changeset 0:785ed8621503 draft default tip

planemo upload commit 13e28726551f8751007f28a3c6cd5d00ba278056

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/netboxr_r.R	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,117 @@
+# Set up R error handling to go to stderr
+options(show.error.messages = FALSE,
+        error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)})
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+# Import required libraries and data
+suppressPackageStartupMessages({
+  library(netboxr)
+  library(igraph)
+  library(RColorBrewer)
+})
+
+data(netbox2010)
+args <- commandArgs(TRUE)
+# Vars
+gene_list <- scan(args[2], what = character(), sep = "\n")
+cutoff <- args[4]
+community <- args[6]
+global_model <- args[8]
+global_iterations <- args[10]
+global_number <- args[12]
+local_model <- args[14]
+local_iterations <- args[16]
+
+network_plot <- args[18]
+plot_width <- args[20]
+output_sif <- args[22]
+neighbor_list <- args[24]
+modmem <- args[26]
+nt <- args[28]
+
+sink("metadata.txt")
+sink(stdout(), type = "message")
+# Network analysis as described in netboxr vignette
+sif_network <- netbox2010$network
+graph_reduced <- networkSimplify(sif_network, directed = FALSE)
+threshold <- cutoff
+results <- print(geneConnector(geneList = gene_list, networkGraph = graph_reduced,
+                         directed = FALSE, pValueAdj = "BH", pValueCutoff = threshold,
+                         communityMethod = community, keepIsolatedNodes = FALSE))
+
+# Check the p-value of the selected linker
+linker_df <- results$neighborData
+linker_df[linker_df$pValueFDR < threshold, ]
+graph_layout <- layout_with_fr(results$netboxGraph)
+
+# Global Network Null Model
+if (global_model) {
+  global_test <- globalNullModel(netboxGraph = results$netboxGraph, networkGraph = graph_reduced,
+                                iterations = global_iterations, numOfGenes = global_number)
+  global_test
+}
+
+# Local Network Null Model
+if (local_model) {
+  local_test <- localNullModel(netboxGraph = results$netboxGraph, iterations = local_iterations)
+  local_test
+}
+
+## Output
+# Plot the edge annotated graph
+if (network_plot) {
+
+  edges <- results$netboxOutput
+  interaction_type <- unique(edges[, 2])
+  interaction_type_color <- brewer.pal(length(interaction_type), name = "Spectral")
+  edge_colors <- data.frame(interaction_type, interaction_type_color, stringsAsFactors = FALSE)
+  colnames(edge_colors) <- c("INTERACTION_TYPE", "COLOR")
+  netbox_graph_annotated <- annotateGraph(netboxResults = results, edgeColors =
+                                          edge_colors, directed = FALSE, linker = TRUE)
+  pdf("network_plot.pdf", width = plot_width)
+  plot(results$netboxCommunity, netbox_graph_annotated, layout = graph_layout,
+       vertex.size = 10, vertex.shape = V(netbox_graph_annotated)$shape, edge.color
+       = E(netbox_graph_annotated)$interactionColor, edge.width = 3)
+
+  # Add interaction type annotations
+  legend(x = -1.8, y = -1, legend = interaction_type, col =
+           interaction_type_color, lty = 1, lwd = 2, bty = "n", cex = 1)
+  dev.off()
+}
+
+# Local Network Null Model
+if (local_model) {
+  pdf("localModel_histogram.pdf")
+  h <- hist(local_test$randomModularityScore, breaks = 35, plot = FALSE)
+  h$density <- h$counts / sum(h$counts)
+  plot(h, freq = FALSE, ylim = c(0, 0.1), xlim = c(0.1, 0.6), col = "lightblue")
+  abline(v = local_test$modularityScoreObs, col = "red")
+  dev.off()
+}
+
+# NetBox algorithm output in SIF format.
+if (output_sif) {
+  write.table(results$netboxOutput, file = "network.sif", sep = "\t", quote = FALSE,
+              col.names = FALSE, row.names = FALSE)
+}
+
+# Save neighbor data
+if (neighbor_list) {
+  write.table(results$neighborData, file = "neighbor_data.txt", sep = "\t",
+              quote = FALSE, col.names = TRUE, row.names = FALSE)
+}
+
+#Save identified pathway module numbers
+if (modmem) {
+ write.table(results$moduleMembership, file = "community.membership.txt", sep = "\t",
+              quote = FALSE, col.names = FALSE, row.names = FALSE)
+}
+
+# Save file that indicates whether the node is a 'linker' or 'candidate'
+if (nt) {
+  write.table(results$nodeType, file = "nodeType.txt", sep = "\t", quote = FALSE, col.names = FALSE,
+              row.names = FALSE)
+}
+sink(NULL)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/netboxr_xml.xml	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,151 @@
+<tool id="netboxr" name="netboxr" version="1.6.0">
+    <description>enables automated discovery of biological process modules by network analysis.</description>
+    <requirements>
+        <requirement type="package" version="1.6.0">bioconductor-netboxr</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/netboxr_r.R'
+--geneList '$geneList'
+--cutoff '$cutoff'
+--community $community
+--globalModel $globalModel
+--globalIterations '$globalIterations'
+--globalNumber '$globalNumber'
+--localModel $localModel
+--localIterations '$localIterations'
+--networkPlot $networkPlot
+--plotWidth '$plotWidth'
+--outputSIF $outputSIF
+--neighborList $neighborList
+--modmem $modmem
+--nt $nt
+	]]></command>
+    <inputs>
+        <param argument="--geneList" type="data" format="txt" label="Gene list" help="A newline-delimited text file that contains a list of genes of interest" />
+        <param argument="--cutoff" type="float" value="0.05" label="P-Value Cut-Off" help="The corrected p-value (or q-value) cut-off to apply for the graph output. Default: 0.05" />
+        <param argument="--community" type="select" label="Community detection method" help="Community detection methods include edge betweenness score (EBC), leading eigenvector method (LEC), Louvain method (LOUV), or Leiden method (LEID). Default: EBC">
+            <option value="ebc">EBC</option>
+            <option value="lec">LEC</option>
+            <option value="louvain">LOUV</option>
+            <option value="leiden">LEID</option>
+        </param>
