comparison clean_ltr.R @ 3:6ae4a341d1f3 draft

"planemo upload commit 8bd6029a4de4a8f5031a5cc71303bb06217cc88a"

2:f131886ea194

                                                          TE_DLTP_info$seqs_representative,
                                                          word_size = word_size
)

TE_DLT_plus_DLP_info_multiplicity <- verify_based_on_multiplicity(TE_DLT_plus_DLP_info)

# create additional library from rank 2 verified by multiplicity
id_for_additional_library <- setdiff(
  TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
  TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified)

  }else {
    seq_representative <- TE_DLTP_info$seqs_representative
  }
}


# TE  rank 3
TE_DL_info_DLTP_verified <- compare_TE_datasets(
  s_te$DL,
  TE_DLTP_info$seqs_representative, min_coverage = 0.98,
  ncpus = ncpus

c1 <- g$ID %in% ID[id_of_good_te]
c2 <- sapply(g$Parent, function(x)ifelse(length(x) == 0, "", x)) %in% ID[id_of_good_te]

gff_out <- g[c1 | c2]


writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib.fasta"))
export(gff_out, paste0(opt$output, "_clean.gff3"), format = "gff3")

3:6ae4a341d1f3

                                                          TE_DLTP_info$seqs_representative,
                                                          word_size = word_size
)

TE_DLT_plus_DLP_info_multiplicity <- verify_based_on_multiplicity(TE_DLT_plus_DLP_info)
# create additional library from rank 2 verified by multiplicity
id_for_additional_library <- setdiff(
  TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
  TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified)

  }else {
    seq_representative <- TE_DLTP_info$seqs_representative
  }
}

# TE  rank 3
TE_DL_info_DLTP_verified <- compare_TE_datasets(
  s_te$DL,
  TE_DLTP_info$seqs_representative, min_coverage = 0.98,
  ncpus = ncpus

c1 <- g$ID %in% ID[id_of_good_te]
c2 <- sapply(g$Parent, function(x)ifelse(length(x) == 0, "", x)) %in% ID[id_of_good_te]

gff_out <- g[c1 | c2]

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$LTR %in% "3LTR"]
full_te <- getSeqNamed(s, gff_te)
ltr5 <-  getSeqNamed(s, gff_5ltr)
ltr3 <-  getSeqNamed(s, gff_3ltr)
inc <-  gff_te$Rank != "DL"

writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib_non_redundant.fasta"))
writeXStringSet(full_te, paste0(opt$output, "_RM_lib_full_TE.fasta"))
writeXStringSet(ltr5, paste0(opt$output, "_RM_lib_5LTR.fasta"))
writeXStringSet(ltr3, paste0(opt$output, "_RM_lib_3LTR.fasta"))

export(gff_out, paste0(opt$output, "_clean.gff3"), format = "gff3")

lv <- sort(unique(gff_te$Final_Classification))
te_count <- table(factor(gff_te$Final_Classification, levels=lv))

pdf(paste0(opt$output, "_summary.pdf"), width = 13, height=8, pointsize = 10)
par(mfrow=c(1,2), mar=c(5,7,2,0), las=1)
boxplot(width(gff_te) ~ factor(gff_te$Final_Classification, levels=lv),
        horizontal = TRUE, xlab="length[bp]", ylab="",
        names = paste0(gsub("^.+[|]", "", lv), " (", te_count, ")"),
        main = 'Full TE', at = seq_along(lv)*4
)
boxplot(width(gff_te[inc]) ~ factor(gff_te$Final_Classification[inc], levels=lv),
        horizontal = TRUE, xlab="length[bp]", ylab="",
        names = rep("", length(lv)),
        main = 'Full TE', at = seq_along(lv)*4-1, add=TRUE, col=2
)
par(mar=c(5,0,2,7))
boxplot(width(gff_5ltr) ~ factor(gff_5ltr$Final_Classification, levels=lv),
        horizontal = TRUE, xlab="length[bp]", ylab="",
        names = rep("", length(lv)),
        main = "5'LTR", at = seq_along(lv)*4
)
boxplot(width(gff_5ltr[inc]) ~ factor(gff_5ltr$Final_Classification[inc], levels=lv),
        horizontal = TRUE, xlab="length[bp]", ylab="",
        names = rep("", length(lv)),
        main = "5'LTR", at = seq_along(lv)*4-1, add=TRUE, col=2
)
legend('bottomright', col=c("grey","2"), legend=c("All TE", "TE with PBS/TSD"), pch=15)
dev.off()