[Bioperl-l] Creating a fastq format file?

[Michael Muratet]

On Apr 22, 2009, at 8:32 AM, Dan Bolser wrote:

> In the Bio::SeqIO::fastq page:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/SeqIO/fastq.pm#write_seq
>
>
> I read:
>
> "This object can transform Bio::Seq and Bio::Seq::Quality objects to
> and from fastq flat file databases."
>
> I'm not sure how to code the link between the fastq IO object and the
> qual object that I have created using the code from the previous
> thread...
>
> Any suggestions? What am I missing?

Howdy

This might be a good place to ask the question: having looked at the  
fastq.pm page, is the fastq format defined (only) by a "@'" followed  
by a sequence line and a "+" header followed by a quality line and the  
two headers have to agree? Now that Illumina is using phred scaling,  
are 'Sanger' and 'Illumina' versions the same?

Thanks

Mike
>
>
>
> 2009/4/22 Dan Bolser <dan.bolser at gmail.com>:
>> Creating a fastq format file from fasta and 'fasta quality file'?
>>
>>
>> Hi,
>>
>> I'm sure this is easy, but I'm still not able to 'think bioperl'...
>>
>> I have a 'fasta quality file' and a fasta file, and I would like to
>> output a fastq file. I followed the discussion on the previous thread
>> here:
>>
>> http://bioperl.org/pipermail/bioperl-l/2008-July/028013.html
>>
>>
>> With the conclusion seeming to be 'just do it'. Could someone point  
>> me
>> at a way to do this, or was that suggestion an error? i.e. the poster
>> was working out a way to create a fastq the only way possible...
>>
>> I get the feeling that this should be a one-liner, but perhaps the
>> above thread was demonstrating the code I need to copy.
>>
>>
>> Thanks for any suggestions,
>>
>> Dan.
>>
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