+        <param argument="--globalModel" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Global network null model" help="Perform global network null model analysis. The global network null model calculates the empirical p-value as the number of times (over a set of iterations) the size of the largest connected component (the giant component) in the network coming from the same number of randomly selected genes equals or exceeds the size of the largest connected component in the observed network. Default: Yes" />
+        <param argument="--globalIterations" type="integer" value="10" label="Global network null model iterations" help="Global network null model iterations. Recommended: 1000" />
+        <param argument="--globalNumber" type="integer" value="274" label="Global network model number of genes" help="Global network null model number of genes." />
+        <param argument="--localModel" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Local network null model" help="Perform local network null model analysis. The local network null model evaluates the deviation of modularity in the observed network from modularity distribution in the random network. Default: Yes" />
+        <param argument="--localIterations" type="integer" value="10" label="Local network null model iterations" help="Local network null model iterations. Recommended: 1000" />
+        <param argument="--networkPlot" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Network plot" help="Output the annotated graph of netboxr output. Default: Yes" />
+        <param argument="--plotWidth" type="integer" value="8" label="Network plot width" help="Plot width. Recommended: 9" />
+        <param argument="--outputSIF" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Network in SIF format" help="Output the network in SIF format. Default: Yes" />
+        <param argument="--neighborList" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Neighbor list" help="Output a table containing the information of all neighbor nodes. Default: Yes" />
+        <param argument="--modmem" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Module membership" help="Output a table containing the identified pathway module numbers. Default: Yes" />
+        <param argument="--nt" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Node type" help="Output a table containing the information of node types. Default: Yes" />
+    </inputs>
+    <outputs>
+        <data name="output_pdf" format="pdf" from_work_dir="network_plot.pdf" label="${tool.name} on ${on_string}: Network plot">
+            <filter>output_pdf is True</filter>
+        </data>
+        <data name="localModel_pdf" format="pdf" from_work_dir="localModel_histogram.pdf" label="${tool.name} on ${on_string}: Local model histogram">
+            <filter>localModel is True</filter>
+        </data>
+        <data name="output_sif" format="sif" from_work_dir="network.sif" label="${tool.name} on ${on_string}: SIF network">
+            <filter>outputSIF is True</filter>
+        </data>
+        <data name="output_neighbor" format="tabular" from_work_dir="neighbor_data.txt" label="${tool.name} on ${on_string}: Neighbor data">
+            <filter>output_neighbor is True</filter>
+        </data>
+        <data name="moduleMembership" format="tabular" from_work_dir="community.membership.txt" label="${tool.name} on ${on_string}: Module membership">
+            <filter>moduleMembership is True</filter>
+        </data>
+        <data name="nodeType" format="tabular" from_work_dir="nodeType.txt" label="${tool.name} on ${on_string}: Node type">
+            <filter>nodeType is True</filter>
+        </data>
+        <data name="metadata" format="txt" from_work_dir="metadata.txt" label="${tool.name} on ${on_string}: Metadata" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="geneList" value="netbox2010_data.txt" />
+            <param name="cutoff" value="0.05" />
+            <param name="community" value="ebc" />
+            <param name="globalModel" value="True" />
+            <param name="globalIterations" value="10" />
+            <param name="globalNumber" value="274" />
+            <param name="localModel" value="True" />
+            <param name="localIterations" value="10" />
+            <param name="networkPlot" value="True" />
+            <param name="plotWidth" value="8" />
+            <param name="outputSIF" value="True" />
+            <param name="neighborList" value="True" />
+            <param name="modmem" value="True" />
+            <param name="nt" value="True" />
+            <output name="output_pdf" file="network_plot.pdf" compare="sim_size" />
+            <output name="localModel_pdf" file="localModel_histogram.pdf" compare="sim_size" />
+            <output name="output_sif" file="network.sif">
+                <assert_contents>
+                    <has_text_matching expression="CBL\tPP\tPIK3R1" />
+                    <has_text_matching expression="PIK3R1\tIN_SAME_COMPONENT\tAGAP2" />
+                </assert_contents>
+            </output>
+            <output name="output_neighbor" file="neighbor_data.txt">
+                <assert_contents>
+                    <has_text_matching expression="idx\tname\tlocalDegree\tglobalDegree\tpValueRaw\toddsRatio\tpValueFDR" />
+                    <has_text_matching expression="1712\tCRK\t11\t81\t2.39208791593171e-05\t1.70873218314362\t0.0186673141177578" />
+                    <has_text_matching expression="6187\tRPS27\t2\t186\t0.975923212389053\t-0.825808759394024\t0.975923212389053" />
+                </assert_contents>
+            </output>
+            <output name="moduleMembership" file="community.membership.txt">
+                <assert_contents>
+                    <has_text_matching expression="CBL\t1" />
+                    <has_text_matching expression="CCT6A\t10" />
+                </assert_contents>
+            </output>
+            <output name="nodeType" file="nodeType.txt">
+                <assert_contents>
+                    <has_text_matching expression="CDKN2B\tcandidate" />
+                    <has_text_matching expression="PTPN11\tlinker" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+NetBox is a network-based approach that combines prior knowledge with a
+network clustering algorithm. The algorithm allows for the identification
+of functional modules and allows for combining multiple data types, such as
