Sha256: a40a5f5b419616ddbdd71a4e07f4071875e8dcec37824d6f51e36bc28199cb1e
Contents?: true
Size: 937 Bytes
Versions: 28
Compression:
Stored size: 937 Bytes
Contents
#!/usr/bin/env ruby
require 'scbi_fasta'
# GOOD_QUAL=50
# BAD_QUAL=10
# DOWN_CASE=('a'..'z')
class Array
def count
self.length
end
end
if ARGV.count < 4
puts "#{$0} FASTA QUAL OUTPUT_NAME SEQ_NAMES_FILE"
exit
else
fasta = ARGV.shift
qual = ARGV.shift
output_name = ARGV.shift
seqs_file=ARGV.shift
seqs=[]
f=File.open(seqs_file).each_line do |line|
seqs.push line.strip.chomp
end
# puts seqs.join(';')
fqr=FastaQualFile.new(fasta,qual)
output_fasta=File.new(output_name+'.fasta','a')
output_qual=File.new(output_name+'.fasta.qual','a')
fqr.each do |seq_name,seq_fasta,seq_qual|
if seqs.index(seq_name)
output_fasta.puts ">#{seq_name}"
output_fasta.puts seq_fasta
output_qual.puts ">#{seq_name}"
output_qual.puts seq_qual
seqs.delete(seq_name)
if seqs.empty?
break
end
end
end
output_qual.close
output_fasta.close
fqr.close
end
Version data entries
28 entries across 28 versions & 1 rubygems