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view fasta2database.R @ 15:3151a72a6671 draft

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author petr-novak
date Tue, 03 Sep 2019 05:20:02 -0400
parents d0431a839606
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library(Biostrings)
input_fasta = commandArgs(T)[1]
## for testing input_fasta="/mnt/raid/454_data/RE2_benchmark/REPET_annotation/Prunus_persica/DANTE_proteins_filtered.fasta"
s = readAAStringSet(input_fasta)
names_table = do.call("rbind", strsplit(names(s)," "))
head(names_table)
classification_table = paste(names_table[,1], gsub("|","\t",names_table[,3], fixed = TRUE), sep="\t")
cat(unique(classification_table), sep="\n", file = paste(input_fasta, ".classification", sep = ""))

new_fasta_names = paste("NA-", names_table[,2], "__", names_table[,1], sep="")

names(s) = new_fasta_names

writeXStringSet(s, filepath = paste(input_fasta, ".db",sep=''))