+mutations and copy number alterations. NetBox performs network analysis on
+human interaction networks, and comes pre-loaded with a Human Interaction
+Network (HIN) derived from four literature curated data sources, including
+the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway
+Interaction (PID) Database, and the MSKCC Cancer Cell Map.
+
+-----
+
+**INPUTS**
+
+**Gene list**
+A newline-delimited text file that contains a list of genes of interest is
+required.
+
+Example of text file contents:
+
+EGFR
+TP53
+ACTB
+GAPDH
+
+**Cutoff value**
+The corrected p-value (or q-value) cut-off to apply for the graph output.
+The default p-value is 0.05.
+
+
+**OUTPUTS**
+
+* A PDF with a plot of the edge annotated graph (optional)
+
+* A text file with tabular data containing information of all neighbor nodes (optional)
+
+  	]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pone.0234669</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/community.membership.txt	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,72 @@
+CBL	1
+ADAM12	1
+PIK3R1	1
+PTPN11	1
+KIT	1
+MPDZ	1
+KDR	1
+ERBB2	1
+SPRY2	1
+FRS2	1
+TEK	1
+GAB1	1
+PDGFRA	1
+IFNG	1
+VLDLR	1
+DOCK1	1
+EGFR	1
+JAK2	1
+CRK	1
+PIK3C2B	1
+PTPRB	1
+PTEN	1
+SH3GL2	1
+FGF23	1
+MAPK11	1
+PIK3CA	1
+HLA-DRA	1
+AVIL	1
+AGAP2	1
+TBP	2
+RB1	2
+TAF1	2
+CDK6	2
+CDKN2A	2
+TP53	2
+HSPA1A	2
+RBBP5	2
+SNAPC3	2
+MDM4	2
+MDM2	2
+KLF6	2
+CDKN2C	2
+CDK4	2
+PIM1	2
+BNC2	2
+EPHA3	2
+CCND2	2
+CDKN2B	2
+IFNW1	3
+IFNA2	3
+IFNB1	3
+IFNAR1	3
+IFNA1	3
+KCNA5	4
+PTPRD	4
+PTPRE	4
+CNTN2	5
+NCAM1	5
+NUP50	6
+THOC4	6
+NUP107	6
+SNRPE	6
+DCTN2	7
+TUBGCP2	7
+FGFR1OP	7
+TUBGCP6	7
+A2M	8
+LYZ	8
+PPARA	9
+STAC3	9
+CCT2	10
+CCT6A	10

Binary file test-data/localModel_histogram.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/neighbor_data.txt	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,893 @@
+idx	name	localDegree	globalDegree	pValueRaw	oddsRatio	pValueFDR
+1712	CRK	11	81	2.39208791593171e-05	1.70873218314362	0.0186673141177578
+4546	IFNAR1	6	23	4.18549643895914e-05	2.51872572932126	0.0186673141177578
+20	CBL	14	140	6.50546994954036e-05	1.3610568890526	0.0193429306499667
+500	GAB1	8	57	0.000248319689968565	1.75112196905105	0.0488782736525554
+414	CDK6	5	21	0.000300851540057881	2.40690610751877	0.0488782736525554
+84	PTPN11	14	163	0.000328777625465619	1.19140466680817	0.0488782736525554
+883	NRCAM	3	6	0.000479055427005265	3.49957222828438	0.0610453486983852
+1589	EGF	8	67	0.00075960357041191	1.56599925702267	0.0623864456740024
+723	E4F1	3	7	0.000820026182632156	3.24814652197521	0.0623864456740024
+2002	UBE2A	3	7	0.000820026182632156	3.24814652197521	0.0623864456740024
+2011	CCNG1	3	7	0.000820026182632156	3.24814652197521	0.0623864456740024
+9028	SH3BGRL3	2	2	0.000871691877932093	5.10566742579647	0.0623864456740024
+1075	IFNAR2	6	39	0.000909219499733219	1.86759645259685	0.0623864456740024
+3417	CCND1	7	55	0.0011040563656313	1.64273421305669	0.0703441627245085
+152	SOS1	10	109	0.00140677841553983	1.26617116982172	0.0788613246697833
+5758	YES1	5	30	0.00169479306853121	1.97058463576423	0.0788613246697833
+475	FES	5	30	0.00169479306853121	1.97058463576423	0.0788613246697833
+6824	IL1B	5	30	0.00169479306853121	1.97058463576423	0.0788613246697833
+1514	EPB41L1	4	19	0.00204257619053189	2.26516348792102	0.0788613246697833
+95	CRKL	7	62	0.00224497452402098	1.50713186104734	0.0788613246697833
+2777	MAP2K3	5	32	0.00228227989570501	1.89485396857421	0.0788613246697833
+188	GRB2	16	245	0.00248499401989919	0.890626990123815	0.0788613246697833
+4	GRB7	4	20	0.00249450743931036	2.20253170411913	0.0788613246697833
+6547	NUMA1	4	20	0.00249450743931036	2.20253170411913	0.0788613246697833
+13	ERRFI1	2	3	0.002563877147336	4.00694389623609	0.0788613246697833
+6366	TRIAP1	2	3	0.002563877147336	4.00694389623609	0.0788613246697833
+485	TIE1	2	3	0.002563877147336	4.00694389623609	0.0788613246697833
+1027	KCNE4	2	3	0.002563877147336	4.00694389623609	0.0788613246697833
+6197	CELSR2	2	3	0.002563877147336	4.00694389623609	0.0788613246697833
+469	PDGFRB	7	67	0.00350325776782824	1.42031176303995	0.104163530963426
+30	SHB	4	23	0.00425236950480855	2.03514326447932	0.118016403072892
+5820	RAP1A	6	54	0.00497475252068343	1.49590202180316	0.118016403072892
+5794	IL1R1	4	24	0.00498597603079399	1.98502136739822	0.118016403072892
+5506	BTC	2	4	0.00502760461521287	3.49600701920192	0.118016403072892
+4450	ZNHIT1	2	4	0.00502760461521287	3.49600701920192	0.118016403072892
+5888	NQO1	2	4	0.00502760461521287	3.49600701920192	0.118016403072892
+92	PTPRO	2	4	0.00502760461521287	3.49600701920192	0.118016403072892
+6017	ECM1	2	4	0.00502760461521287	3.49600701920192	0.118016403072892
+302	SH3KBP1	5	39	0.00551594038987694	1.6672993555707	0.126159457122314
+1259	RAD54B	3	13	0.00587280182975435	2.40018073325415	0.128668086485739
+7	PIK3R2	5	40	0.0061548531624999	1.63861431990281	0.128668086485739
+890	STAT5B	5	40	0.0061548531624999	1.63861431990281	0.128668086485739
+109	PTK2	9	113	0.00620260955032151	1.11272217001549	0.128668086485739
+44	SOCS1	6	57	0.00649453744645887	1.43554846037083	0.131661986414575
+1663	ITGB4	5	41	0.00684405330209209	1.61072308010184	0.135664345454803
+2718	ANGPT2	3	14	0.00731280617614375	2.30909759027298	0.140937424013585
+32	TEC	4	27	0.0076830666388411	1.84811132829167	0.140937424013585
+9027	PIK3C2A	2	5	0.00821608301424488	3.15942351693386	0.140937424013585
+2681	SERTAD1	2	5	0.00821608301424488	3.15942351693386	0.140937424013585
+5515	MAGEB18	2	5	0.00821608301424488	3.15942351693386	0.140937424013585
+5889	MTSS1	2	5	0.00821608301424488	3.15942351693386	0.140937424013585
+5669	GTPBP3	2	5	0.00821608301424488	3.15942351693386	0.140937424013585
+497	PIK3CB	3	15	0.00894359163891158	2.225604604155	0.145048795307439
+662	SNX6	3	15	0.00894359163891158	2.225604604155	0.145048795307439
+4988	PHB	3	15	0.00894359163891158	2.225604604155	0.145048795307439
+49	VAV2	4	29	0.00992912036910822	1.76621023236459	0.158156703022224
+141	VEGFA	6	63	0.0105025498546494	1.32467387885121	0.158521475773754
+1309	SMARCB1	3	16	0.0107701332049099	2.14853217343368	0.158521475773754
+1750	NFYB	3	16	0.0107701332049099	2.14853217343368	0.158521475773754
+5760	SERPINA3	3	16	0.0107701332049099	2.14853217343368	0.158521475773754
