= scbi_fastq

• http://www.scbi.uma.es/downloads

== DESCRIPTION:

scbi_fastq is a ruby gem to read/write FASTQ files (DNA/RNA sequences) with qualities in a variety of formats (Sanger, Solexa, Ilumina).

== FEATURES/PROBLEMS:

• Read FASTQ files in Sanger Solexa and Ilumina, making the appropriate quality values conversions
• Quality values can be automatically splitted
• Write FASTQ files in Sanger format
• Iteration over large files without extra memory usage
• Can read gzip files directly

== SYNOPSIS:

=== Reading a compressed FASTQ in gzip with iterator:

require 'scbi_fastq'

# open gzip file in sanger mode fqr=FastqFile.new('file1.fastq.gz')

fqr.each do |name,seq_fasta,qual,comments|

puts name
puts seq_fasta
puts qual
puts comments

end

fqr.close

=== Reading a FASTQ with iterator:

require 'scbi_fastq'

# open file in sanger mode fqr=FastqFile.new('file1.fastq')

fqr.each do |name,seq_fasta,qual,comments|

puts name
puts seq_fasta
puts qual
puts comments

end

fqr.close

=== Reading a FASTQ one sequence at a time:

require 'scbi_fastq'

# open file in sanger mode fqr=FastqFile.new('file1.fastq')

begin

# read one sequence
name,seq_fasta,qual,comments=fqr.next_seq

# name will be nil if there are not more sequences available
  if !name.nil?
  puts name
  puts seq_fasta
  puts qual
  puts comments
end
end until name.nil?

fqr.close

=== Writing a FASTQ:

require 'scbi_fastq'

# open new file f=FastqFile.new('file.fastq','w')

# prepare sample data name = 'seq1' seq_fasta= 'acgtacgtacact' seq_qual= [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40]

# write sequence to disk
f.write_seq(name,seq_fasta,seq_qual,'comments')

# close file f.close

== REQUIREMENTS:

• This is a standalone gem.

== INSTALL:

• gem install scbi_fastq

Contributing

1. Fork it ( https://github.com/[my-github-username]/scbi_fastq/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request