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Changeset 26:ac5415190777 (2017-02-15)

Previous changeset 25:9098bc982b6a (2017-02-06) Next changeset 27:fd7bfd438a65 (2017-02-15)

Commit message:
Uploaded

modified:
getGSMdata/getGSMdata.R
getGSMdata/getGSMdata.xml

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/.Rhistory
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/.Rhistory Wed Feb 15 10:21:18 2017 -0500

@@ -0,0 +1,7 @@
+??options
+options(warn = -1)
++options("download.file.method"="wget")
+options("download.file.method"="wget")
+options(warn = -1,"download.file.method"="wget")
+??getPlatform
+??getPlatform

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/._.DS_Store

Binary file getGSMdata/geo_data-05050b50d4f8/GEO/._.DS_Store has changed

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.R Wed Feb 15 10:21:18 2017 -0500

[

@@ -0,0 +1,54 @@
+require("BiocGenerics", quietly = TRUE)
+require("data.table", quietly = TRUE)
+require("GEOquery", quietly = TRUE)
+require("rtracklayer", quietly = TRUE)
+require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
+
+options("download.file.method.GEOquery"="wget")
+options(warn = -1)
+
+args <- commandArgs(trailingOnly = TRUE)
+GSMTable = args[1]
+MetaTable = args[2]
+IlmnTable = args[3]
+gmTable = args[4]
+
+TAB = fread(GSMTable)
+
+if (is.null(TAB)) {
+  stop("Must specify input files")
+} else {
+  GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
+  IlmnIDTable <- Table(GEODataTable)
+  MetaData <- data.frame(Meta(GEODataTable))
+
+
+  write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
+}
+
+hm450.hg19 <- getPlatform()
+
+IlmnInfo <-
+  data.table(
+    IlmnID = names(hm450.hg19),
+    CHR = as.data.frame(hm450.hg19@seqnames)$value,
+    BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
+  )
+
+
+write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
+
+
+if (length(TAB$ID) > 1) {
+  mysamples <-
+    do.call("data.table", lapply(TAB$ID[-1], function(x)
+      Table(getGEO(x, getGPL = FALSE))[, -1]))
+
+  gmSet <- data.table(IlmnIDTable[, -1], mysamples)
+
+} else {
+  gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
+}
+
+
+write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/getGEO.xml Wed Feb 15 10:21:18 2017 -0500

[

@@ -0,0 +1,39 @@
+<tool id="GEO" name="getGEO" version="1.16.2">
+  <requirements>
+         <requirement type="package" version="3.2.1">R</requirement>
+     </requirements>
+<stdio>
+    <exit_code range="1:" />
+ </stdio>
+  <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
+  <inputs>
+    <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="csv" name="MetaTable" label="MetaData.csv"/>
+    <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
+    <data format="csv" name="gmTable" label="gmSet.csv"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="test">
+      <element name="test-data">
+          <collection type="data">
+              <element name="GSMTable" value="test-data/input.csv" />
+          </collection>
+        </element>
+        </param>
+        <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
+        <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
+        <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
+        </test>
+    </tests>
+  <help>
+**Description**
+</help>
+<citations>
+GEO
+</citations>
+</tool>

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._.DS_Store

Binary file getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._.DS_Store has changed

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._input.csv

Binary file getGSMdata/geo_data-05050b50d4f8/GEO/test-data/._input.csv has changed

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/IlmnTable.csv Wed Feb 15 10:21:18 2017 -0500

