# HG changeset patch
# User testtool
# Date 1486376276 18000
# Node ID 5e1d49abfc99dd81ec2205c2ebb096370cfc6db4
# Parent 3eb1073638d7c26d8ac8d463d1e4c49dccb12205
Uploaded
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/.Rhistory
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/.Rhistory Mon Feb 06 05:17:56 2017 -0500
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+GSMTable <- ("test-data/GSMTable.txt")
+write.table(samples, GSMTable, row.names = FALSE, sep = "\t")
+?write.table
+GSE <- "GSE51547"
+search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
+require("rentrez", quietly = TRUE)
+search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
+rec2 <- entrez_summary(db = "gds",
+id = search1$ids,
+version = "2.0")
+extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
+samples <- extract$samples
+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)
+write.table(samples, file=GSMTable.txt, row.names = FALSE, sep = "\t",quote = FALSE)
+write.table(samples, file="GSMTable.txt", row.names = FALSE, sep = "\t",quote = FALSE)
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/._.DS_Store
Binary file getGSMdata/._.DS_Store has changed
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/getGSMdata.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/getGSMdata.R Mon Feb 06 05:17:56 2017 -0500
@@ -0,0 +1,20 @@
+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",
+ id = search1$ids,
+ version = "2.0")
+
+extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
+
+samples <- extract$samples
+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)
+
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/getGSMdata.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/getGSMdata.xml Mon Feb 06 05:17:56 2017 -0500
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+ Rscript $__tool_directory__/getGSMdata.R "$GSE" "$GSMTable"
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+**Description**
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+GEO
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diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/test-data/._.DS_Store
Binary file getGSMdata/test-data/._.DS_Store has changed
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/test-data/GSMTable.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/test-data/GSMTable.txt Mon Feb 06 05:17:56 2017 -0500
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+ID Phenotype
+GSM1247797 genomic DNA from Sample HEM.d_gDNA_2
+GSM1247734 genomic DNA from Sample MM37
+GSM1247757 genomic DNA from Sample MM10
+GSM1247794 genomic DNA from Sample HEM.m_gDNA_1
+GSM1247771 genomic DNA from Sample MM52
+GSM1247765 genomic DNA from Sample MM93
+GSM1247768 genomic DNA from Sample MM08
+GSM1247752 genomic DNA from Sample MM17
+GSM1247749 genomic DNA from Sample MM25
+GSM1247789 genomic DNA from Sample HT144
+GSM1247792 genomic DNA from Sample HEM.l_gDNA_1
+GSM1247774 genomic DNA from Sample MM57
+GSM1247751 genomic DNA from Sample MM19
+GSM1247800 genomic DNA from Sample HDF.a_gDNA_1
+GSM1247777 genomic DNA from Sample MM78
+GSM1247760 genomic DNA from Sample MM80
+GSM1247754 genomic DNA from Sample MM01
+GSM1247763 genomic DNA from Sample MM68
+GSM1247786 genomic DNA from Sample MM383
+GSM1247784 genomic DNA from Sample SKMEL5
+GSM1247787 genomic DNA from Sample SKMEL3
+GSM1247747 genomic DNA from Sample MM71
+GSM1247741 genomic DNA from Sample MM60
+GSM1247778 genomic DNA from Sample MM50
+GSM1247744 genomic DNA from Sample MM09
+GSM1247755 genomic DNA from Sample MM58
+GSM1247781 genomic DNA from Sample MM53
+GSM1247758 genomic DNA from Sample MM94
+GSM1247742 genomic DNA from Sample MM43
+GSM1247795 genomic DNA from Sample HEM.m_gDNA_2
+GSM1247779 genomic DNA from Sample MM16
+GSM1247802 genomic DNA from Sample Blood
+GSM1247736 genomic DNA from Sample MM03
+GSM1247739 genomic DNA from Sample MM38
+GSM1247776 genomic DNA from Sample MM95
+GSM1247733 genomic DNA from Sample MM44
+GSM1247770 genomic DNA from Sample MM18
+GSM1247750 genomic DNA from Sample MM11
+GSM1247773 genomic DNA from Sample MM21
+GSM1247745 genomic DNA from Sample MM47
+GSM1247748 genomic DNA from Sample MM61
+GSM1247788 genomic DNA from Sample A7
+GSM1247791 genomic DNA from Sample CHL1
+GSM1247785 genomic DNA from Sample WM852
+GSM1247780 genomic DNA from Sample MM40
+GSM1247783 genomic DNA from Sample A2058
+GSM1247766 genomic DNA from Sample MM24
+GSM1247761 genomic DNA from Sample MM42
+GSM1247746 genomic DNA from Sample MM22
+GSM1247769 genomic DNA from Sample MM27
+GSM1247764 genomic DNA from Sample MM51
+GSM1247772 genomic DNA from Sample MM31
+GSM1247767 genomic DNA from Sample MM34
+GSM1247738 genomic DNA from Sample MM13
+GSM1247735 genomic DNA from Sample MM04
+GSM1247743 genomic DNA from Sample MM20
+GSM1247737 genomic DNA from Sample MM41
+GSM1247799 genomic DNA from Sample HEK.a_gDNA_2
+GSM1247740 genomic DNA from Sample MM81
+GSM1247793 genomic DNA from Sample HEM.l_gDNA_2
+GSM1247796 genomic DNA from Sample HEM.d_gDNA_1
+GSM1247790 genomic DNA from Sample WM239A
+GSM1247775 genomic DNA from Sample MM02
+GSM1247798 genomic DNA from Sample HEK.a_gDNA_1
+GSM1247801 genomic DNA from Sample HDF.a_gDNA_2
+GSM1247756 genomic DNA from Sample MM82
+GSM1247759 genomic DNA from Sample MM14
+GSM1247782 genomic DNA from Sample MM86
+GSM1247762 genomic DNA from Sample MM45
+GSM1247753 genomic DNA from Sample MM83
diff -r 3eb1073638d7 -r 5e1d49abfc99 getGSMdata/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getGSMdata/tool_dependencies.xml Mon Feb 06 05:17:56 2017 -0500
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