+1764	KLF4	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+5912	MNDA	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+1335	EID1	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+1340	CREG1	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+6427	SERPINB2	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+342	CNTNAP1	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+8133	CNOT3	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+578	IFNGR2	2	6	0.0120845968078647	2.90799781062469	0.158521475773754
+631	GRB14	3	17	0.0127964386470709	2.07696180745733	0.158533656572046
+5047	MSX1	3	17	0.0127964386470709	2.07696180745733	0.158533656572046
+5521	EHMT2	3	17	0.0127964386470709	2.07696180745733	0.158533656572046
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+984	STAT5A	6	67	0.0139941938994954	1.25697377365741	0.166437612777999
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+5307	HMGB1	5	52	0.0182687697962566	1.34607637319496	0.173358964449584
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+961	FER	3	23	0.029268081337397	1.73001689802986	0.196294199646302
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+4535	IL27	2	17	0.0885802621838938	1.67001030720214	0.287322159520121
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+4724	LZTS1	3	36	0.0894470133146053	1.23744601876555	0.289082376364594
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+1698	NGFR	4	59	0.0964705714746852	0.985153705330878	0.302829642199571
+131	VAV3	2	18	0.0977745929971708	1.60737852340025	0.302829642199571
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+148	SPI1	2	26	0.178697198200999	1.21117392493556	0.334148447105062
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+306	POLA1	3	50	0.183497430220692	0.886697500426964	0.341711289680286
+4739	CDC25A	2	27	0.189444089412398	1.17105705164571	0.350589476671907
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+1365	UBE3A	3	51	0.191007601556957	0.865751587971867	0.352751098527548
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+5736	CEP70	4	77	0.193212977223658	0.702234738405826	0.35535252718248
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+1735	RAF1	5	110	0.226069055119377	0.541588489562003	0.387051050223579
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+2179	CDK5	2	49	0.427728202076045	0.546548789076441	0.571158018341066
+731	DNM1	2	49	0.427728202076045	0.546548789076441	0.571158018341066
+2799	SNRPD2	5	145	0.428596294776488	0.251144951117547	0.571461726368651
+2080	U2AF2	5	146	0.434444453724017	0.243939722073431	0.57839470555496
+3752	FAS	2	50	0.437904484236684	0.525602876621346	0.579282968008018
+5302	MAX	2	50	0.437904484236684	0.525602876621346	0.579282968008018
+1267	CSNK1A1	2	50	0.437904484236684	0.525602876621346	0.579282968008018
+4197	CSNK2B	2	50	0.437904484236684	0.525602876621346	0.579282968008018
+1658	IRS1	3	82	0.439008168580067	0.368085555073812	0.579282968008018
+733	ARNT	3	82	0.439008168580067	0.368085555073812	0.579282968008018
+1099	APP	3	83	0.446827100117769	0.355473165161716	0.58592355125135
+2240	IL2RG	3	83	0.446827100117769	0.355473165161716	0.58592355125135
+329	ATN1	3	83	0.446827100117769	0.355473165161716	0.58592355125135
+4151	POLR2F	6	181	0.447277562609643	0.195522314878721	0.58592355125135
+1315	CTBP1	2	51	0.44798190801953	0.505082166931531	0.58592355125135
+96	DOK1	2	51	0.44798190801953	0.505082166931531	0.58592355125135
+4815	ARF1	2	52	0.457957409046696	0.484969649657103	0.597219311212942
+4979	POU2F1	2	52	0.457957409046696	0.484969649657103	0.597219311212942
+1809	POLR2E	6	184	0.463001124887172	0.178232369655213	0.602628954759795
+1087	TRAF6	4	118	0.46345679704621	0.254336759547928	0.602628954759795
+806	SOCS3	2	53	0.467828189098096	0.465249315189017	0.606169270729882
+275	PRKCE	2	53	0.467828189098096	0.465249315189017	0.606169270729882
+5303	POLR2L	6	185	0.468218192301445	0.172532274891068	0.606169270729882
+181	GAB2	2	54	0.4775917031503	0.445906077666677	0.615697051352885
+1006	PRKCZ	3	87	0.477648385130265	0.306529780639897	0.615697051352885
+2821	INSR	3	87	0.477648385130265	0.306529780639897	0.615697051352885
+4672	FN1	3	88	0.485230501296624	0.294652648902425	0.622669222169922
+4931	NCBP1	5	155	0.486380352085156	0.181258773332132	0.622669222169922
+4825	ARRB2	2	55	0.487245646944625	0.426925705250288	0.622669222169922
+2865	HLA-A	2	55	0.487245646944625	0.426925705250288	0.622669222169922
+7637	VAMP2	2	55	0.487245646944625	0.426925705250288	0.622669222169922
+1867	BMPR2	2	55	0.487245646944625	0.426925705250288	0.622669222169922
+861	LRP1	2	56	0.496787945064708	0.408294756850696	0.633955432042518
+6346	ERCC3	3	90	0.500234704662845	0.271305613331481	0.637441937941796
+3202	ACVR1	2	57	0.506216739504444	0.390000524611995	0.64414455297855
+4737	POLR2H	6	193	0.509411944055755	0.128020269003112	0.647286971649193
+3503	POLR2K	6	194	0.514482722459127	0.122587503435642	0.65119223304771
+7199	CPSF2	4	126	0.514675475671116	0.185898839241157	0.65119223304771
+457	YWHAB	4	126	0.514675475671116	0.185898839241157	0.65119223304771
+4842	CREB1	2	58	0.515530378707894	0.372030981530526	0.651349996894392
+197	GTF2F2	5	161	0.520070541387391	0.141486884065638	0.654455523695549
+2090	SFRS11	4	127	0.520923118636592	0.177655941801713	0.654455523695549
+7200	CPSF3	4	127	0.520923118636592	0.177655941801713	0.654455523695549
+7233	DHX38	4	127	0.520923118636592	0.177655941801713	0.654455523695549
+3959	PSMA3	3	93	0.52231803106705	0.237257534135729	0.654624960979805
+1009	TERT	2	59	0.524727407063409	0.354374733669392	0.654624960979805
+394	DAXX	2	59	0.524727407063409	0.354374733669392	0.654624960979805
+4621	HCK	2	59	0.524727407063409	0.354374733669392	0.654624960979805
+5770	PSEN1	2	59	0.524727407063409	0.354374733669392	0.654624960979805
+4313	CDC40	4	128	0.527132828688427	0.169478597889976	0.655791468884347
+7558	SFRS6	4	128	0.527132828688427	0.169478597889976	0.655791468884347
+841	PPP1CC	3	94	0.529560806262049	0.226156046696764	0.65789448354561
+6837	MAGOH	4	129	0.533303649207608	0.161365758426208	0.661327009600941
+2338	B2M	2	60	0.53380655483484	0.337020976493092	0.661327009600941
+3833	RBM8A	4	130	0.539434662650956	0.153316399309228	0.667372703307424
+654	PDPK1	2	61	0.542766728513317	0.319959454903158	0.669637512909929
+4575	POLA2	2	61	0.542766728513317	0.319959454903158	0.669637512909929
