
+FBgn0052320	0.0175484790610184
+FBgn0011854	NA
+FBgn0011855	NA
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+FBgn0013342	0.0997732174769658
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+FBgn0035256	0.0084684991828538
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+FBgn0267484	0.219296879255093
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+FBgn0250911	NA
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+FBgn0266436	-0.0270372935632874
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+FBgn0086068	-0.0435761742858795
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+FBgn0054047	-0.0084183607797989
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+FBgn0267306	-0.013212713682036
+FBgn0011986	NA
+FBgn0052420	NA
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+FBgn0267307	-0.0084183607797989
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+FBgn0085371	-0.0815713957048884
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+FBgn0065097	NA
+FBgn0003486	0.0128800515721138
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+FBgn0052404	-0.0680082009011717
+FBgn0020641	-0.00758984673039062
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+FBgn0086900	NA
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+FBgn0036080	NA
+FBgn0267666	0.0939039065859802
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+FBgn0266953	-0.360228521385059
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+FBgn0262437	NA
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+FBgn0267545	-0.013212713682036
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+FBgn0036221	0.0144199024639676
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+FBgn0264488	-0.0665980867084628
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+FBgn0267554	NA
+FBgn0036617	0.0275429169209358
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+FBgn0267525	NA
+FBgn0267697	-0.0378450803539929
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+FBgn0266689	0.0570689667845828
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+FBgn0043577	-0.0104715474396846
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+FBgn0036665	0.11115091503864
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+FBgn0262895	0.0258665240125204
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+FBgn0263381	NA
+FBgn0036703	0.0116907700445181
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+FBgn0036704	-0.055408366818876
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+FBgn0266985	NA
+FBgn0262376	NA
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+FBgn0036715	0.0425670212417659
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+FBgn0036731	0.211913384976934
+FBgn0263478	NA
+FBgn0266675	NA
+FBgn0023197	0.0583541239880988
+FBgn0036738	-0.0935440557125241
+FBgn0086080	NA
+FBgn0261454	0.0116907700445181
+FBgn0265759	0.0116907700445181
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+FBgn0262531	-0.0339474959848732
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+FBgn0085280	-0.013212713682036
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+FBgn0261401	0.0164501260126716
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+FBgn0052189	NA
+FBgn0266685	-0.00413459690897029
+FBgn0054002	0.0542797970009038
+FBgn0262533	-0.0807654891432418
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+FBgn0260721	NA
+FBgn0036767	-0.0132510749453709
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+FBgn0267794	0.057841703303948
+FBgn0266942	-0.0482928994220537
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+FBgn0266769	-0.0404080581288139
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+FBgn0267599	NA
+FBgn0267598	-0.0238637209139179
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+FBgn0036784	0.0172427507160337
+FBgn0262998	-0.013212713682036
+FBgn0036785	-0.013212713682036
+FBgn0015946	NA
+FBgn0267637	NA
+FBgn0267636	NA
+FBgn0036786	0.0674846902976554
