Sha256: 5d369dc36f9ea7a525a7e8c7a4cd604fd66aa26d4cf33ee4f6fec208a610fe91
Contents?: true
Size: 696 Bytes
Versions: 28
Compression:
Stored size: 696 Bytes
Contents
#!/usr/bin/env ruby
require 'scbi_fastq'
class Array
def count
self.length
end
end
if ARGV.count != 3
puts "#{$0} FASTQ OUTPUT_NAME SEQ_NAMES_FILE"
exit
else
fasta = 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=FastqFile.new(fasta)
output_fastq=FastqFile.new(output_name+'.fastq','w')
fqr.each do |seq_name,seq_fasta,seq_qual|
if seqs.index(seq_name)
output_fastq.write_seq(seq_name,seq_fasta,seq_qual)
seqs.delete(seq_name)
if seqs.empty?
break
end
end
end
output_fastq.close
fqr.close
end
Version data entries
28 entries across 28 versions & 1 rubygems