Save the sequence of the predicted LTR Transposons in a fasta file

This function allows users to save the sequence of the predicted LTR Transposons or LTRs in a fasta file.

pred2fasta(LTRpred.tbl, prediction.file, output = "output.fa")

Arguments

LTRpred.tbl	the data.frame generated by LTRpred.
prediction.file	the fasta file storing either the full LTR Transposon sequence or only the LTR sequence as returned by the LTRpred function.
output	the fasta file to which the output sequences shall be stored in.

Details

The output data.frames returned by LTRpred contain all information of the predicted LTR retrotransposons that can be used for post-filtering steps. After these post-filtering steps sequences of the remaining (filtered) candidates can be retrieved by this function.

See also

LTRharvest, LTRdigest, LTRpred, read.prediction

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# Hypothetical Example
# Generate LTR transposon prediction for A. thaliana 
Ath.Pred <- LTRpred(input.gff3        = "TAIR10_chr_all/TAIR10_chr_all_Prediction.gff", 
                    genome.file       = "Genome/TAIR10_chr_all.fas",
                    trnas             = "araTha1-tRNAs.fa",
                    hmms              = "hmm_*",
                    cores             = 1)

# Filter for LTR transposons having 100 pec. sequence similarity between their LTRs
FilteredLTRTransposons <- dplyr::filter(Ath.Pred, ltr_similarity == 100)

# Write the sequences of these filtered LTR transposons to a fasta file
pred2fasta(LTRpred.tbl = FilteredLTRTransposons, 
           prediction.file = "TAIR10_chr_all-ltrdigest_complete.fas", 
           output                = "AthalianaPutativeLTRTransposons.fa")
}