b'@@ -0,0 +1,485578 @@\n+"IlmnID","CHR","BP"\n+"cg04913815","chr16",60438\n+"cg01686861","chr16",60700\n+"cg05558259","chr16",61037\n+"cg26978960","chr16",62412\n+"cg03792876","chr16",73195\n+"cg09699726","chr16",91554\n+"cg07549526","chr16",91663\n+"cg02851049","chr16",101212\n+"cg11876012","chr16",101638\n+"cg14820573","chr16",102073\n+"cg14747225","chr16",102976\n+"cg16670573","chr16",103375\n+"cg09499248","chr16",103483\n+"cg00762468","chr16",103568\n+"cg05055400","chr16",103592\n+"cg09969830","chr16",103646\n+"cg00958578","chr16",103715\n+"cg11653271","chr16",103723\n+"cg01188584","chr16",103853\n+"cg03974483","chr16",103985\n+"cg08718695","chr16",104135\n+"cg01062126","chr16",104539\n+"cg00992207","chr16",107404\n+"cg00914902","chr16",108066\n+"cg27248189","chr16",110257\n+"cg06194960","chr16",111362\n+"cg07608562","chr16",111610\n+"cg20220196","chr16",111753\n+"cg09201525","chr16",111823\n+"cg03333116","chr16",112396\n+"cg04721268","chr16",112802\n+"cg01403103","chr16",112804\n+"cg01502407","chr16",113107\n+"cg04322210","chr16",114987\n+"cg26933686","chr16",115957\n+"cg00179196","chr16",117934\n+"cg07405083","chr16",119384\n+"cg06934747","chr16",120902\n+"cg00525011","chr16",122031\n+"cg03948744","chr16",122515\n+"cg00079891","chr16",122716\n+"cg09113560","chr16",122764\n+"cg04995976","chr16",123198\n+"cg06230303","chr16",123353\n+"cg01262217","chr16",123363\n+"cg04260507","chr16",123553\n+"cg17199481","chr16",123676\n+"cg01422009","chr16",125896\n+"cg03462322","chr16",126397\n+"cg16383109","chr16",126403\n+"cg03110993","chr16",126800\n+"cg03492469","chr16",126855\n+"cg05501742","chr16",126844\n+"cg16003913","chr16",127072\n+"cg04257263","chr16",127088\n+"cg15017278","chr16",127401\n+"cg02729269","chr16",127772\n+"cg07395378","chr16",127904\n+"cg01609171","chr16",127949\n+"cg10009236","chr16",127968\n+"cg05397937","chr16",128446\n+"cg15768556","chr16",128630\n+"cg05394456","chr16",129230\n+"cg10143220","chr16",129454\n+"cg00935108","chr16",129562\n+"cg02949481","chr16",131514\n+"cg05791870","chr16",136656\n+"cg07484220","chr16",136761\n+"cg07405534","chr16",139691\n+"cg26925590","chr16",139704\n+"cg07371452","chr16",139732\n+"cg04807152","chr16",147558\n+"cg16730559","chr16",157323\n+"cg02353723","chr16",163133\n+"cg09430181","chr16",175615\n+"cg02028423","chr16",185078\n+"cg01527023","chr16",188138\n+"cg00928894","chr16",188221\n+"cg02369618","chr16",188603\n+"cg09580244","chr16",188684\n+"cg02783232","chr16",188741\n+"cg08524197","chr16",188802\n+"cg02855078","chr16",188815\n+"cg08969593","chr16",188855\n+"cg06171619","chr16",188884\n+"cg00389577","chr16",189052\n+"cg24399405","chr16",189577\n+"cg27009501","chr16",192791\n+"cg06929449","chr16",199366\n+"cg10317591","chr16",199773\n+"cg08957279","chr16",202263\n+"cg10164238","chr16",202320\n+"cg21960110","chr16",202434\n+"cg01839639","chr16",202542\n+"cg25425005","chr16",202905\n+"cg07263153","chr16",202926\n+"cg08400316","chr16",204221\n+"cg02279719","chr16",204474\n+"cg06459847","chr16",204601\n+"cg07498624","chr16",204783\n+"cg01923692","chr16",204949\n+"cg06031493","chr16",210205\n+"cg05390075","chr16",210528\n+"cg07067950","chr16",212416\n+"cg07893512","chr16",214728\n+"cg05057452","chr16",214922\n+"cg25322095","chr16",215002\n+"cg07466193","chr16",215362\n+"cg01744019","chr16",215545\n+"cg09812623","chr16",215733\n+"cg08393070","chr16",215743\n+"cg01558909","chr16",215797\n+"cg26540367","chr16",215816\n+"cg06319822","chr16",215912\n+"cg26976732","chr16",216052\n+"cg21664030","chr16",216244\n+"cg04141813","chr16",216450\n+"cg03309232","chr16",216626\n+"cg12251336","chr16",216719\n+"cg09523819","chr16",216709\n+"cg04321267","chr16",219107\n+"cg04377849","chr16",221536\n+"cg26637826","chr16",221542\n+"cg04938149","chr16",221811\n+"cg15597257","chr16",222837\n+"cg00697413","chr16",222858\n+"cg16263182","chr16",223351\n+"cg05956679","chr16",223360\n+"cg01319583","chr16",224880\n+"cg01704105","chr16",225666\n+"cg08923033","chr16",226002\n+"cg06235582","chr16",226668\n+"cg27452732","chr16",226670\n+"cg10647513","chr16",227155\n+"cg09434193","chr16",227185\n+"cg08923355","chr16",227469\n+"cg05933901","chr16'