+FBgn0262969	0.0253456464979394
+FBgn0265881	NA
+FBgn0265882	-0.013212713682036
+FBgn0036787	0.00100140154930125
+FBgn0028415	NA
+FBgn0028416	NA
+FBgn0265883	NA
+FBgn0265884	NA
+FBgn0036789	-0.0104715474396846
+FBgn0052198	NA
+FBgn0036790	0.040163306387823
+FBgn0266984	NA
+FBgn0036791	0.0116907700445181
+FBgn0003683	0.00849126972077431
+FBgn0266938	NA
+FBgn0266939	-0.013212713682036
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+FBgn0265268	0.0241590774796037
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+FBgn0036796	0.0116907700445181
+FBgn0052201	-0.0136975495798405
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+FBgn0052200	NA
+FBgn0085283	0.0257114584676606
+FBgn0264719	0.00103976281263618
+FBgn0036807	0.0259432465391903
+FBgn0036808	0.00103976281263617
+FBgn0265885	NA
+FBgn0264717	0.0178794074626748
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+FBgn0267600	0.107328822415952
+FBgn0267601	-0.226969635192074
+FBgn0266937	0.00222861242252214
+FBgn0266936	0.057841703303948
+FBgn0262461	NA
+FBgn0036817	NA
+FBgn0036822	0.421487741327471
+FBgn0086661	-0.129834669469101
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+FBgn0262351	NA
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+FBgn0267249	NA
+FBgn0036835	0.0332896938253534
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+FBgn0264484	NA
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+FBgn0264697	NA
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+FBgn0267296	0.248138917349512
+FBgn0266983	-0.0238637209139179
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+FBgn0036872	0.0531379206684464
+FBgn0267714	0.0419671879525755
+FBgn0036873	NA
+FBgn0052213	NA
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+FBgn0036876	0.00616568680529
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+FBgn0265887	NA
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+FBgn0265895	NA
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+FBgn0265893	NA
+FBgn0037014	0.25701654186178
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+FBgn0264573	NA
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+FBgn0037162	0.0046453075757512
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+FBgn0037164	0.0240857747668296
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+FBgn0263004	0.0253456464979394
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+FBgn0266978	NA
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+FBgn0037169	0.302866488330669
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+FBgn0053771	NA
+FBgn0053772	0.0144199024639676
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+FBgn0037174	0.0253456464979394
+FBgn0037175	-0.0360044129953397
+FBgn0037176	-0.0239404434405877
+FBgn0037177	0.0436545744996447
+FBgn0037178	NA
+FBgn0037179	NA
+FBgn0037180	NA
+FBgn0052453	0.0116907700445181
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+FBgn0264980	0.0116524087811832
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+FBgn0011888	NA
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+FBgn0011880	NA
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+FBgn0011955	NA
+FBgn0040502	-0.0157087656977755
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+FBgn0050257	NA
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+FBgn0053664	NA
+FBgn0053669	NA
+FBgn0053668	NA
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+FBgn0065071	-0.0362799938261874
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+FBgn0029930	-0.136605371285031
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+FBgn0011952	NA
+FBgn0011975	NA
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+FBgn0011948	NA
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+FBgn0011950	NA
+FBgn0011951	NA
+FBgn0011980	NA
+FBgn0011982	NA
+FBgn0053247	NA
+FBgn0053246	NA
+FBgn0053245	NA
+FBgn0053244	NA
+FBgn0053243	NA
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+FBgn0053240	NA
