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1 #!/usr/bin/env Rscript
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2 library(optparse)
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3 option_list <- list(
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4 make_option(c("-c", "--cluster_table"), default=NA, type = "character",
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5 help="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"),
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6
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7 make_option(c("-m", "--comparative_counts"),default = NA,type = "character",
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8 help="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"),
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9 make_option(c("-o", "--output"), type="character",
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10 help="output file name")
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11 )
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12
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13
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14 opt = parse_args(OptionParser(option_list = option_list))
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15
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16 ## for testing
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17 cluster_annotation = opt$cluster_table
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18 header_line = grep(".*Cluster.*Supercluster.*Size", readLines(cluster_annotation))
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19 annot = read.table(cluster_annotation, sep="\t",header=TRUE,as.is=TRUE, skip = header_line - 1)
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20
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21
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22 input_read_counts = as.numeric(strsplit(
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23 grep("Number_of_analyzed_reads",
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24 readLines(con=cluster_annotation, n=header_line),
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25 value=TRUE)
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26 ,split="\t")[[1]][2]
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27 )
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28
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29 ## complete classification table:
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30 unique_groups = sort(unique(annot$Final_annotatio))
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31
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32 groups_to_remove = grep("contamination|organelle", unique_groups, value=TRUE)
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33 groups_to_keep = unique_groups[!(unique_groups %in% groups_to_remove)]
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34
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35 if (length(groups_to_remove)>0){
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36 input_count_reads_corrected = input_read_counts - sum(annot$Size_adjusted[annot$Final_annotation %in% groups_to_remove])
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37
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38 }else{
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39 input_count_reads_corrected = input_read_counts
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40 }
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41
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42 proportion = numeric()
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43 sum_of_reads = numeric()
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44 for (g in groups_to_keep){
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45 sum_of_reads[g] = sum(annot$Size_adjusted[annot$Final_annotation %in% g])
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46 proportion[g] = sum_of_reads[g] / input_count_reads_corrected
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47 }
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48
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49
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50
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51 summary_table = data.frame(Annotation = groups_to_keep,
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52 Number_of_reads = sum_of_reads,
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53 "Proportion[%]" = proportion * 100 , check.names = FALSE)
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54
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55 print(opt$output)
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56 write.table(summary_table,file = opt$output,
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57 row.names = FALSE, col.names = TRUE, sep="\t")
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