+4922	SFRS5	4	131	0.545524990051943	0.145329520629654	0.671183849829425
+7630	UPF3B	4	131	0.545524990051943	0.145329520629654	0.671183849829425
+2568	SFRS9	4	132	0.551573790504199	0.137404145913899	0.674942997810319
+4293	SRRM1	4	132	0.551573790504199	0.137404145913899	0.674942997810319
+6551	U2AF1	4	132	0.551573790504199	0.137404145913899	0.674942997810319
+418	RBX1	2	62	0.55160700157368	0.303180426604606	0.674942997810319
+4729	CPSF1	4	133	0.557580260629053	0.129539321397448	0.680785694206002
+1790	CCNH	3	98	0.557908455677789	0.18291918173463	0.680785694206002
+216	SUMO1	2	63	0.5603266056202	0.286674628475601	0.680941869500297
+449	NCOR2	2	63	0.5603266056202	0.286674628475601	0.680941869500297
+1994	IKBKG	2	63	0.5603266056202	0.286674628475601	0.680941869500297
+3830	SFRS4	4	134	0.563543634028422	0.121734115326116	0.683919621161024
+298	ZAP70	2	64	0.568924921906782	0.270433245649594	0.68951226948485
+1823	CDK7	3	100	0.571694067040413	0.161968180517216	0.691928233107257
+2567	SFRS3	4	136	0.575338206586045	0.106298937546605	0.69257986541802
+3984	RNPS1	4	136	0.575338206586045	0.106298937546605	0.69257986541802
+7434	NUP43	4	136	0.575338206586045	0.106298937546605	0.69257986541802
+491	RAC1	4	136	0.575338206586045	0.106298937546605	0.69257986541802
+2057	RIPK1	2	65	0.577401473217381	0.254447883051571	0.694126838423051
+3201	NUP133	4	137	0.581168052746696	0.0986672064590168	0.695841480604098
+4658	NUP37	4	137	0.581168052746696	0.0986672064590168	0.695841480604098
+7431	NUP160	4	137	0.581168052746696	0.0986672064590168	0.695841480604098
+372	ITGAV	2	66	0.585755916092849	0.238710539158346	0.699456863661073
+7311	HADH	2	66	0.585755916092849	0.238710539158346	0.699456863661073
+2083	SFRS2	4	138	0.586952095009321	0.0910915738363167	0.699948220251757
+1466	SNRPD1	4	139	0.592689743244591	0.0835712083869158	0.705846797028271
+207	SMAD4	6	211	0.597217447460633	0.03430622963758	0.709870533142958
+3249	SNRPF	4	140	0.598380440780564	0.0761052971568104	0.709870533142958
+29	SYK	3	104	0.598455875474781	0.121311866881211	0.709870533142958
+530	GNB2L1	2	68	0.602097727166834	0.207949725661472	0.713241929127245
+2472	ATXN1	4	142	0.609618920645795	0.0613336740332846	0.721193736360808
+3890	AURKB	3	106	0.61142188548388	0.101574030154429	0.722368638214067
+1465	SNRPD3	4	143	0.615165751336626	0.054026423197195	0.725830489672315
+2507	PRPF6	3	109	0.630341500647569	0.0726630289862156	0.74275378940242
+5444	SNRPG	4	146	0.631511546705121	0.0324100225431483	0.743150791109456
+5086	CDC27	2	72	0.633314106811008	0.149090633526689	0.743310767467656
+1110	TNF	2	72	0.633314106811008	0.149090633526689	0.743310767467656
+5128	ATP5C1	3	110	0.63650547966149	0.0632045983233613	0.745095653357019
+5398	NHP2L1	3	110	0.63650547966149	0.0632045983233613	0.745095653357019
+5481	NUDT21	3	111	0.642597745351728	0.0538326919929109	0.751241400856804
+1468	CSNK2A2	2	74	0.648192874131279	0.120892541097651	0.755801364346537
+2882	EIF2S2	2	74	0.648192874131279	0.120892541097651	0.755801364346537
+2854	NCBP2	4	150	0.65260533208556	0.00427441200995293	0.759302274774633
+5352	RBMX	3	113	0.654566420657891	0.0353421441497863	0.759302274774633
+416	GSK3B	2	75	0.655451515220255	0.107081557686945	0.759302274774633
+7648	ZW10	2	75	0.655451515220255	0.107081557686945	0.759302274774633
+176	UNC119	2	75	0.655451515220255	0.107081557686945	0.759302274774633
+6107	SNRPB	4	151	0.657751773672216	-0.00264141271440188	0.76097870572713
+1293	YWHAQ	2	76	0.662590482337636	0.093455686891101	0.764593415582369
+3480	UBE2D1	2	76	0.662590482337636	0.093455686891101	0.764593415582369
+7477	POLR2I	4	153	0.667890728234075	-0.0163358229351998	0.769713862512655
+3962	PSMC3	2	77	0.66961047702957	0.0800099918131192	0.770700058723066
+5728	CCDC85B	3	116	0.671978241822442	0.00821693326824047	0.772428597558787
+5843	PSMB5	2	78	0.676512263959974	0.0667397304448683	0.774159344785468
+1818	CUL1	2	78	0.676512263959974	0.0667397304448683	0.774159344785468
+3390	CDK2	4	155	0.677823372508353	-0.0298512993987368	0.774159344785468
+3649	POLR2J	4	155	0.677823372508353	-0.0298512993987368	0.774159344785468
+4799	POLR2B	4	155	0.677823372508353	-0.0298512993987368	0.774159344785468
+1804	CALM1	4	156	0.682712016063659	-0.0365434118670436	0.777424268622409
+4570	POLR2D	4	156	0.682712016063659	-0.0365434118670436	0.777424268622409
+7552	SEC13	2	79	0.683296666591893	0.0536403455422727	0.777424268622409
+1788	GTF2F1	4	157	0.68754875353766	-0.0431925370195092	0.781025875959636
+772	RPA1	2	80	0.689964563067481	0.0407074551495583	0.781025875959636
+151	SETDB1	2	80	0.689964563067481	0.0407074551495583	0.781025875959636
+5795	PSMC2	2	80	0.689964563067481	0.0407074551495583	0.781025875959636
+4469	POLR2G	4	158	0.692333522426773	-0.0497992333080548	0.782714197724565
+4019	CDCA8	2	82	0.702954600121172	0.0153244538111954	0.792712393562687
+4730	SKIL	2	82	0.702954600121172	0.0153244538111954	0.792712393562687
+615	YBX1	3	122	0.704855009795715	-0.0439727337296008	0.793851854466892
+3275	RANGAP1	2	84	0.715490349046785	-0.00944114719251843	0.803800240994625
+1354	PSMC5	2	84	0.715490349046785	-0.00944114719251843	0.803800240994625
+28	TGFBR1	4	164	0.719949925614054	-0.0885783504823259	0.805580422769966
+4332	POLR2C	4	164	0.719949925614054	-0.0885783504823259	0.805580422769966
+1334	NDC80	2	85	0.721590535642604	-0.0216017506540833	0.805580422769966
+1786	GTF2H4	2	85	0.721590535642604	-0.0216017506540833	0.805580422769966
+6638	GTF2H3	2	85	0.721590535642604	-0.0216017506540833	0.805580422769966
+226	DHX9	3	126	0.725343229982971	-0.077348527566647	0.808757701431013
+4018	INCENP	2	86	0.72758042557091	-0.0336189307106238	0.809229101757172
+6353	GTF2H2	2	86	0.72758042557091	-0.0336189307106238	0.809229101757172
+4720	ERCC2	2	88	0.739233985932631	-0.0572364032115953	0.821166519865388
+6578	ACTA1	2	89	0.744900058914621	-0.0688430980190402	0.826431408646569
+833	CASP8	2	91	0.755916971773536	-0.0916675985510222	0.837612346362725
+3119	UBQLN4	3	134	0.762973380645887	-0.141016852084409	0.842041456376351
+7144	ATP5D	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7145	ATP5E	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7146	ATP5F1	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7147	ATP5G1	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7148	ATP5I	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7151	ATP5O	2	93	0.766522043248427	-0.113992664653757	0.842041456376351
