class Bio::Assembly::Contig
Attributes
consensus_seq[RW]
from[RW]
name[RW]
orientation[RW]
quality[RW]
reads[RW]
seq[RW]
to[RW]
Public Class Methods
new(str="")
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# File lib/bio-assembly/contig.rb, line 10 def initialize(str="") @reads = Hash.new @seq = Bio::Sequence::NA.new(str) # counter for Reads @rds_parsed = 0 end
Public Instance Methods
add_read(read)
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# File lib/bio-assembly/contig.rb, line 40 def add_read(read) # TODO do some checks for pos location @reads[read.name] = read end
each_read() { |read| ... }
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# File lib/bio-assembly/contig.rb, line 45 def each_read @reads.each_value { |read| yield read } end
find_read_by_name(name)
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# File lib/bio-assembly/contig.rb, line 17 def find_read_by_name(name) @reads[name] end
find_reads_in_range(clear_range_from, clear_range_to)
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# File lib/bio-assembly/contig.rb, line 21 def find_reads_in_range(clear_range_from, clear_range_to) reads_in_range = Array.new each_read do |read| # Read starts in region if read.from+read.clear_range_from > clear_range_from and read.from+read.clear_range_from < clear_range_to reads_in_range.push read # Read ends in region elsif read.to+read.clear_range_to < clear_range_to and read.to+read.clear_range_to > clear_range_from reads_in_range.push read # Read encompasses region elsif read.from+read.clear_range_from < clear_range_from and read.to+read.clear_range_to > clear_range_to reads_in_range.push read end end reads_in_range; end
num_base_segments()
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# File lib/bio-assembly/contig.rb, line 61 def num_base_segments num_base_sequences = 0 each_read do |read| num_base_sequences += read.base_sequences.size unless read.base_sequences.nil? end num_base_sequences end
num_bases()
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# File lib/bio-assembly/contig.rb, line 53 def num_bases seq.length end
num_reads()
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# File lib/bio-assembly/contig.rb, line 49 def num_reads @reads.size end
seq=(str)
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# File lib/bio-assembly/contig.rb, line 57 def seq=(str) @seq = Bio::Sequence::NA.new(str) end