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95
|
1 args <- commandArgs(trailingOnly = TRUE)
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2
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|
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3 imgt.dir = args[1]
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4 merged.file = args[2]
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|
99
|
5 gene = args[3]
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|
95
|
6
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7 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
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8
|
|
101
|
9 print(head(merged$best_match))
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10
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|
99
|
11 if(gene != "-"){
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12 merged = merged[grepl(gene, merged$best_match),]
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|
13 }
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|
|
14
|
|
97
|
15 merged = merged[!grepl("unmatched", merged$best_match),]
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|
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16
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|
95
|
17 for(f in list.files(imgt.dir, pattern="*.txt$")){
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18 print(paste("filtering", f))
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|
19 path = paste(imgt.dir, f, sep="")
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20 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
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21
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|
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22 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
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|
|
23
|
|
99
|
24 if(nrow(dat) > 0 & "FR1.IMGT" %in% colnames(dat)){
|
|
95
|
25 dat$FR1.IMGT = ""
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|
|
26 }
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|
|
27
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|
|
28 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
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|
|
29 }
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