+7247	EEF2	2	94	0.771673374487262	-0.124974715381536	0.843544914267938
+3749	RPL11	2	94	0.771673374487262	-0.124974715381536	0.843544914267938
+6328	ATP5H	2	94	0.771673374487262	-0.124974715381536	0.843544914267938
+7150	ATP5L	2	94	0.771673374487262	-0.124974715381536	0.843544914267938
+7149	ATP5J	2	95	0.776725654906272	-0.135839898279018	0.847756374911252
+210	SMAD2	4	179	0.780901550503423	-0.179623649584213	0.847756374911252
+5465	PSMD11	2	96	0.78168021176687	-0.146590700238478	0.847756374911252
+1273	XPO1	3	140	0.788375889852397	-0.186311424374199	0.847756374911252
+6771	ATP5A1	2	98	0.791301504158898	-0.167758719503444	0.847756374911252
+4481	ACTB	2	99	0.795970929653815	-0.178180530833305	0.847756374911252
+253	RPL18A	2	99	0.795970929653815	-0.178180530833305	0.847756374911252
+6038	ATP5B	2	100	0.80054800848266	-0.188497155323098	0.847756374911252
+7588	SNRNP70	2	100	0.80054800848266	-0.188497155323098	0.847756374911252
+1836	POLR2A	4	187	0.808860827298371	-0.225107230199428	0.847756374911252
+7078	AASS	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+2853	SNRPA1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+5331	SNRPA	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+5748	CLP1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7201	CPSF7	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7207	CSTF3	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7227	DDX23	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7237	DNAJC8	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7322	HNRNPA0	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7323	HNRNPA1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7324	HNRNPA2B1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7325	HNRNPA3	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7327	HNRNPD	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7328	HNRNPF	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7329	HNRNPH1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7330	HNRNPH2	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7331	HNRNPL	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7332	HNRNPM	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7333	HNRNPR	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7334	HNRNPU	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7335	HNRNPUL1	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7446	PCF11	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7459	PHF5A	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7555	SF3B14	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7556	SF3B5	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7557	SF4	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7586	SNRNP200	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+7587	SNRNP40	2	103	0.813738704638071	-0.218836844469312	0.847756374911252
+6329	ATP5J2	2	104	0.81795993658245	-0.22875334948814	0.847756374911252
+5496	RBM5	2	104	0.81795993658245	-0.22875334948814	0.847756374911252
+7487	PRPF8	2	104	0.81795993658245	-0.22875334948814	0.847756374911252
+2695	RPL5	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+2087	SF3A3	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+2424	SNRPB2	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+2473	TXNL4A	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+2816	CSTF1	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+3365	CCAR1	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+4595	SF3B2	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+6192	EFTUD2	2	105	0.822095587778289	-0.238574681196091	0.847756374911252
+1486	PAPOLA	2	106	0.826147005130104	-0.248302670138155	0.848989779465498
+1691	CD2BP2	2	106	0.826147005130104	-0.248302670138155	0.848989779465498
+2422	SF3A2	2	106	0.826147005130104	-0.248302670138155	0.848989779465498
+1766	SF3A1	2	107	0.830115531036522	-0.257939094556514	0.849154878078644
+3059	PRPF4	2	107	0.830115531036522	-0.257939094556514	0.849154878078644
+3517	PABPN1	2	107	0.830115531036522	-0.257939094556514	0.849154878078644
+7326	HNRNPC	2	107	0.830115531036522	-0.257939094556514	0.849154878078644
+4297	SF3B3	2	108	0.834002502480785	-0.267485682364305	0.852153759693998
+2988	PCBP2	2	109	0.837809250178602	-0.276944113027159	0.855063902928276
+4468	SF3B4	2	110	0.841537097780771	-0.286316019357612	0.857886961394797
+665	SF3B1	2	111	0.845187361128093	-0.295602989227195	0.860624573203492
+3964	PTBP1	2	113	0.85226035524807	-0.31392825609699	0.865849928110796
+439	VIM	2	113	0.85226035524807	-0.31392825609699	0.865849928110796
+3919	RPS7	2	115	0.859038577822236	-0.33193177808228	0.870752740247085
+287	SMAD1	2	115	0.859038577822236	-0.33193177808228	0.870752740247085
+2815	CSTF2	2	117	0.865532209448699	-0.349624797847373	0.876339081530352
+2801	LSM2	2	118	0.868675436084772	-0.358358223296043	0.878524363931538
+3442	SMC1A	2	121	0.877705505480484	-0.384121445080123	0.886651541210183
+3825	PCBP1	2	122	0.88058634707523	-0.392567559856226	0.888555454288581
+677	RPS3A	2	124	0.886161358114687	-0.409254341477723	0.89317054399808
+683	BUB3	2	134	0.910596051541953	-0.488854243172278	0.916762616225081
+2675	BUB1B	2	138	0.918923494761648	-0.51904788356207	0.924103446817801
+4732	MAD2L1	2	139	0.920888734702681	-0.526460135724721	0.925036882156297
+1684	CDC20	2	142	0.926519520852894	-0.548382633000971	0.928601587191889
+4003	EEF1G	2	142	0.926519520852894	-0.548382633000971	0.928601587191889
+4955	EEF1A1	2	168	0.961736895547538	-0.721112630716305	0.962816286002699
+6187	RPS27	2	186	0.975923212389053	-0.825808759394024	0.975923212389053

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/netbox2010_data.txt	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,517 @@
+CDKN2B
+EGFR
+CDKN2A
+MTAP
+PTEN
+TP53
+SEC61G
+LANCL2
+DMRTA1
+IFNE
+IFNA1
+ELAVL2
+IFNA8
+IFNA2
+IFNA13
+IFNA6
+KLHL9
+IFNA5
+IFNA14
+CYP27B1
+IFNA10
+IFNA16
+IFNA7
+IFNW1
+IFNA21
+CDK4
+TSPAN31
+VOPP1
+MARCH9
+VSTM2A
+KIAA1797
+AGAP2
+METTL1
+TSFM
+FAM119B
+AVIL
+MLLT3
+PTPLAD2
+IFNB1
+CTDSP2
+HLA-DRA
+NF1
+XRCC6BP1
+MDM2
+OS9
+GSX2
+SLC24A2
+RPL21P44
+PDGFRA
+CHIC2
+SEPT14
+NME7
+RB1
+C9orf82
+MARS
+SLC35E3
+DTX3
+PLAA
+CPM
+MBD6
+PIP4K2C
+SLC26A10
+LRRC19
+KIT
