[BioRuby] fastq files reading

[Anurag Priyam]

Hello xyz,

You should be able to solve this problem by parallel iteration over the two
files. An external iterator will be required  here. You can call next on an
external iterator to get the next object. It will raise a StopIteration
exception when there is no more item to iterate over. You will have to add a
case to handle that too.

Give something like the following a try:

require 'bio'

#open the two files
one = Bio::FlatFile.open(Bio::Fastq, 'readsA.fastq')
two = Bio::FlatFile.open(Bio::Fastq, 'readsB.fastq')

#get an external iterator for two
two_iterator = two.to_enum

#now iterate
one.each do |ff1|
 ff1.each do |entry1|

   header1 = entry1.entry_id
   seq1 = entry1.seq

   puts seq1.to_fasta(header1 + "qwa")

   entry2 = two_iterator.next
   header2 = entry2.entry_id
   seq2 = entry2.seq
   puts seq2.to_fasta(header2 + "qwa")
 end
end

#close the files
one.close
two.close

I did not have any fasta file to test it on, but it should work.

On Sat, May 29, 2010 at 5:44 PM, xyz <mitlox at op.pl> wrote:

> Hello,
> I would like to read at the same time two fastq files in order to
> save them to fasta file.
>
> require 'bio'
> Bio::FlatFile.open(Bio::Fastq, 'readsA.fastq') do |ff1|
>  ff1.each do |entry1|
>
>    header1 = entry1.entry_id
>    seq1 = entry1.seq
>
>    puts seq1.to_fasta(header1 + "qwa")
>
>    #header2 = entry2.entry_id
>    #seq2 = entry2.seq
>    #puts seq2.to_fasta(header2 + "qwa")
>  end
> end
>
> I have already the following code, but unfortunately I do not know
> how to read both files at the same time.
>
> How is it possible to read two files at the same time and write them
> to fasta file?
>
> Thank you in advance.
>
> Best regards,
>
>
> _______________________________________________
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>



-- 
Anurag Priyam,
2nd Year Undergraduate,
Department of Mechanical Engineering,
IIT Kharagpur.
+91-9775550642