Sha256: beacbe318cce4db639b30239d1336e77ae303ad822df70123f4bf66e63d02baa
Contents?: true
Size: 788 Bytes
Versions: 28
Compression:
Stored size: 788 Bytes
Contents
#!/usr/bin/env ruby
require 'scbi_fastq'
class Array
def count
self.length
end
end
if ARGV.count < 3
puts "#{$0} FASTA OUTPUT_NAME SEQ_NAME_FILE [MORE_SEQ_NAMES]"
exit
else
fasta = ARGV.shift
qual = ARGV.shift
output_name = ARGV.shift
seqs=ARGV
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