cosmetics

R/bio/bioinfo_commons.R

@@ -16,6 +16,14 @@ read.fasta <- function(fileName){
     return(fastaDataDF)
 }
 
+
+write.fasta <- function(seq_names, sequences, file){
+    fastaData <- AAStringSet(sequences)
+    names(fastaData) <- seq_names;
+    writeXStringSet(fastaData, file=file, format="fasta", width=80)
+}
+
+
 getSeqLengthFromFasta <- function(fileName){
     assembly <- mutate(read.fasta(fileName), seq_len=nchar(Sequence))
     assembly$Sequence = NULL
@@ -23,9 +31,21 @@ getSeqLengthFromFasta <- function(fileName){
 }
 
 
-write.fasta <- function(seq_names, sequences, file){
-    fastaData <- AAStringSet(sequences)
-    names(fastaData) <- seq_names;
-    writeXStringSet(fastaData, file=file, format="fasta", width=80)
+## necessary to disable scientific number formats for long integers
+options(scipen=100)
+
+## writes a table in bed format expecting columns being ordered according to bed spec already
+write.bed <- function(bedData, file){
+    write.table(bedData, file=file, quote=FALSE, sep ="\t", na="NA", row.names=FALSE, col.names=FALSE)
 }
 
+#write.bed <- function(bedData, file){
+#    oldScipen<-getOption("scipen")
+#
+#     ## necessary to disable scientific number formats for long integers
+#    options(scipen=100)
+#
+#    write.table(bedData, file=file, quote=FALSE, sep ="\t", na="NA", row.names=FALSE, col.names=FALSE)
+#
+#    options(oldScipen)
+#}

R/core_commons.R

@@ -198,15 +198,6 @@ write.delim <- function(df, file, header=TRUE,...){
     write.table(df, file, row.names=FALSE, col.names=header, sep="\t", ...)
 }
 
-## writes a table in bed format expecting columns being ordered according to bed spec already
-write.bed <- function(bedData, file){
-    write.table(bedData, file=file, quote=FALSE, sep ="\t", na="NA", row.names=FALSE, col.names=FALSE)
-}
-#options(scipen=100) ## necessary to disable scientific number formats for long integers
-
-
-
-
 rmSomeElements <- function(vec, toDel) vec[!(vec %in% toDel)]
 
 rmLastElement <- function(vec) vec[-length(vec)]