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+FBgn0053238	NA
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+FBgn0011974	NA
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+FBgn0031423	0.0377818545513836
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+FBgn0031432	0.0910136260581415
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+FBgn0263330	0.0144199024639676
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+FBgn0260955	NA
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+FBgn0264362	-0.00758984687345976
+FBgn0264365	0.0179565700386897
+FBgn0040992	NA
+FBgn0260228	NA
+FBgn0040993	NA
+FBgn0259201	NA
+FBgn0027074	0.0145301818849389
+FBgn0051752	-0.071256844471063
+FBgn0003896	0.00785132758019629
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+FBgn0265951	-0.0132510749453709
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+FBgn0032751	NA
+FBgn0032753	0.00339494792431007
+FBgn0053315	0.00714352468535558
+FBgn0032754	0.154814781542154
+FBgn0002023	-0.108951416957479
+FBgn0032755	NA
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+FBgn0266210	0.0865476614794824
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+FBgn0265263	0.00103976281263618
+FBgn0267726	0.0846068687415834
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+FBgn0265078	NA
+FBgn0051797	-0.0713549981951631
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+FBgn0265079	0.0144199024639676
+FBgn0032768	0.00103976281263618
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+FBgn0267264	-0.0660576874359208
+FBgn0266796	NA
+FBgn0032770	0.345703063467278
+FBgn0032771	0.0120609297790053
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+FBgn0016675	0.226074408204236
+FBgn0053532	-0.201550814226259
+FBgn0053533	-0.00807298177968498
+FBgn0000964	0.0647957389876318
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+FBgn0043022	0.0116524087811832
+FBgn0003923	-0.013212713682036
+FBgn0032824	0.0402733158979063
+FBgn0003922	NA
+FBgn0043021	NA
+FBgn0032827	-0.0287786588984212
+FBgn0262543	0.10151707731605
+FBgn0044811	-0.013212713682036
+FBgn0053117	-0.013212713682036
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+FBgn0262140	0.00103976281263618
+FBgn0032834	-0.013212713682036
+FBgn0032835	0.149091268073848
+FBgn0267265	NA
+FBgn0032836	0.0307066936049185
+FBgn0042129	0.0116907700445181
+FBgn0014000	-0.0316286257991082
+FBgn0264443	0.0705112609371053
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+FBgn0266212	0.031324690767414
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+FBgn0032851	0.0258665240125204
+FBgn0032853	0.00103976281263618
+FBgn0259996	0.00244524496396793
+FBgn0058172	NA
+FBgn0250817	-0.0132510749453709
+FBgn0259998	0.114060098955332
+FBgn0260000	-0.386922052996486
+FBgn0040996	0.0259432465391903
+FBgn0263333	0.12020564458903
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+FBgn0026756	0.0928440108344353
+FBgn0032856	-0.0709262200110599
+FBgn0032857	0.204774313088697
+FBgn0083038	-0.0249717718270943
+FBgn0083026	NA
+FBgn0083037	-0.0157087656977755
+FBgn0083036	-0.0328813012095911
+FBgn0083025	-0.013212713682036
+FBgn0083035	-0.0323892278124207
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+FBgn0083034	-0.0231585382702343
+FBgn0083023	-0.00190562967735426
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+FBgn0083032	-0.0813160602658234
+FBgn0083022	-0.0256893514234041
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+FBgn0083021	0.00100140154930126
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+FBgn0083029	-0.0916748460354697
+FBgn0032860	-0.0806235023933274
+FBgn0051683	-0.0121664923135047
+FBgn0266315	NA
+FBgn0262878	-0.013212713682036
+FBgn0262879	-0.00309975278532033
+FBgn0266901	0.0144199024639676
+FBgn0262455	NA
+FBgn0266900	-0.0132510749453709
+FBgn0266899	0.0144199024639676
+FBgn0054007	0.0116907700445181
+FBgn0267266	-0.013212713682036
+FBgn0265256	NA
+FBgn0267271	NA
+FBgn0266886	NA
