Mercurial > repos > petr-novak > dante_ltr
comparison clean_ltr.R @ 6:b91ca438a1cb draft
"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
author | petr-novak |
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date | Thu, 19 May 2022 08:21:55 +0000 |
parents | 93d35ae65e1b |
children | c33d6583e548 |
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5:0c3111ab729b | 6:b91ca438a1cb |
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175 gff_out <- g[c1 | c2] | 175 gff_out <- g[c1 | c2] |
176 | 176 |
177 gff_te <- gff_out[gff_out$type %in% "transposable_element"] | 177 gff_te <- gff_out[gff_out$type %in% "transposable_element"] |
178 gff_5ltr <- gff_out[gff_out$LTR %in% "5LTR"] | 178 gff_5ltr <- gff_out[gff_out$LTR %in% "5LTR"] |
179 gff_3ltr <- gff_out[gff_out$LTR %in% "3LTR"] | 179 gff_3ltr <- gff_out[gff_out$LTR %in% "3LTR"] |
180 | |
180 full_te <- getSeqNamed(s, gff_te) | 181 full_te <- getSeqNamed(s, gff_te) |
182 names(full_te) <- paste0(gff_te$ID,":",names(full_te)) | |
181 ltr5 <- getSeqNamed(s, gff_5ltr) | 183 ltr5 <- getSeqNamed(s, gff_5ltr) |
184 names(ltr5) <- paste0(gff_5ltr$Parent,":",names(ltr5)) | |
182 ltr3 <- getSeqNamed(s, gff_3ltr) | 185 ltr3 <- getSeqNamed(s, gff_3ltr) |
183 inc <- gff_te$Rank != "DL" | 186 names(ltr3) <- paste0(gff_3ltr$Parent,":",names(ltr3)) |
187 inc <- gff_te$Rank != "DL" | |
184 | 188 |
185 writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib_non_redundant.fasta")) | 189 writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib_non_redundant.fasta")) |
186 writeXStringSet(full_te, paste0(opt$output, "_RM_lib_full_TE.fasta")) | 190 writeXStringSet(full_te, paste0(opt$output, "_RM_lib_full_TE.fasta")) |
187 writeXStringSet(ltr5, paste0(opt$output, "_RM_lib_5LTR.fasta")) | 191 writeXStringSet(ltr5, paste0(opt$output, "_RM_lib_5LTR.fasta")) |
188 writeXStringSet(ltr3, paste0(opt$output, "_RM_lib_3LTR.fasta")) | 192 writeXStringSet(ltr3, paste0(opt$output, "_RM_lib_3LTR.fasta")) |