Mercurial > repos > petr-novak > dante_ltr

comparison clean_ltr.R @ 6:b91ca438a1cb draft

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"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
author petr-novak
date Thu, 19 May 2022 08:21:55 +0000
parents 93d35ae65e1b
children c33d6583e548
comparison
equal deleted inserted replaced
5:0c3111ab729b 6:b91ca438a1cb
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"))