FASTQ output

[Chris Fields-5]

I am working on FASTQ output and noticed a real oddity.  Apparently,  
there are three write_* methods for this module, with the odd choice  
of write_seq for Bio::SeqIO::fastq writing FASTA, not FASTQ.  
write_qual() writes Qual format:

http://www.bioperl.org/wiki/Qual_sequence_format

and write_fastq() writes FASTQ.  Now, maybe it's just me, but I think  
an implementation of write_seq() for a specific format should probably  
output that format and not something else entirely unexpected.  Also,  
is there a reason for duplicating output code for qual and FASTA  
output within Bio::SeqIO::fastq, i.e. should we call Bio::SeqIO::fasta/
qual instead?

I would consider the write_seq() issue a bug, the others are really  
just maintenance issues.  Anyone have problems with me changing that  
up a bit?

chris
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[Hilmar Lapp]

On Jul 1, 2009, at 5:48 AM, Chris Fields wrote:

> I am working on FASTQ output and noticed a real oddity.  Apparently,  
> there are three write_* methods for this module, with the odd choice  
> of write_seq for Bio::SeqIO::fastq writing FASTA, not FASTQ.  
> write_qual() writes Qual format:

Maybe the motivating thought was that a SeqIO module ought to write  
sequences when write_seq() is called. I agree though that a writer for  
a format ought to write that format and not something else.

> [...] is there a reason for duplicating output code for qual and  
> FASTA output within Bio::SeqIO::fastq

Hopefully not.

> [...]  Anyone have problems with me changing that up a bit?

Go ahead.

        -hilmar
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