# HG changeset patch
# User davidvanzessen
# Date 1481190669 18000
# Node ID 80c4eebf7bc91cb2684986873882daa0a153e0eb
# Parent c0ecc31829bd0d03088b52ec457e0fe3aa5c43da
Uploaded
diff -r c0ecc31829bd -r 80c4eebf7bc9 aa_histogram.r
--- a/aa_histogram.r Wed Dec 07 08:17:09 2016 -0500
+++ b/aa_histogram.r Thu Dec 08 04:51:09 2016 -0500
@@ -16,15 +16,15 @@
for(gene in genes){
if(gene == ""){
- mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
- absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
+ mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
+ absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
} else {
- mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
- absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
+ mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
+ absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
}
print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
if(nrow(mutations.by.id.gene) == 0){
- next
+ next
}
mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
diff -r c0ecc31829bd -r 80c4eebf7bc9 shm_csr.xml
--- a/shm_csr.xml Wed Dec 07 08:17:09 2016 -0500
+++ b/shm_csr.xml Thu Dec 08 04:51:09 2016 -0500
@@ -27,7 +27,7 @@
-
+
diff -r c0ecc31829bd -r 80c4eebf7bc9 wrapper.sh
--- a/wrapper.sh Wed Dec 07 08:17:09 2016 -0500
+++ b/wrapper.sh Thu Dec 08 04:51:09 2016 -0500
@@ -187,6 +187,9 @@
if [ -e "$outdir/aa_histogram_.png" ]; then
mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
+ mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
+ mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
+ mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
fi
genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
@@ -592,6 +595,12 @@
echo "| AA mutation data per sequence ID | Download |
" >> $output
echo "| Absent AA location data per sequence ID | Download |
" >> $output
+echo "| The data used to generate the aa mutation frequency plot | Download |
" >> $output
+echo "| The data used to generate the aa mutation frequency plot for IGA | Download |
" >> $output
+echo "| The data used to generate the aa mutation frequency plot for IGG | Download |
" >> $output
+echo "| The data used to generate the aa mutation frequency plot for IGM | Download |
" >> $output
+echo "| The data used to generate the aa mutation frequency plot for IGE | Download |
" >> $output
+
echo "| Baseline PDF (http://selection.med.yale.edu/baseline/) | Download |
" >> $output
echo "| Baseline data | Download |
" >> $output
echo "| Baseline IGA PDF | Download |
" >> $output