..b'16637094\n+"cg09804407","chrY",16733251\n+"cg08816194","chrY",16733442\n+"cg07795413","chrY",16733930\n+"cg01073572","chrY",16924422\n+"cg01498999","chrY",16939335\n+"cg03278611","chrY",16941543\n+"cg09300505","chrY",16942106\n+"cg05939513","chrY",16942232\n+"cg02340092","chrY",16945913\n+"cg25667057","chrY",17567474\n+"cg23834181","chrY",17567486\n+"cg03672679","chrY",17567897\n+"cg04792227","chrY",17568097\n+"cg00679624","chrY",17568445\n+"cg20764275","chrY",17568616\n+"cg14742615","chrY",17569363\n+"cg01882666","chrY",17571429\n+"cg03905640","chrY",19625260\n+"cg01209756","chrY",19671414\n+"cg17115812","chrY",19678480\n+"cg14151065","chrY",19678487\n+"cg25012987","chrY",19691491\n+"cg16292375","chrY",19691502\n+"cg16894943","chrY",20488221\n+"cg06060201","chrY",20488232\n+"cg04170994","chrY",20488245\n+"cg09408193","chrY",20501241\n+"cg10252249","chrY",20508275\n+"cg23308414","chrY",20508314\n+"cg26046487","chrY",20736099\n+"cg10646950","chrY",20748734\n+"cg00479827","chrY",21036938\n+"cg10691859","chrY",21041339\n+"cg15281205","chrY",21100424\n+"cg05230942","chrY",21155222\n+"cg13765957","chrY",21208573\n+"cg26251715","chrY",21236181\n+"cg03244189","chrY",21238424\n+"cg13845521","chrY",21238886\n+"cg10811597","chrY",21239219\n+"cg11816202","chrY",21239284\n+"cg00212031","chrY",21239300\n+"cg15345074","chrY",21239413\n+"cg11684211","chrY",21239559\n+"cg06628792","chrY",21240004\n+"cg00121626","chrY",21664248\n+"cg15027426","chrY",21664556\n+"cg00876332","chrY",21664717\n+"cg15794778","chrY",21664973\n+"cg09228985","chrY",21666030\n+"cg06065495","chrY",21666261\n+"cg03533500","chrY",21668372\n+"cg06231362","chrY",21726406\n+"cg25756647","chrY",21728575\n+"cg06502680","chrY",21728904\n+"cg20864678","chrY",21728989\n+"cg14492024","chrY",21729001\n+"cg05725925","chrY",21729010\n+"cg05621349","chrY",21729021\n+"cg10076560","chrY",21729144\n+"cg15682993","chrY",21729203\n+"cg07731488","chrY",21729314\n+"cg05672930","chrY",21729555\n+"cg17660627","chrY",21729665\n+"cg14931215","chrY",21867654\n+"cg00308367","chrY",21868484\n+"cg27509967","chrY",21877683\n+"cg15329860","chrY",21906636\n+"cg25815185","chrY",21906868\n+"cg27049643","chrY",21906893\n+"cg26517491","chrY",21906895\n+"cg15662272","chrY",21906974\n+"cg02522936","chrY",22680010\n+"cg10799208","chrY",22681388\n+"cg26928789","chrY",22682345\n+"cg09081202","chrY",22735272\n+"cg01988452","chrY",22736480\n+"cg13308744","chrY",22736536\n+"cg10172760","chrY",22736785\n+"cg10620659","chrY",22737343\n+"cg15422579","chrY",22737376\n+"cg15059553","chrY",22737505\n+"cg01644972","chrY",22737508\n+"cg02233190","chrY",22737591\n+"cg26983535","chrY",22737594\n+"cg11225091","chrY",22737615\n+"cg03750315","chrY",22737848\n+"cg02884332","chrY",22737946\n+"cg08715207","chrY",22737921\n+"cg08820785","chrY",22738029\n+"cg10593480","chrY",22738723\n+"cg00063477","chrY",22741795\n+"cg01900066","chrY",22754881\n+"cg07747963","chrY",22917039\n+"cg10841270","chrY",22917104\n+"cg01943289","chrY",22917296\n+"cg17741448","chrY",22917782\n+"cg02012379","chrY",22917846\n+"cg00676506","chrY",22917913\n+"cg06322277","chrY",22917937\n+"cg26058907","chrY",22917894\n+"cg02050847","chrY",22918038\n+"cg14029254","chrY",22918213\n+"cg02352633","chrY",23561638\n+"cg03416979","chrY",23566240\n+"cg05051262","chrY",23566524\n+"cg25427172","chrY",23566730\n+"cg10666546","chrY",23566863\n+"cg25640065","chrY",23569324\n+"cg16552926","chrY",23694843\n+"cg25918849","chrY",23753284\n+"cg11021362","chrY",23756676\n+"cg14467015","chrY",23757241\n+"cg15516537","chrY",24036834\n+"cg05999368","chrY",24044030\n+"cg15462332","chrY",24052484\n+"cg26497631","chrY",24331310\n+"cg06865724","chrY",24445690\n+"cg25914522","chrY",24452543\n+"cg13808036","chrY",24453658\n+"cg10267609","chrY",24453709\n+"cg00335297","chrY",24454479\n+"cg03827298","chrY",24454879\n+"cg26983430","chrY",24549675\n+"cg22051787","chrY",24549677\n+"cg01757887","chrY",25114762\n+"cg00061679","chrY",25314123\n+"cg03930849","chrY",26716241\n+"cg17939569","chrY",27009430\n+"cg13365400","chrY",27210334\n+"cg21106100","chrY",28555488\n+"cg08265308","chrY",28555502\n+"cg14273923","chrY",28555912\n'

