| Previous changeset 12:6b66c1c57f22 (2016-11-10) Next changeset 14:59765d2c8890 (2016-11-11) |
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Commit message:
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modified:
merge_and_filter.r shm_csr.xml |
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| diff -r 6b66c1c57f22 -r 933fb21568ce merge_and_filter.r --- a/merge_and_filter.r Thu Nov 10 08:36:18 2016 -0500 +++ b/merge_and_filter.r Fri Nov 11 03:49:30 2016 -0500 |
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| @@ -187,11 +187,13 @@ stop("No data remaining after filter") } +result$best_match_class = gsub(",.*", "", result$best_match) #gsub so the unmatched don't have a class after it + result$past = do.call(paste, c(result[unlist(strsplit(unique.type, ","))], sep = ":")) result = result[!(duplicated(result$past)), ] -result = result[,!(names(result) %in% c("past"))] +result = result[,!(names(result) %in% c("past", "best_match_class"))] print(paste("Number of sequences in result after", unique.type, "filtering:", nrow(result))) |
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| diff -r 6b66c1c57f22 -r 933fb21568ce shm_csr.xml --- a/shm_csr.xml Thu Nov 10 08:36:18 2016 -0500 +++ b/shm_csr.xml Fri Nov 11 03:49:30 2016 -0500 |
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| @@ -22,14 +22,14 @@ <option value="no">No</option> </param> <param name="unique" type="select" label="Remove duplicates based on" help="" > - <option value="VGene,AA.JUNCTION,best_match">Top.V.Gene, CDR3 (AA), C region</option> + <option value="VGene,AA.JUNCTION,best_match_class">Top.V.Gene, CDR3 (AA), C region</option> <option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3 (AA)</option> - <option value="AA.JUNCTION,best_match">CDR3 (AA), C region</option> + <option value="AA.JUNCTION,best_match_class">CDR3 (AA), C region</option> <option value="AA.JUNCTION">CDR3 (AA)</option> - <option value="VGene,CDR3.IMGT.seq,best_match">Top.V.Gene, CDR3.nt.Seq, C region</option> + <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3.nt.Seq, C region</option> <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option> - <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option> + <option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option> <option value="CDR3.IMGT.seq">CDR3 (nt)</option> <option value="Sequence.ID" selected="true">Don't remove duplicates</option> </param> |