Mercurial > repos > petr-novak > dante_ltr
diff clean_ltr.R @ 6:b91ca438a1cb draft
"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
| author | petr-novak |
|---|---|
| date | Thu, 19 May 2022 08:21:55 +0000 |
| parents | 93d35ae65e1b |
| children | c33d6583e548 |
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--- a/clean_ltr.R Mon May 16 07:50:41 2022 +0000 +++ b/clean_ltr.R Thu May 19 08:21:55 2022 +0000 @@ -177,10 +177,14 @@ gff_te <- gff_out[gff_out$type %in% "transposable_element"] gff_5ltr <- gff_out[gff_out$LTR %in% "5LTR"] gff_3ltr <- gff_out[gff_out$LTR %in% "3LTR"] + full_te <- getSeqNamed(s, gff_te) +names(full_te) <- paste0(gff_te$ID,":",names(full_te)) ltr5 <- getSeqNamed(s, gff_5ltr) +names(ltr5) <- paste0(gff_5ltr$Parent,":",names(ltr5)) ltr3 <- getSeqNamed(s, gff_3ltr) -inc <- gff_te$Rank != "DL" +names(ltr3) <- paste0(gff_3ltr$Parent,":",names(ltr3)) +inc <- gff_te$Rank != "DL" writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib_non_redundant.fasta")) writeXStringSet(full_te, paste0(opt$output, "_RM_lib_full_TE.fasta"))