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changeset 11:1d5883a9ec3a draft

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Deleted selected files
author petr-novak
date Wed, 14 Aug 2019 11:24:42 -0400
parents d0431a839606
children ddc6bab20889
files fasta2database.R
diffstat 1 files changed, 0 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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=''))