[Bioperl-l] FASTQ output

Chris Fields cjfields at illinois.edu
Tue Jun 30 23:48:11 EDT 2009


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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