+ZNF713
+B4GALNT1
+TEK
+IFT74
+DDIT3
+GEFT
+KIF5A
+LINGO2
+C9orf11
+MOBKL2B
+NUP107
+DCTN2
+FKBP9
+IFNK
+PTPRD
+PAOX
+ERBB2
+PIK3R1
+GLI1
+CPSF6
+ARHGAP9
+PIK3CA
+FRS2
+LYZ
+INHBC
+C9orf72
+INHBE
+YEATS4
+LNX1
+LRIG3
+MDM4
+ECHS1
+KDR
+KISS1
+GBAS
+RAB3IP
+PLEKHA6
+CCT2
+ETNK2
+MRPS17
+LRRN2
+REN
+PPP1R15B
+SOX13
+LRRC10
+PIK3C2B
+GOLT1A
+C1orf157
+CLRN3
+C10orf90
+HMGA2
+PPM1H
+TYRP1
+TPD52L3
+DOCK1
+LAX1
+NPS
+FAM196A
+hCG_1757335
+BEST3
+FOXI2
+PRELP
+TCERG1L
+SNRPE
+SRD5A3
+CCT6A
+TMEM165
+GRIP1
+RAP1B
+ATP2B4
+PSPH
+EBF3
+GLRX3
+PTPRE
+SLC16A7
+ZC3H11A
+OPTC
+ADAM12
+FIP1L1
+C9orf150
+NFASC
+MKI67
+R3HDM2
+PSIP1
+NKX6-2
+C9orf93
+RCL1
+INSL6
+PPAPDC2
+CNOT2
+AK3
+ERMP1
+AVPR1A
+NOTUM
+KIAA2026
+CD274
+RANBP6
+KIAA1432
+MLANA
+MON2
+RASL11B
+CCND2
+SCFD2
+INSL4
+BNIP3
+GLDC
+ATAD1
+EPHA3
+KCNV2
+MGMT
+STAC3
+SNAPC3
+DUX4
+HELB
+JAK2
+GLIS3
+FRG2B
+LRRC66
+LRRC27
+KDM4C
+CAND1
+USP15
+DCUN1D4
+SGCB
+CDC37L1
+BNC2
+PPP2R2D
+SRGAP1
+LMO7
+FMOD
+TTC39B
+FAM19A2
+FREM1
+ZDHHC21
+KLRC3
+C10orf92
+SUMF2
+STK32C
+C10orf91
+C9orf123
+SPATA18
+C12orf61
+PDCD1LG2
+RFX3
+USP46
+KIAA0020
+NFIB
+TDRD3
+C9orf68
+PWWP2B
+CNTLN
+RLN2
+SH3GL2
+IL33
+JAKMIP3
+MPDZ
+C10orf93
+RNLS
+KCNMB4
+INPP5A
+ACER2
+VLDLR
+SLC1A1
+DPYSL4
+CLOCK
+CER1
+SMARCA2
+TMEM5
+DST
+PHKG1
+CHCHD2
+UHRF2
+CHIT1
+IRAK3
+MYO3A
+CELSR1
+PRAP1
+C22orf9
+ZNF511
+GAD2
+PANX2
+ADAMTSL1
+RIBC2
+NCRNA00168
+GTSE1
+TSPO
+KIAA1644
+PIP4K2A
+SLC12A6
+GALNT8
+LPHN3
+CALY
+MDM1
+TMEM19
+DYRK4
+RAPGEF3
+C12orf66
+SMC1B
+ZBED4
+C22orf40
+BIK
+PARVG
+ARID2
+PKDREJ
+MSRB3
+TMEM81
+TAF1
+CRELD2
+OR6C74
+MCAT
+CDKN2C
+DACH1
+KCNQ1
+EDNRB
+SLC6A12
+RAD51AP1
+TSPAN9
+A2BP1
+DENND4C
+RP3-474I12.5
+MIOX
+SBF1
+ENO1
+DIAPH3
+CCR6
+UCHL3
+DSTYK
+GRAMD4
+PARP11
+TBC1D4
+RPAP3
+BTG2
+NUP50
+HDAC10
+RPS6
+WDR27
+CACNA1C
+PHF21B
+PIBF1
+BRD1
+RBBP5
+EFCAB4B
+NMU
+IL26
+TTC38
+PNPLA5
+ZFC3H1
+CERK
+PNPLA3
+WIF1
+NDUFA9
+SLC2A5
+LDOC1L
+ATAD2B
+NTF3
+TBK1
+SLFN11
+PHACTR3
+NDFIP2
+SLAIN1
+FGF6
+PITRM1
+RASSF4
+LARP4B
+HAUS6
+KLF5
+DOCK5
+DIP2C
+PFKP
+SLITRK1
+TUBGCP2
+UPK3A
+DMRT2
+C12orf4
+C12orf56
+UNC93A
+KCNA1
+ARHGAP8
+RRAGA
+C6orf124
+RERE
+RAB21
+PIM1
+PCDH9
+HSPA1A
+CTNNA3
+DMRT3
+PIM3
+TTLL2
+PHF10
+GTSF1
+HDAC7
+APBB1IP
+RNASET2
+C13orf37
+AKR1E2
+SLITRK5
+KLF12
+PTPRR
+IFNG
+GTPBP4
+FGF23
+PRMT8
+TYMP
+SPRY2
+MAPK8IP2
+SFT2D1
+LLPH
+C13orf34
+PLIN2
+DYRK2
+MAPK12
+KLHDC7B
+WDR37
+SLITRK6
+KCTD12
+ADM2
+MLC1
+PDCL2
+OR10A7
+PDCD2
+XPOT
+C6orf70
+TBC1D22A
+T
+EXOC1
+AKR1C3
+TCTE3
+SAPS2
+VDR
+LARP4
+NCKAP1L
+FAM116B
+AKR1C1
+CNTN2
+NDUFA4L2
+AKR1C4
+BCL11A
+KLHL1
+SCEL
+ADORA1
+SLC45A1
+SLC2A7
+DMRT1
+SPAG6
+MYCBP2
+C12orf5
+FAM118A
+A2M
+FBXL3
+OMG
+PLXNB2
+PSMB1
+RAB11FIP4
+RBM26
+FAM154A
+ATXN10
+PCDH17
+GNS
+TRABD
+FBLN1
+ARSA
+CLN5
+SLC48A1
+PARVB
+KLF6
+PAPSS2
+COMMD6
+TBC1D15
+DACT2
+PTPRB
+CHI3L1
+CDC123
+CHKB
+BBS10
+TBP
+C12orf64
+GPR157
+AKR1CL1
+EVI2B
+DNAJC1
+MYBPH
+KCNA5
+FGFR1OP
+THAP2
+ADAMTS20
+IDI2
+RASSF3
+MPPED1
+TMBIM4
+ALG12
+RPS6KA2
+MOV10L1
+FAM120B
+CPT1B
+THOC4
+ADARB2
+ODF3B
+C10orf10
+PRR18
+RNF219
+SLFN13
+ZNF479
+IL17REL
+LMF2
+TTLL8
+PDE10A
+C22orf26
+TTLL12
+SLFN12
+TRMU
+ADAM8
+C10orf125
+AKR1C2
+NCAM1
+COMMD3
+IDI1
+ZMYND11
+FAF1
+CA6
+TUBGCP6
+TCP10
+C6orf120
+THBS2
+PPARA
+P11
+FAM19A5
+PRR5
+IL22
+SULT4A1
+DIS3
+MAPK11
+ST7
+DLL1
+BRP44L
+BMI1
+CTRB1
+AKAP3
+SCUBE1
+GPR31
+PTPRZ1
+SAMM50
+WNT7B
+SCO2
+LEMD3
+POU4F1
+NCAPH2
+EFCAB6
+KCNA6
+RP3-402G11.5
+RABL2B
+PCDH20
+LOC553158

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/network.sif	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,152 @@
+CBL	PP	PIK3R1
+ADAM12	PP	PIK3R1
+CBL	PP	PTPN11
+PIK3R1	PP	PTPN11
+CBL	PP	KIT
+PIK3R1	PP	KIT
+PTPN11	PP	KIT
+KIT	PP	MPDZ
+CBL	PP	KDR
+PIK3R1	STATE_CHANGE	KDR
+PTPN11	PP	KDR
+TBP	PP	RB1
+PIK3R1	PP	RB1
+TBP	PP	TAF1
+RB1	PP	TAF1
+PIK3R1	PP	ERBB2
+PTPN11	PP	ERBB2
+CBL	PP	SPRY2
+PTPN11	PP	SPRY2
+CBL	PP	FRS2
+PIK3R1	STATE_CHANGE	FRS2
+PTPN11	PP	FRS2
+KDR	PP	FRS2
+RB1	PP	CDK6
+CDK6	PP	CDKN2A
+PIK3R1	PP	TEK
+PTPN11	PP	TEK
+PIK3R1	PP	GAB1
+PTPN11	PP	GAB1
+KIT	STATE_CHANGE	GAB1
+KDR	STATE_CHANGE	GAB1
+FRS2	PP	GAB1
+CBL	PP	PDGFRA
+PIK3R1	PP	PDGFRA
+PTPN11	PP	PDGFRA
+CBL	STATE_CHANGE	IFNG
+PTPN11	STATE_CHANGE	IFNG
+PDGFRA	INTERACTS_WITH	IFNG
+TBP	PP	TP53
+TP53	PP	HSPA1A
+PIK3R1	IN_SAME_COMPONENT	VLDLR
+CBL	CO_CONTROL_INDEPENDENT_SIMILAR	DOCK1
+PIK3R1	CO_CONTROL_INDEPENDENT_SIMILAR	DOCK1
+RB1	PP	RBBP5
+TBP	IN_SAME_COMPONENT	SNAPC3
+RB1	PP	SNAPC3
+RB1	PP	MDM4
+TP53	PP	MDM4
+TBP	PP	MDM2
+RB1	PP	MDM2
+TAF1	PP	MDM2
+CDKN2A	PP	MDM2
+TP53	PP	MDM2
+MDM4	PP	MDM2
+CBL	PP	EGFR
+PIK3R1	PP	EGFR
+PTPN11	PP	EGFR
+ERBB2	PP	EGFR
+GAB1	PP	EGFR
+IFNG	CO_CONTROL_INDEPENDENT_ANTI	EGFR
+CBL	STATE_CHANGE	JAK2
+PIK3R1	PP	JAK2
+PTPN11	PP	JAK2
+KIT	PP	JAK2
+ERBB2	PP	JAK2
+GAB1	STATE_CHANGE	JAK2
+IFNG	IN_SAME_COMPONENT	JAK2
+EGFR	PP	JAK2
+CBL	PP	CRK
+PIK3R1	PP	CRK
+KIT	PP	CRK
+KDR	PP	CRK
+FRS2	PP	CRK
+TEK	STATE_CHANGE	CRK
+GAB1	PP	CRK
+PDGFRA	PP	CRK
+DOCK1	PP	CRK
+EGFR	PP	CRK
+TP53	PP	KLF6
+KCNA5	PP	PTPRE
+PTPRD	PP	PTPRE
+ERBB2	PP	PIK3C2B
+EGFR	PP	PIK3C2B
+TEK	PP	PTPRB
+PIK3R1	CO_CONTROL_INDEPENDENT_ANTI	PTEN
+GAB1	CO_CONTROL_INDEPENDENT_SIMILAR	PTEN
+TP53	PP	PTEN
+CBL	IN_SAME_COMPONENT	SH3GL2
+EGFR	IN_SAME_COMPONENT	SH3GL2
+CBL	STATE_CHANGE	FGF23
+CDK6	PP	CDKN2C
+CDKN2A	PP	CDKN2C
+TP53	PP	CDKN2C
+CNTN2	IN_SAME_COMPONENT	NCAM1
+RB1	PP	CDK4
+CDK6	IN_SAME_COMPONENT	CDK4
+CDKN2A	PP	CDK4
+CDKN2C	PP	CDK4
+NUP50	STATE_CHANGE	THOC4
+PIK3R1	STATE_CHANGE	MAPK11
+KDR	STATE_CHANGE	MAPK11
+NUP50	IN_SAME_COMPONENT	NUP107
+THOC4	STATE_CHANGE	NUP107
+DCTN2	IN_SAME_COMPONENT	TUBGCP2
+PIK3R1	PP	IFNAR1
+PTPN11	PP	IFNAR1
+IFNW1	PP	IFNAR1
+IFNA2	PP	IFNAR1
+IFNB1	PP	IFNAR1
+IFNG	METABOLIC_CATALYSIS	IFNAR1
+PTPN11	METABOLIC_CATALYSIS	A2M
+RB1	PP	BNC2
+TP53	PP	EPHA3
+CRK	PP	EPHA3
+PIM1	PP	EPHA3
+RB1	PP	CCND2
+CDK6	PP	CCND2
+CDK4	PP	CCND2
+CDK4	PP	CDKN2B
+PPARA	PP	STAC3
+IFNAR1	PP	IFNA1
+CBL	CO_CONTROL_INDEPENDENT_SIMILAR	PIK3CA
+PIK3R1	PP	PIK3CA
+PTPN11	IN_SAME_COMPONENT	PIK3CA
+KDR	STATE_CHANGE	PIK3CA
+FRS2	STATE_CHANGE	PIK3CA
+TEK	STATE_CHANGE	PIK3CA
+GAB1	IN_SAME_COMPONENT	PIK3CA
+VLDLR	IN_SAME_COMPONENT	PIK3CA
+DOCK1	CO_CONTROL_INDEPENDENT_SIMILAR	PIK3CA
+EGFR	IN_SAME_COMPONENT	PIK3CA
+JAK2	CO_CONTROL_INDEPENDENT_SIMILAR	PIK3CA
+CRK	CO_CONTROL_INDEPENDENT_SIMILAR	PIK3CA
+PTEN	CO_CONTROL_INDEPENDENT_ANTI	PIK3CA
