[Bioperl-l] A picky question about "fasta.qual" files

[Ewan Birney]

On Thu, 30 Jan 2003, Nancy Hansen wrote:

> 
> Hi!
> 
> 	I've been doing a lot of qual file reading with SeqIO lately, and
> am bothered by the fact that qual.pm assumes a space at the end of each
> line (i.e., following the last quality value on each line).  Is this a
> standard that I've just never picked up until now?  In any case, I've been
> given qual files with no space at the end of each line, and the
> PrimaryQual object SeqIO returned has joined qualities, e.g. '5161' where
> 51 was the last quality on the first line, and 61 the first on the next
> line, etc.
> 
> 	It seems like qual.pm could check for the space at the end of the
> line, and add it if it doesn't exist, just to forgive (and make
> parsable) the qual files that were created without knowledge of this
> standard.

Sounds v. sane. Make the change, send us the new qual.pm and/or patch and
we will apply.


> 
> 	Thanks,
> 	--Nancy
> 
> *************************************
> Nancy F. Hansen, PhD	nhansen at nhgri.nih.gov
> Bioinformatics Group
> NIH Intramural Sequencing Center (NISC)
> 8717 Grovemont Circle, Rm. 152L
> Gaithersburg, MD 20877
> Phone: (301) 435-1560	Fax: (301) 435-6170
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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