+FBgn0263533	NA
+FBgn0266214	-0.0238637209139179
+FBgn0051677	NA
+FBgn0263583	0.0116524087811832
+FBgn0032867	NA
+FBgn0262445	0.0116524087811832
+FBgn0262425	NA
+FBgn0032868	-0.0132510749453709
+FBgn0262688	0.0376559194464528
+FBgn0051680	-0.0484384748431004
+FBgn0261058	0.00747142871687574
+FBgn0082938	NA
+FBgn0082937	0.0227910114074387
+FBgn0082936	NA
+FBgn0265076	0.0613752015172003
+FBgn0265077	0.0334876307707455
+FBgn0266844	NA
+FBgn0032878	-0.0704054219860202
+FBgn0000251	0.055036030735351
+FBgn0264995	-0.013212713682036
+FBgn0053322	0.040163306387823
+FBgn0067311	-0.0317890942807231
+FBgn0067312	0.0779550705308147
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+FBgn0032894	0.0525267201196996
+FBgn0032896	0.00103976281263618
+FBgn0032898	-0.149830857659899
+FBgn0263996	NA
+FBgn0053318	0.20889400703169
+FBgn0053319	-0.0132510749453709
+FBgn0265817	-0.0503408445195435
+FBgn0032911	0.0915006857040727
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+FBgn0264353	0.00100140154930126
+FBgn0032916	0.0804382314875433
+FBgn0264865	-0.073222237269809
+FBgn0086041	NA
+FBgn0266215	NA
+FBgn0263050	NA
+FBgn0263051	NA
+FBgn0263474	0.0930800764374396
+FBgn0051988	0.0810613108959105
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+FBgn0267277	0.160820223439083
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+FBgn0032945	0.0452005735590661
+FBgn0051616	NA
+FBgn0051615	NA
+FBgn0051754	NA
+FBgn0053801	NA
+FBgn0053910	NA
+FBgn0053802	NA
+FBgn0053909	NA
+FBgn0053803	NA
+FBgn0051617	NA
+FBgn0061209	NA
+FBgn0051618	NA
+FBgn0053727	NA
+FBgn0051611	NA
+FBgn0051613	NA
+FBgn0053804	NA
+FBgn0053908	NA
+FBgn0053805	NA
+FBgn0053907	NA
+FBgn0053806	NA
+FBgn0053807	NA
+FBgn0053906	NA
+FBgn0053808	NA
+FBgn0053728	NA
+FBgn0053905	NA
+FBgn0053809	NA
+FBgn0053810	NA
+FBgn0053904	NA
+FBgn0053811	NA
+FBgn0053903	NA
+FBgn0053812	NA
+FBgn0053813	NA
+FBgn0053902	NA
+FBgn0053814	NA
+FBgn0053729	NA
+FBgn0053901	NA
+FBgn0053815	NA
+FBgn0053816	NA
+FBgn0053900	NA
+FBgn0053817	NA
+FBgn0053730	NA
+FBgn0053899	NA
+FBgn0053818	NA
+FBgn0053819	NA
+FBgn0053898	NA
+FBgn0053820	NA
+FBgn0053731	NA
+FBgn0053897	NA
+FBgn0053821	NA
+FBgn0053822	NA
+FBgn0053896	NA
+FBgn0053823	NA
+FBgn0053732	NA
+FBgn0053895	NA
+FBgn0053824	NA
+FBgn0053825	NA
+FBgn0053894	NA
+FBgn0053826	NA
+FBgn0053733	NA
+FBgn0053893	NA
+FBgn0053827	NA
+FBgn0053828	NA
+FBgn0053892	NA
+FBgn0053829	NA
+FBgn0053734	NA
+FBgn0053891	NA
+FBgn0053830	NA
+FBgn0053831	NA
+FBgn0053890	NA
+FBgn0053832	NA
+FBgn0053735	NA
+FBgn0053889	NA
+FBgn0053833	NA
+FBgn0053834	0.012866135181923
+FBgn0053888	NA
+FBgn0053835	NA
+FBgn0053736	NA
+FBgn0053887	NA
+FBgn0053836	NA
+FBgn0053837	NA
+FBgn0053886	NA
+FBgn0053838	NA
+FBgn0053737	NA
+FBgn0053885	NA
+FBgn0053839	NA
+FBgn0053840	NA
+FBgn0053884	NA
+FBgn0053841	NA
+FBgn0053738	NA
+FBgn0053883	NA
+FBgn0053842	NA
+FBgn0053843	NA
+FBgn0053882	-0.013212713682036
+FBgn0053844	NA
+FBgn0053739	NA
+FBgn0053881	NA
+FBgn0053845	NA
+FBgn0053846	NA
+FBgn0053880	NA
+FBgn0053847	NA
+FBgn0053740	NA
+FBgn0053879	NA
+FBgn0053848	NA
+FBgn0053849	NA
+FBgn0053878	NA
+FBgn0053850	NA
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+FBgn0053877	NA
+FBgn0053851	NA
+FBgn0053852	NA
+FBgn0053876	NA
+FBgn0053853	NA
+FBgn0053742	NA
+FBgn0053875	NA
+FBgn0053854	NA
+FBgn0053855	NA
+FBgn0053874	NA
+FBgn0053856	NA
+FBgn0053743	NA
+FBgn0053873	NA
+FBgn0053857	NA
+FBgn0053858	NA
+FBgn0053872	NA
+FBgn0053859	NA
+FBgn0053744	NA
+FBgn0053871	NA
+FBgn0053860	NA
+FBgn0053861	NA
+FBgn0053870	NA
+FBgn0053862	NA
+FBgn0053745	NA
+FBgn0053869	NA
+FBgn0053863	NA
+FBgn0053864	NA
+FBgn0053865	NA
+FBgn0053746	NA
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+FBgn0260718	-0.150309256047457
+FBgn0260719	-0.0820629001352134
+FBgn0267735	-0.125357055699434
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+FBgn0051703	-0.0102405703224315
+FBgn0040519	-0.000261638855324046
+FBgn0262885	NA
+FBgn0264265	-0.0318648021405151
+FBgn0263091	-0.111667489131942
