rbbt-util 5.21.86 → 5.21.87

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 14c71affcd04cfc765824f452e0455dd0a59befe
-  data.tar.gz: 57821f59ec541b8cb173fbcf64861ca793a0a032
+  metadata.gz: 88ef613a2ceb07588403878b6f87982221a4d7fb
+  data.tar.gz: d9d54cd91f619d9bead8d8d072f115eff635774b
 SHA512:
-  metadata.gz: 81cd59fb9a32bddf24ca25a7bb614faab5ced6bfdff678454b688992674c84029312d8c52dc2a29f9c3511945daf6be91e90375ba8b661e184a08330229be203
-  data.tar.gz: 2e45a91dcd62e667d9f16e83ff1c20f58bbf2111ab631e82a0e287cfa97a8e5c46af6fe6f0c79f75b99c30d6fceb62d91dcca2fe72eec4bc28d313386483df1f
+  metadata.gz: 65fc0ea4c70a2ca5902e786addebf0741d11f6ad402087cf1e8516b953365fa1ae8c42091185a8a6d6352e710cb1b7269dba00c7c149ea8b55bfb93445865c28
+  data.tar.gz: f5a050a28355d674cbb95d887686bb13a74feac6ecd1540548912acc34ac4442c829e103223871d9e98d2a925324562734c829237df05de924ae5bddebc04b10

data/lib/rbbt/tsv/util.rb

@@ -237,7 +237,7 @@ module TSV
         new[k] = [v]
       end
     when :list
-      self
+      return self
     end
     self.annotate(new)
     new.type = :list

data/lib/rbbt/util/misc/system.rb

@@ -92,6 +92,7 @@ end
   end
 
   def self.is_filename?(string)
+    return true if defined? PATH and Path === string
     return true if string.respond_to? :exists
     return true if String === string and string.length < 265 and File.exist? string
     return false

data/share/Rlib/util.R

@@ -89,29 +89,32 @@ rbbt.load.data <- function(filename, sep = "\t",  ...){
 
 rbbt.flat.tsv <- function(filename, sep = "\t", comment.char ="#", ...){
   f = file(filename, 'r');
-  headers = readLines(f, 1);
-  if (length(grep("^#: ", headers)) > 0){ 
-      headers = readLines(f, 1); 
+  line = readLines(f, 1);
+  if (length(grep("^#: ", line)) > 0){ 
+      line = readLines(f, 1); 
+  } 
+  if (comment.char=="" || length(grep("^# ", line)) > 0){ 
+      line = readLines(f, 1); 
   } 
   result = list();
   while( TRUE ){
-    line = readLines(f, 1);
-    if (length(line) == 0){ break;}
     parts = unlist(strsplit(line, sep, fixed = TRUE));
     id = parts[1];
     result[[id]] = parts[2:length(parts)];
+    line = readLines(f, 1);
+    if (length(line) == 0){ break;}
   }
   close(f);
   return(result);
 }
 
-rbbt.tsv.columns <- function(filename, sep="\t"){
+rbbt.tsv.columns <- function(filename, sep="\t", comment.char="#"){
   f = file(filename, 'r');
   headers = readLines(f, 1);
   if (length(grep("^#:", headers)) > 0){ 
       headers = readLines(f, 1); 
   } 
-  if (length(grep("^#", headers)) > 0){
+  if (comment.char == "" || length(grep("^#", headers)) > 0){
       fields = strsplit(headers, sep)[[1]];
       close(f);
       return(fields);
@@ -121,9 +124,14 @@ rbbt.tsv.columns <- function(filename, sep="\t"){
 }
 
 rbbt.tsv <- function(filename, sep = "\t", comment.char ="#", row.names=1, check.names=FALSE, fill=TRUE, as.is=TRUE, quote='',  ...){
-  data=read.table(file=filename, sep=sep, fill=fill, as.is=as.is, quote=quote, row.names= row.names, comment.char = comment.char, ...);
+ 
+  if (comment.char == ""){
+      data=read.table(file=filename, sep=sep, fill=fill, as.is=as.is, quote=quote, row.names= row.names, comment.char = comment.char, skip=1, ...);
+  }else{
+      data=read.table(file=filename, sep=sep, fill=fill, as.is=as.is, quote=quote, row.names= row.names, comment.char = comment.char, ...);
+  }
 
-  columns = rbbt.tsv.columns(filename, sep)
+  columns = rbbt.tsv.columns(filename, sep, comment.char=comment.char)
   if (! is.null(columns)){
       names(data) <- columns[2:length(columns)];
   }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.86
+  version: 5.21.87
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-06-22 00:00:00.000000000 Z
+date: 2017-06-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake