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comparison summarize_gff.R @ 10:d0431a839606 draft

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author petr-novak
date Wed, 14 Aug 2019 11:24:15 -0400
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children ddc6bab20889
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9:ed4d9ede9cb4 10:d0431a839606
1 ## summarize hits
2 output = commandArgs(T)[2] ## output table
3 filepath = commandArgs(T)[1] ## input dante gff3
4 summarized_by = commandArgs(T)[-(1:2)]
5
6 readGFF3fromDante = function(filepath){
7 dfraw=read.table(filepath, as.is = TRUE)
8 gff_df = dfraw[,1:8]
9 colnames(gff_df) = c("seqid", "source", "type", "start", "end", "score",
10 "strand", "phase")
11 ## assume same order, same attributes names
12 gffattr = do.call(rbind,
13 lapply(
14 strsplit(dfraw[,9],split=c("=|;")),
15 function(x)x[c(FALSE,TRUE)]
16 )
17 )
18 gff_df$Name = gffattr[,1]
19 gff_df$Final_Classification = gffattr[,2]
20 gff_df$Region_Hits_Classifications = gffattr[,3]
21 gff_df$Best_Hit = gffattr[,4]
22 gff_df$Best_Hit_DB_Pos = gffattr[,5]
23 gff_df$DB_Seq = gffattr[,6]
24 gff_df$Query_Seq = gffattr[,7]
25 gff_df$Identity = as.numeric(gffattr[,8])
26 gff_df$Similarity = as.numeric(gffattr[,9])
27 gff_df$Relat_Length = as.numeric(gffattr[,10])
28 gff_df$Relat_Interruptions = as.numeric(gffattr[,11])
29 gff_df$Hit_to_DB_Length = as.numeric(gffattr[,12])
30 return(gff_df)
31 }
32
33 gff = readGFF3fromDante(filepath)
34 # summarize_by = c("Final_Classification", "Name", "seqid")
35
36 tbl = data.frame(table(gff[,summarize_by]))
37 write.table(tbl, file = filepath, row.names =FALSE, quote = FALSE)