+FBgn0264548	0.0302954301006288
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+FBgn0267433	-0.0100513068226799
+FBgn0267489	-0.0134656733826486
+FBgn0267608	NA
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+FBgn0001313	0.146569379876571
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+FBgn0259838	0.0116907700445181
+FBgn0085673	-0.013212713682036
+FBgn0259850	0.0116907700445181
+FBgn0259851	NA
+FBgn0259852	NA
+FBgn0259861	NA
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+FBgn0259863	-0.0132510749453709
+FBgn0259843	NA
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+FBgn0267446	-0.013212713682036
+FBgn0085505	0.0116907700445181
+FBgn0046697	0.0415629566141163
+FBgn0058441	NA
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+FBgn0267449	0.0410940497301336
+FBgn0267610	NA
+FBgn0259860	NA
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+FBgn0265047	0.171038551486606
+FBgn0085831	-0.0132510749453709
+FBgn0085790	-0.0241637759028751
+FBgn0085791	NA
+FBgn0085788	NA
+FBgn0085644	NA
+FBgn0085520	0.089778181402086
+FBgn0267490	NA
+FBgn0267411	NA
+FBgn0267412	NA
+FBgn0267418	NA
+FBgn0267413	NA
+FBgn0267419	NA
+FBgn0267420	NA
+FBgn0267492	NA
+FBgn0267494	NA
+FBgn0267493	NA
+FBgn0267422	NA
+FBgn0267423	NA
+FBgn0267417	NA
+FBgn0267491	NA
+FBgn0267424	NA
+FBgn0262795	NA
+FBgn0267426	NA
+FBgn0267427	NA
+FBgn0046698	0.0259048852758553
+FBgn0046323	0.0255014730403305
+FBgn0267592	0.0128022456752535
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+FBgn0267734	0.0741122156818308
+FBgn0264793	-0.0107656898021209
+FBgn0039900	0.0151062405847882
+FBgn0266618	NA
+FBgn0263385	-0.0798848245086766
+FBgn0264794	0.0575738813004444
+FBgn0266619	0.1858337006464
+FBgn0266726	-0.0985039138908206
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+FBgn0266727	-0.0997409181499728
+FBgn0039939	0.0171071999189566
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+FBgn0053797	NA
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+FBgn0083990	0.0216889984381714
+FBgn0264823	0.00100140154930125
+FBgn0039930	0.113783920160028
+FBgn0024913	0.0797294610910849
+FBgn0013696	NA
+FBgn0013703	NA
+FBgn0013700	NA
+FBgn0013680	NA
+FBgn0013709	NA
+FBgn0013690	NA
+FBgn0013710	NA
+FBgn0013674	NA
+FBgn0013699	NA
+FBgn0013675	NA
+FBgn0013697	NA
+FBgn0013691	NA
+FBgn0013673	NA
+FBgn0013672	NA
+FBgn0013676	NA
+FBgn0013694	NA
+FBgn0013681	NA
+FBgn0013689	NA
+FBgn0013704	NA
+FBgn0013701	NA
+FBgn0013705	NA
+FBgn0013692	NA
+FBgn0013693	NA
+FBgn0013684	NA
+FBgn0013695	NA
+FBgn0262952	NA
+FBgn0013683	NA
+FBgn0013707	NA
+FBgn0013702	NA
+FBgn0013685	NA
+FBgn0013678	NA
+FBgn0013706	NA
+FBgn0013679	NA
+FBgn0013698	NA
+FBgn0013686	NA
+FBgn0013708	NA
+FBgn0013688	NA
+FBgn0261386	NA
+FBgn0040038	NA
+FBgn0267508	NA
+FBgn0267509	NA
+FBgn0267510	NA
+FBgn0085753	NA
+FBgn0267511	NA
+FBgn0267505	NA
+FBgn0085802	NA
+FBgn0267512	NA
+FBgn0267496	NA
+FBgn0267497	NA
+FBgn0267506	NA
+FBgn0267498	NA
+FBgn0267499	NA
+FBgn0267500	NA
+FBgn0267507	NA
+FBgn0267501	NA
+FBgn0267502	NA
+FBgn0267503	NA
+FBgn0267504	NA
+FBgn0085692	NA
+FBgn0085828	NA
+FBgn0085816	NA
+FBgn0085817	NA
+FBgn0267594	NA
+FBgn0259837	NA
+FBgn0085777	NA
+FBgn0259839	NA
+FBgn0259840	NA
+FBgn0267596	NA
+FBgn0259842	NA
+FBgn0259817	NA
+FBgn0085805	NA
+FBgn0259849	NA
+FBgn0085807	NA
+FBgn0085755	NA
+FBgn0085808	NA
+FBgn0085744	NA
+FBgn0085760	NA
+FBgn0085494	NA
+FBgn0085540	NA
+FBgn0085746	NA
+FBgn0085751	NA
+FBgn0085773	NA
+FBgn0267595	NA
+FBgn0259864	NA
+FBgn0085752	NA
+FBgn0085795	NA
+FBgn0085827	NA
+FBgn0085822	NA
+FBgn0085803	NA
+FBgn0085506	NA
+FBgn0085768	NA
+FBgn0085757	NA
+FBgn0085758	NA
+FBgn0085764	NA
+FBgn0259870	NA
+FBgn0085761	NA
+FBgn0085748	NA
+FBgn0085756	NA
+FBgn0085799	NA
+FBgn0085759	NA
+FBgn0085826	NA
+FBgn0085737	NA
+FBgn0085511	NA
+FBgn0085766	NA
+FBgn0085772	NA
+FBgn0085825	NA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pathways.tabular	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,2 @@
+00010
+00480