[Biopython] reading two fastq files at the same time

xyz mitlox at op.pl
Mon Sep 6 13:24:14 UTC 2010


Hi,
How is it possible to read two fastq files at the same time in 
BioPython? I have the following BioRuby example:

require 'bio'

begin
   fq1 = Bio::FlatFile.open(Bio::Fastq, ARGV[2])
   fq2 = Bio::FlatFile.open(Bio::Fastq, ARGV[3])

   while (entry1 = fq1.next_entry) and (entry2 = fq2.next_entry)

     fastq_A1 = entry1.entry_id
     fastq_A2 = entry1.seq

     fastq_B1 = entry2.entry_id
     fastq_B2 = entry2.seq
   end

rescue => err
   raise "Exception: #{err}"
end

Thank you in advance.



More information about the Biopython mailing list