# HG changeset patch
# User davidvanzessen
# Date 1441027718 14400
# Node ID d592dab2fca14a502ee559edbb9008501c3bb913
# Parent 32d8a5abed4cb01e20c0a135739f792a5b774467
Uploaded
diff -r 32d8a5abed4c -r d592dab2fca1 RScript.r
--- a/RScript.r Wed Aug 26 05:51:20 2015 -0400
+++ b/RScript.r Mon Aug 31 09:28:38 2015 -0400
@@ -156,8 +156,11 @@
patient1.fuzzy = patient1[!(patient1$merge %in% merge.list),]
patient2.fuzzy = patient2[!(patient2$merge %in% merge.list),]
- patient1.fuzzy$merge = paste(patient1.fuzzy$V_Segment_Major_Gene, patient1.fuzzy$J_Segment_Major_Gene, patient1.fuzzy$CDR3_Sense_Sequence)
- patient2.fuzzy$merge = paste(patient2.fuzzy$V_Segment_Major_Gene, patient2.fuzzy$J_Segment_Major_Gene, patient2.fuzzy$CDR3_Sense_Sequence)
+ #patient1.fuzzy$merge = paste(patient1.fuzzy$V_Segment_Major_Gene, patient1.fuzzy$J_Segment_Major_Gene, patient1.fuzzy$CDR3_Sense_Sequence)
+ #patient2.fuzzy$merge = paste(patient2.fuzzy$V_Segment_Major_Gene, patient2.fuzzy$J_Segment_Major_Gene, patient2.fuzzy$CDR3_Sense_Sequence)
+
+ patient1.fuzzy$merge = paste(patient1.fuzzy$locus_V, patient1.fuzzy$locus_J, patient1.fuzzy$CDR3_Sense_Sequence)
+ patient2.fuzzy$merge = paste(patient2.fuzzy$locus_V, patient2.fuzzy$locus_J, patient2.fuzzy$CDR3_Sense_Sequence)
merge.freq.table = data.frame(table(c(patient1.fuzzy$merge, patient2.fuzzy$merge)))
merge.freq.table.gt.1 = merge.freq.table[merge.freq.table$Freq > 1,]
@@ -171,7 +174,7 @@
current.merge.in.2 = patient2.fuzzy[patient2.fuzzy$merge == current.merge.1,]
#agrep/adist the two samples
- agrep.match = agrep(current.clone.seq.1, current.merge.in.2$Clone_Sequence, max.distance = 1, costs=list(insertions=0.1, deletions=0.1, substitutions=1))
+ agrep.match = agrep(current.clone.seq.1, current.merge.in.2$Clone_Sequence, max.distance = 9, costs=list(insertions=1, deletions=1, substitutions=10))
if(length(agrep.match) == 1){
@@ -233,7 +236,7 @@
} else if (length(agrep.match) > 1){
#multiple matches, whatdo?
- cat(paste("| ", "Multiple matches found for ", current.merge.1, " in ", patient, " |
", sep=""), file=logfile, append=T)
+ cat(paste("| ", "Multiple matches found for ", current.merge.1, ", ", current.clone.seq.1, " in ", patient, ", ", oneSample, " |
", sep=""), file=logfile, append=T)
}
patient1.fuzzy = patient1.fuzzy[-1,]
}
diff -r 32d8a5abed4c -r d592dab2fca1 wrapper.sh
--- a/wrapper.sh Wed Aug 26 05:51:20 2015 -0400
+++ b/wrapper.sh Mon Aug 31 09:28:38 2015 -0400
@@ -16,6 +16,7 @@
cp $dir/script.js $outputDir
cp $dir/style.css $outputDir
cp $dir/tabber.js $outputDir
+mv "$outputFile" "$outputDir/log.html"
echo "Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $outputFile