+MAPK11	STATE_CHANGE	PIK3CA
+A2M	PP	LYZ
+CBL	IN_SAME_COMPONENT	HLA-DRA
+PTPN11	STATE_CHANGE	HLA-DRA
+IFNG	METABOLIC_CATALYSIS	HLA-DRA
+JAK2	CO_CONTROL_INDEPENDENT_SIMILAR	HLA-DRA
+CRK	PP	AVIL
+CCT2	IN_SAME_COMPONENT	CCT6A
+DCTN2	IN_SAME_COMPONENT	FGFR1OP
+TUBGCP2	IN_SAME_COMPONENT	FGFR1OP
+NUP50	STATE_CHANGE	SNRPE
+THOC4	IN_SAME_COMPONENT	SNRPE
+NUP107	STATE_CHANGE	SNRPE
+DCTN2	IN_SAME_COMPONENT	TUBGCP6
+TUBGCP2	IN_SAME_COMPONENT	TUBGCP6
+FGFR1OP	IN_SAME_COMPONENT	TUBGCP6
+PIK3R1	IN_SAME_COMPONENT	AGAP2
+PIK3CA	IN_SAME_COMPONENT	AGAP2

Binary file test-data/network_plot.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nodeType.txt	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,280 @@
+CDKN2B	candidate
+EGFR	candidate
+CDKN2A	candidate
+MTAP	candidate
+PTEN	candidate
+TP53	candidate
+SEC61G	candidate
+IFNA1	candidate
+ELAVL2	candidate
+IFNA8	candidate
+IFNA2	candidate
+KLHL9	candidate
+IFNA5	candidate
+CYP27B1	candidate
+IFNW1	candidate
+CDK4	candidate
+AGAP2	candidate
+METTL1	candidate
+AVIL	candidate
+MLLT3	candidate
+IFNB1	candidate
+CTDSP2	candidate
+HLA-DRA	candidate
+NF1	candidate
+XRCC6BP1	candidate
+MDM2	candidate
+OS9	candidate
+PDGFRA	candidate
+CHIC2	candidate
+NME7	candidate
+RB1	candidate
+C9orf82	candidate
+MARS	candidate
+DTX3	candidate
+PLAA	candidate
+CPM	candidate
+MBD6	candidate
+KIT	candidate
+TEK	candidate
+DDIT3	candidate
+KIF5A	candidate
+MOBKL2B	candidate
+NUP107	candidate
+DCTN2	candidate
+PTPRD	candidate
+PAOX	candidate
+ERBB2	candidate
+PIK3R1	candidate
+GLI1	candidate
+CPSF6	candidate
+ARHGAP9	candidate
+PIK3CA	candidate
+FRS2	candidate
+LYZ	candidate
+INHBC	candidate
+INHBE	candidate
+YEATS4	candidate
+LNX1	candidate
+MDM4	candidate
+ECHS1	candidate
+KDR	candidate
+KISS1	candidate
+RAB3IP	candidate
+CCT2	candidate
+ETNK2	candidate
+REN	candidate
+PPP1R15B	candidate
+SOX13	candidate
+PIK3C2B	candidate
+HMGA2	candidate
+TYRP1	candidate
+TPD52L3	candidate
+DOCK1	candidate
+LAX1	candidate
+PRELP	candidate
+SNRPE	candidate
+CCT6A	candidate
+GRIP1	candidate
+RAP1B	candidate
+ATP2B4	candidate
+PTPRE	candidate
+ZC3H11A	candidate
+OPTC	candidate
+ADAM12	candidate
+FIP1L1	candidate
+NFASC	candidate
+MKI67	candidate
+R3HDM2	candidate
+PSIP1	candidate
+CNOT2	candidate
+AVPR1A	candidate
+KIAA2026	candidate
+CD274	candidate
+RASL11B	candidate
+CCND2	candidate
+BNIP3	candidate
+GLDC	candidate
+EPHA3	candidate
+KCNV2	candidate
+MGMT	candidate
+STAC3	candidate
+SNAPC3	candidate
+HELB	candidate
+JAK2	candidate
+GLIS3	candidate
+CAND1	candidate
+SGCB	candidate
+CDC37L1	candidate
+BNC2	candidate
+PPP2R2D	candidate
+SRGAP1	candidate
+LMO7	candidate
+FMOD	candidate
+ZDHHC21	candidate
+KLRC3	candidate
+SUMF2	candidate
+RFX3	candidate
+KIAA0020	candidate
+NFIB	candidate
+RLN2	candidate
+SH3GL2	candidate
+IL33	candidate
+MPDZ	candidate
+INPP5A	candidate
+VLDLR	candidate
+SLC1A1	candidate
+DPYSL4	candidate
+CLOCK	candidate
+CER1	candidate
+SMARCA2	candidate
+DST	candidate
+PHKG1	candidate
+UHRF2	candidate
+IRAK3	candidate
+MYO3A	candidate
+CELSR1	candidate
+C22orf9	candidate
+GAD2	candidate
+PANX2	candidate
+RIBC2	candidate
+TSPO	candidate
+SLC12A6	candidate
+TMEM19	candidate
+RAPGEF3	candidate
+SMC1B	candidate
+BIK	candidate
+PARVG	candidate
+ARID2	candidate
+TAF1	candidate
+CRELD2	candidate
+CDKN2C	candidate
+DACH1	candidate
+KCNQ1	candidate
+EDNRB	candidate
+SLC6A12	candidate
+RAD51AP1	candidate
+SBF1	candidate
+ENO1	candidate
+DIAPH3	candidate
+CCR6	candidate
+UCHL3	candidate
+PARP11	candidate
+TBC1D4	candidate
+BTG2	candidate
+NUP50	candidate
+HDAC10	candidate
+RPS6	candidate
+CACNA1C	candidate
+BRD1	candidate
+RBBP5	candidate
+EFCAB4B	candidate
+NMU	candidate
+WIF1	candidate
+NDUFA9	candidate
+NTF3	candidate
+TBK1	candidate
+PHACTR3	candidate
+NDFIP2	candidate
+FGF6	candidate
+RASSF4	candidate
+KLF5	candidate
+PFKP	candidate
+TUBGCP2	candidate
+UPK3A	candidate
+KCNA1	candidate
+ARHGAP8	candidate
+RRAGA	candidate
+RERE	candidate
+PIM1	candidate
+HSPA1A	candidate
+CTNNA3	candidate
+PIM3	candidate
+PHF10	candidate
+HDAC7	candidate
+APBB1IP	candidate
+KLF12	candidate
+PTPRR	candidate
+IFNG	candidate
+GTPBP4	candidate
+FGF23	candidate
+PRMT8	candidate
+TYMP	candidate
+SPRY2	candidate
+MAPK8IP2	candidate
+C13orf34	candidate
+DYRK2	candidate
+MAPK12	candidate
+WDR37	candidate
+MLC1	candidate
+PDCL2	candidate
+PDCD2	candidate
+XPOT	candidate
+EXOC1	candidate
+AKR1C3	candidate
+SAPS2	candidate
+VDR	candidate
+CNTN2	candidate
+NDUFA4L2	candidate
+AKR1C4	candidate
+BCL11A	candidate
+KLHL1	candidate
+SCEL	candidate
+ADORA1	candidate
+SPAG6	candidate
+MYCBP2	candidate
+A2M	candidate
+OMG	candidate
+PLXNB2	candidate
+PSMB1	candidate
+RAB11FIP4	candidate
+ATXN10	candidate
+PCDH17	candidate
+FBLN1	candidate
+ARSA	candidate
+PARVB	candidate
+KLF6	candidate
+COMMD6	candidate
+PTPRB	candidate
+TBP	candidate
+DNAJC1	candidate
+MYBPH	candidate
+KCNA5	candidate
+FGFR1OP	candidate
+RPS6KA2	candidate
+FAM120B	candidate
+CPT1B	candidate
+THOC4	candidate
+C10orf10	candidate
+PDE10A	candidate
+NCAM1	candidate
+COMMD3	candidate
+ZMYND11	candidate
+FAF1	candidate
+CA6	candidate
+TUBGCP6	candidate
+TCP10	candidate
+THBS2	candidate
+PPARA	candidate
+IL22	candidate
+DIS3	candidate
+MAPK11	candidate
+ST7	candidate
+DLL1	candidate
+BRP44L	candidate
+BMI1	candidate
+CTRB1	candidate
+AKAP3	candidate
+SCUBE1	candidate
+PTPRZ1	candidate
+SAMM50	candidate
+WNT7B	candidate
+LEMD3	candidate
+POU4F1	candidate
+RABL2B	candidate
+CRK	linker
+IFNAR1	linker
+CBL	linker
+GAB1	linker
+CDK6	linker
+PTPN11	linker

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_conf.xml	Wed Aug 24 08:27:40 2022 +0000
@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<tool_dependency>
+<package name="R" version="4.0.0">
+<repository name="package_r_4_0_0" owner="iuc" />
+</package>
+<package name="netboxr" version="1.6.0">
+<install version="1.0">
+<actions>
+<action type="setup_r_environment">
+<repository name="package_r_3_2_1" owner="iuc">
+<package name="R" version="3.2.1" />
+</repository>
+<package name = "igraph">
+https://cran.r-project.org/src/contrib/igraph_1.3.0.tar.gz
+</package>
+<package name = "netboxr">
+https://www.bioconductor.org/packages/release/bioc/src/contrib/netboxr_1.6.
+0.tar.gz
+</package>
+</action>
+</actions>
+</install>
+</package>
+</tool_dependency>