Mercurial > repos > davidvanzessen > mutation_analysis
changeset 59:79696e273853 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 16 Mar 2016 11:18:55 -0400 |
| parents | 8bb4d6009e08 |
| children | 1558fbbc19ef |
| files | aa_histogram.r merge_and_filter.r mutation_analysis.xml wrapper.sh |
| diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/merge_and_filter.r Tue Mar 01 06:53:40 2016 -0500 +++ b/merge_and_filter.r Wed Mar 16 11:18:55 2016 -0400 @@ -12,7 +12,7 @@ method=args[9] functionality=args[10] unique_type=args[11] -filter_unique=args[12] == "yes" +filter_unique=args[12] summ = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="") sequences = read.table(sequencesfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="") @@ -92,8 +92,7 @@ print(paste("filter uniques: ", filter_unique)) -if(filter_unique){ - +if(filter_unique != "no"){ clmns = names(result) result$unique.def = paste(result$CDR1.Seq, result$CDR2.Seq, result$CDR3.Seq, result$FR1.IMGT, result$FR2.IMGT, result$FR3.IMGT) @@ -104,6 +103,10 @@ result = result[fltr,] + if(filter_unique == "keep"){ + result = result.removed + } + result = result[,clmns] #write.table(inputdata.removed, "unique_removed.csv", sep=",",quote=F,row.names=F,col.names=T)
--- a/mutation_analysis.xml Tue Mar 01 06:53:40 2016 -0500 +++ b/mutation_analysis.xml Wed Mar 16 11:18:55 2016 -0400 @@ -36,6 +36,7 @@ <param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once."> <option value="yes">Yes</option> <option value="no" selected="true">No</option> + <option value="keep">Keep uniques and filter out the duplicates</option> </param> </inputs> <outputs>