@type = options[:type]
@qual = options[:qual]
- if @qual and @seq.length != @qual.length
+ if @seq and @qual and @seq.length != @qual.length
raise SeqError, "Sequence length and score length mismatch: #{@seq.length} != #{@qual.length}"
end
end
raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
raise SeqError, "Missing seq" if self.seq.nil? or self.seq.empty?
- seq_name = self.seq_name.to_s
- seq = self.seq.to_s
+ seq_name = self.seq_name
+ seq = self.seq.dup
unless wrap.nil?
seq.gsub!(/(.{#{wrap}})/) do |match|
# Method to reverse the sequence.
def reverse
- Seq.new(
+ entry = Seq.new(
seq_name: self.seq_name,
seq: self.seq.reverse,
type: self.type,
qual: (self.qual ? self.qual.reverse : self.qual)
)
+
+ entry
end
# Method to reverse the sequence.
regex_start = Regexp.new(start_codons.join('|'), true)
regex_stop = Regexp.new(stop_codons.join('|'), true)
- while pos_beg and pos_beg < self.length - size_min
- if pos_beg = self.seq.index(regex_start, pos_beg)
- if pos_end = self.seq.index(regex_stop, pos_beg)
- length = (pos_end - pos_beg) + 3
+ while pos_beg = self.seq.index(regex_start, pos_beg)
+ pos_end = pos_beg + 3
+
+ while pos_end = self.seq.index(regex_stop, pos_end)
+ length = (pos_end - pos_beg) + 3
- if (length % 3) == 0
- if size_min <= length and length <= size_max
- subseq = self.subseq(pos_beg, length)
+ if (length % 3) == 0
+ if size_min <= length and length <= size_max
+ subseq = self.subseq(pos_beg, length)
- orfs << [subseq, pos_beg, pos_end + 3]
- end
+ orfs << [subseq, pos_beg, pos_end + 3]
end
+
+ break
end
- pos_beg += 1
+ pos_end += 1
end
+
+ pos_beg += 1
end
if pick_longest