[Bioperl-l] Help with manipulating quality objects PLUS write_seq(args)

[Brian Desany]

>Subject: [Bioperl-l] Help with manipulating quality objects
>

>under certain circumstances write_seq does not return the same
>sequence as
>qual - specifically write_seq drops the last quality value -
>but only when
>the last value would be on a line by itself.

I haven't been able to reproduce this problem with Bio::SeqIO::qual from
either the 1.0 release or bioperl-live.


On a separate note:

One thing I did notice is that write_seq takes named arguments, and uses
_rearrange to get SOURCE.  OTOH, Bio::SeqIO::fasta::write_seq takes an array
of Seq objects.

In my code I like to have the correct module chosen at runtime and call
write_seq without necessarily knowing ahead of time whether it's a fasta or
qual IO. So therefore I would also like to call write_seq in the same way
for both.

Does anyone mind if I change qual.pm so that you can write_seq with

$io->write_seq($qual);

in addition to

$io->write_seq('-source'=>$qual);


I can basically keep it as it is, except that if you pass it one $argument
it treats it as if you passed in '-source'=>$argument. I wouldn't want to
break anyone that depends on the existing behavior.

-Brian.