Mercurial > repos > davidvanzessen > mutation_analysis
changeset 79:0513b46178c4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 12 May 2016 07:35:07 -0400 |
| parents | b523ce95d857 |
| children | a4c2ddeadec0 |
| files | merge_and_filter.r mutation_analysis.xml sequence_overview.r wrapper.sh |
| diffstat | 4 files changed, 9 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/merge_and_filter.r Wed May 11 10:29:33 2016 -0400 +++ b/merge_and_filter.r Thu May 12 07:35:07 2016 -0400 @@ -69,7 +69,7 @@ if(any(higher_than)){ #summ = summ[higher_than,] } -print(paste("Number of matched sequences:", nrow(summ))) +print(paste("Number of matched sequences:", sum(!grepl("^unmatched", summ$best_match)))) if(nrow(summ) == 0){ stop("No data remaining after filter")
--- a/mutation_analysis.xml Wed May 11 10:29:33 2016 -0400 +++ b/mutation_analysis.xml Thu May 12 07:35:07 2016 -0400 @@ -33,7 +33,7 @@ <option value="AA.JUNCTION">AA.JUNCTION</option> <option value="none">Don't remove duplicates</option> </param> - <param name="class_filter" type="select" label="Class/Sublass filter" help="" > + <param name="class_filter" type="select" label="Class/Subclass filter" help="" > <option value="70_70" selected="true">>70% class and >70% subclass</option> <option value="70_0">>70% class</option> <option value="60_0">>60% class</option>
--- a/sequence_overview.r Wed May 11 10:29:33 2016 -0400 +++ b/sequence_overview.r Thu May 12 07:35:07 2016 -0400 @@ -21,11 +21,11 @@ #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")]) -dat = data.frame(table(dat$best_match, dat$seq_conc)) +dat = data.frame(table(dat$best_match, dat$seq_conc, dat$Functionality)) dat = dat[dat$Freq > 1,] -names(dat) = c("best_match", "seq_conc", "Freq") +names(dat) = c("best_match", "seq_conc", "Functionality", "Freq") dat$seq_conc = factor(dat$seq_conc) @@ -39,7 +39,7 @@ cat("<table border='1'>", file=main.html, append=F) cat("<caption>CDR1+CDR2+CDR3+FR2+FR3 sequences that show up more than once</caption>", file=main.html, append=T) -cat("<tr><th>Sequence</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T) +cat("<tr><th>Sequence</th><th>Functionality</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T) for(i in 1:nrow(dat)){ ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",] @@ -53,6 +53,8 @@ cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",] id = as.numeric(dat[i,"seq_conc"]) + + functionality = dat[i,"Functionality"] if(nrow(ca1) > 0){ cat(tbl(ca1), file=paste("ca1_", id, ".html", sep="")) @@ -92,7 +94,7 @@ cm.html = make.link(id, "cm", nrow(cm)) - rw = c(as.character(dat[i,"seq_conc"]), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html) + rw = c(as.character(dat[i,"seq_conc"]), as.character(functionality), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html) cat(tr(rw), file=main.html, append=T) }
--- a/wrapper.sh Wed May 11 10:29:33 2016 -0400 +++ b/wrapper.sh Thu May 12 07:35:07 2016 -0400 @@ -142,7 +142,7 @@ done tmp=`cat $outdir/unmatched_${func}_n.txt` - echo "<th><a href='unmatched.txt'>unmatched (N = $tmp)</a></th>" >> $output + echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output tmp=`cat $outdir/all_${func}_n.txt` echo "<th><a href='matched_${func}_all.txt'>all (N = $tmp)</a></th>" >> $output