Mercurial > repos > anmoljh > candidate_compound_select

annotate select_compound.R @ 1:3bd5537cc516 draft default tip

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planemo upload commit 6cabcd537575539c1428b3c5e1780c14a5f36b6e-dirty
author anmoljh
date Wed, 25 Oct 2017 04:39:07 -0400
parents 557baa97ed72
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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1 args <- commandArgs(T)
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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2 arg1 <- args[1] ## Reae Input prediction file
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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3 arg2 <- args[2] ## Less Than
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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4 arg3 <- args[3] ## Greater Than or equal too
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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5 arg4 <- args[4] ## Active / Inactive
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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6 arg5 <- args[5] ## define output file name
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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7 asd <- read.table(arg1,row.names=1,header=T)
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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8 if (arg4 == "Active") {
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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9 refined <- asd[asd[,1] >= as.numeric(arg3) & asd[,1] <= as.numeric(arg2),]
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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10 compound <- rownames(refined)
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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11 refined <- cbind(compound,refined)
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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12 } else if((arg4 == "Inactive") ){
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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13 #refined <- asd[asd[,1] <= as.numeric(arg2),]
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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14 refined <- asd[asd[,2] >= as.numeric(arg3) & asd[,2] <= as.numeric(arg2),]
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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15 compound <- rownames(refined)
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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16 refined <- cbind(compound,refined)}
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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17 ###write.table(dw,file=args3,row.names=FALSE,sep="\t")
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
anmoljh
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18 write.table(refined,file=arg5,row.names=FALSE,sep="\t")
557baa97ed72 planemo upload commit e713bcfa1b1690f9a21ad0bd796c2d385f646e66-dirty
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