# HG changeset patch
# User petr-novak
# Date 1565796282 14400
# Node ID 1d5883a9ec3a562053a37fc4ac887ff5215de6fc
# Parent  d0431a8396067d247aea4ae45cdf95c6d4a52bfc
Deleted selected files

diff -r d0431a839606 -r 1d5883a9ec3a fasta2database.R
--- a/fasta2database.R	Wed Aug 14 11:24:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-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=''))