Mercurial > repos > davidvanzessen > mutation_analysis
changeset 37:4b997f68d769 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 04 Aug 2015 08:52:14 -0400 |
| parents | ac5794b9d300 |
| children | 6b6dbbcc771d |
| files | merge_and_filter.r mutation_analysis.xml wrapper.sh |
| diffstat | 2 files changed, 12 insertions(+), 7 deletions(-) [+] |
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--- a/merge_and_filter.r Thu Jun 25 05:38:55 2015 -0400 +++ b/merge_and_filter.r Tue Aug 04 08:52:14 2015 -0400 @@ -31,10 +31,14 @@ summ = merge(summ, gene_identification, by="Sequence.ID") -if(functionality == "no_results"){ - summ = summ[summ$Functionality != "No results",] -} else if (functionality == "no_result_unproductive"){ - summ = summ[summ$Functionality != "No results" & summ$Functionality != "unproductive",] +summ = summ[summ$Functionality != "No results",] + +if(functionality == "productive"){ + summ = summ[summ$Functionality == "productive (see comment)" | summ$Functionality == "productive",] +} else if (functionality == "unproductive"){ + summ = summ[summ$Functionality == "unproductive (see comment)" | summ$Functionality == "unproductive",] +} else if (functionality == "remove_no_result"){ + summ = summ[summ$Functionality != "No results" & summ$Functionality != "unknown (see comment)" & summ$Functionality != "unknown",] } higher_than=(summ$chunk_hit_percentage >= 70 & summ$nt_hit_percentage >= 70)
--- a/mutation_analysis.xml Thu Jun 25 05:38:55 2015 -0400 +++ b/mutation_analysis.xml Tue Aug 04 08:52:14 2015 -0400 @@ -14,9 +14,10 @@ <option value="no" selected="true">no</option> </param> <param name="functionality" type="select" label="Functionality filter" help="" > - <option value="no_results" selected="true">Remove "No results"</option> - <option value="no_result_unproductive">Remove "No results" and "unproductive"</option> - <option value="dont_remove">Don't filter</option> + <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option> + <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option> + <option value="remove_no_result">Remove "No Results", "unknown" and "unknown (see comment)"</option> + <option value="dont_filter">Don't filter</option> </param> <param name="unique" type="select" label="Remove duplicates based on" help="" >