Mercurial > repos > petr-novak > dante
comparison fasta2database.R @ 10:d0431a839606 draft
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| author | petr-novak |
|---|---|
| date | Wed, 14 Aug 2019 11:24:15 -0400 |
| parents | |
| children |
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| 9:ed4d9ede9cb4 | 10:d0431a839606 |
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| 1 library(Biostrings) | |
| 2 input_fasta = commandArgs(T)[1] | |
| 3 ## for testing input_fasta="/mnt/raid/454_data/RE2_benchmark/REPET_annotation/Prunus_persica/DANTE_proteins_filtered.fasta" | |
| 4 s = readAAStringSet(input_fasta) | |
| 5 names_table = do.call("rbind", strsplit(names(s)," ")) | |
| 6 head(names_table) | |
| 7 classification_table = paste(names_table[,1], gsub("|","\t",names_table[,3], fixed = TRUE), sep="\t") | |
| 8 cat(unique(classification_table), sep="\n", file = paste(input_fasta, ".classification", sep = "")) | |
| 9 | |
| 10 new_fasta_names = paste("NA-", names_table[,2], "__", names_table[,1], sep="") | |
| 11 | |
| 12 names(s) = new_fasta_names | |
| 13 | |
| 14 writeXStringSet(s, filepath = paste(input_fasta, ".db",sep='')) |