changed Seq.new argument to hash

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index fd83ba3282d28c561358fb9383c18e324d9a7ed4..a2d5bbac3462d44401d0e1d97a70101f1b7d3af4 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -93,7 +93,7 @@ class Seq
     type     = record[:SEQ_TYPE].to_sym if record[:SEQ_TYPE]
     qual     = record[:SCORES]
 
-    self.new(seq_name, seq, type, qual)
+    self.new(seq_name: seq_name, seq: seq, type: type, qual: qual)
   end
 
   # Class method that generates all possible oligos of a specifed length and type.
@@ -125,19 +125,19 @@ class Seq
     oligos
   end
 
-  # Initialize a sequence object with the following arguments:
-  # - seq_name: Name of the sequence.
-  # - seq: The sequence.
-  # - type: The sequence type - DNA, RNA, or protein
-  # - qual: An Illumina type quality scores string.
-  def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
-    @seq_name = seq_name
-    @seq      = seq
-    @type     = type
-    @qual     = qual
+  # Initialize a sequence object with the following options:
+  # - :seq_name   Name of the sequence.
+  # - :seq        The sequence.
+  # - :type       The sequence type - DNA, RNA, or protein
+  # - :qual       An Illumina type quality scores string.
+  def initialize(options = {})
+    @seq_name = options[:seq_name]
+    @seq      = options[:seq]
+    @type     = options[:type]
+    @qual     = options[:qual]
 
-    if @qual
-      raise SeqError, "Sequence length and score length mismatch: #{@seq.length} != #{@qual.length}" if @seq.length != @qual.length
+    if @qual and @seq.length != @qual.length
+      raise SeqError, "Sequence length and score length mismatch: #{@seq.length} != #{@qual.length}"
     end
   end
 
@@ -343,7 +343,12 @@ class Seq
 
   # Method to reverse the sequence.
   def reverse
-    Seq.new(self.seq_name, self.seq.reverse, self.type, self.qual ? self.qual.reverse : self.qual)
+    Seq.new(
+      seq_name: self.seq_name,
+      seq:      self.seq.reverse,
+      type:     self.type,
+      qual:     (self.qual ? self.qual.reverse : self.qual)
+    )
   end
 
   # Method to reverse the sequence.
@@ -357,10 +362,11 @@ class Seq
   def complement
     raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
 
-    entry          = Seq.new
-    entry.seq_name = self.seq_name
-    entry.type     = self.type
-    entry.qual     = self.qual
+    entry = Seq.new(
+      seq_name: self.seq_name,
+      type:     self.type,
+      qual:     self.qual
+    )
 
     if self.is_dna?
       entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
@@ -424,7 +430,12 @@ class Seq
 
   # Method to return a new Seq object with shuffled sequence.
   def shuffle
-    Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
+    Seq.new(
+      seq_name: self.seq_name,
+      seq:      self.seq.split('').shuffle!.join,
+      type:     self.type,
+      qual:     self.qual
+    )
   end
 
   # Method to shuffle a sequence randomly inline.
@@ -491,7 +502,7 @@ class Seq
 
     seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
 
-    Seq.new(seq_name, seq, self.type, qual)
+    Seq.new(seq_name: seq_name, seq: seq, type: self.type, qual: qual)
   end
 
   # Method that replaces a sequence with a subsequence from a given start position