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module Bio::PolyploidTools
class ChromosomeArm
attr_accessor :name
attr_reader :genes
attr_reader :loaded_entries
attr_reader :fasta_db
def initialize(name, path_to_fasta)
@name = name
@fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path_to_fasta})
#$stderr.puts "Loading entries for #{name}"
@genes = Hash.new
end
def fetch_contig(contig_id)
@fasta_db.load_fai_entries unless @loaded_entries
@loaded_entries = true
entry = fasta_db.index.region_for_entry(contig_id)
# puts entry
@fasta_db.fetch_sequence(entry.get_full_region)
end
#Loads all the chromosome arms in a folder.
#The current version requires that all the references end with .fa, and start with XXX_*.fa
#Where XXX is the chromosome name
def self.load_from_folder(path_to_contigs)
chromosomeArms = Hash.new
Dir.foreach(path_to_contigs) do |filename |
if File.fnmatch("*.fa", filename)
parsed = /^(?<arm>\d\w+)/.match(filename)
target="#{path_to_contigs}/#{filename}"
# fasta_file = Bio::DB::Fasta::FastaFile.new(target)
#fasta_file.load_fai_entries
arm = ChromosomeArm.new(parsed[:arm], target)
chromosomeArms[arm.name] = arm
end
end
return chromosomeArms
end
end
end
Version data entries
20 entries across 20 versions & 1 rubygems