Sha256: 46d1eb70a9c6bc19916f764c404a22d5e8e179c6508e2f14d6ed2e78cda90650
Contents?: true
Size: 760 Bytes
Versions: 53
Compression:
Stored size: 760 Bytes
Contents
#!/usr/bin/env ruby
found_cointigs = Set.new
Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model, :chunk=>chunk, :total_chunks=>}) do |aln|
if aln.identity > min_identity
exo_f.puts aln.line
unless found_cointigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file.
found_cointigs.add(aln.target_id)
entry = fasta_file.index.region_for_entry(aln.target_id)
raise ExonerateException.new, "Entry not found! #{aln.target_id}. Make sure that the #{target_id}.fai was generated properly." if entry == nil
region = entry.get_full_region
seq = fasta_file.fetch_sequence(region)
contigs_f.puts(">#{aln.target_id}\n#{seq}")
end
end
end
Version data entries
53 entries across 53 versions & 2 rubygems