annotate fasta2database.R @ 10:d0431a839606 draft

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