Mercurial > repos > davidvanzessen > mutation_analysis

diff mutation_analysis.r @ 78:b523ce95d857 draft

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Uploaded
author davidvanzessen
date Wed, 11 May 2016 10:29:33 -0400
parents 13c3710604ef
children e39176ccddc8
line wrap: on
line diff
--- a/mutation_analysis.r	Mon May 09 03:56:38 2016 -0400
+++ b/mutation_analysis.r	Wed May 11 10:29:33 2016 -0400
@@ -169,7 +169,7 @@
 setwd(outputdir)
 
 calculate_result = function(i, gene, dat, matrx, f, fname, name){
-	tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),]
+	tmp = dat[grepl(paste("^", gene, ".*", sep=""), dat$best_match),]
 
 	j = i - 1
 	x = (j * 3) + 1
@@ -267,7 +267,9 @@
   write.table(x=tmp[,c("Sequence.ID", "best_match", "chunk_hit_percentage", "nt_hit_percentage", "start_locations")], file=paste("matched_", name , "_", fname, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
   
   cat(matrx[1,x], file=paste(name, "_", fname, "_value.txt" ,sep=""))
-  cat(length(tmp$Sequence.ID), file=paste(name, "_", fname, "_n.txt" ,sep=""))
+  cat(nrow(tmp), file=paste(name, "_", fname, "_n.txt" ,sep=""))
+  
+  print(paste(fname, name, nrow(tmp)))
   
   matrx
 }