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/MetaTable.csv Wed Feb 15 10:21:18 2017 -0500

@@ -0,0 +1,2 @@
+"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type"
+"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic"

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/gmTable.csv Wed Feb 15 10:21:18 2017 -0500

b'@@ -0,0 +1,485578 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diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/test-data/input.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/test-data/input.csv Wed Feb 15 10:21:18 2017 -0500

@@ -0,0 +1,4 @@
+ID,Phenotype
+GSM1247787,melanoma
+GSM1247784,melanoma
+GSM1247733,healthy

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/geo_data-05050b50d4f8/GEO/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/geo_data-05050b50d4f8/GEO/tool_dependencies.xml Wed Feb 15 10:21:18 2017 -0500

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diff -r 9098bc982b6a -r ac5415190777 getGSMdata/getGSMdata.R
--- a/getGSMdata/getGSMdata.R Mon Feb 06 10:31:24 2017 -0500
+++ b/getGSMdata/getGSMdata.R Wed Feb 15 10:21:18 2017 -0500

[

@@ -1,9 +1,12 @@
require("rentrez", quietly = TRUE)

args <- commandArgs(trailingOnly = TRUE)
+
GSE = args[1]
GSMTable = args[2]

+
+
search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)

rec2 <- entrez_summary(db = "gds",
@@ -16,5 +19,8 @@
colnames(samples)[which(names(samples) == "accession")] <- "ID"
colnames(samples)[which(names(samples) == "title")] <- "Phenotype"

-write.table(samples, GSMTable, row.names = FALSE, sep = "\t",quote = FALSE)
+samples$Phenotype<-gsub("\\s", "",samples$Phenotype)

+write.table(samples, GSMTable, row.names = FALSE,quote=FALSE,sep="\t")
+
+

diff -r 9098bc982b6a -r ac5415190777 getGSMdata/getGSMdata.xml
--- a/getGSMdata/getGSMdata.xml Mon Feb 06 10:31:24 2017 -0500
+++ b/getGSMdata/getGSMdata.xml Wed Feb 15 10:21:18 2017 -0500

@@ -13,7 +13,7 @@
      <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
   </inputs>
   <outputs>
-    <data format="txt" name="GSMTable" label="GSMTable.txt"/>
+    <data format="tab" name="GSMTable" label="GSMTable.tab"/>
   </outputs>
   <tests>
     <test>