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

[Brian Desany]

OK, I can reproduce that.

In short, write_seq loops through qual values 50 at a time and writes them
50 to a line. The conditional that keeps track of where you are and whether
you should stop was looking at "where you are < total length" instead of
"where you are <= total length".

"where you are" is only equal to "total length" in those cases where "total
length" is a (multiple of 50) + 1. Such as was the sequence you provided
(Seq2 at 801 bp).

I've committed a fix to bioperl-live.

-Brian.

Incidentally, the reason I didn't reproduce this originally is that I had
forgotten that in my local copy I had commented out that whole part where it
writes it out in 50 bp chunks.


>-----Original Message-----
>From: Rich LeDuc [mailto:rleduc@uiuc.edu]
>Sent: Wednesday, October 23, 2002 4:05 PM
>To: bdesany@bcm.tmc.edu
>Subject: RE: [Bioperl-l] Help with manipulating quality objects PLUS
>write_seq(args)
>
>
>Brain,
>
>Attached is my show_bug script, and the input file.
>
>The first line of my qual.pm is:
># $Id: qual.pm,v 1.10.2.2 2002/06/04 21:35:53 jason Exp $
>
>Please let me know is your system does not show the bug.
>
>Thanks,
>
>Rich
>
>
>
>At 02:39 PM 10/23/2002 -0500, you wrote:
>>Sure, go right ahead and send it and I'll see if it reproduces for me.
>>
>>Also if you could look at the 1st line of the
>Bio::SeqIO::qual.pm module
>>you're using and report what the version is, e.g.:
>>
>># $Id: qual.pm,v 1.10 2002/02/18 17:17:25 bosborne Exp $
>>
>>-Brian.
>>
>>
>> >
>> >Brian-
>> >
>> >If you are willing, I would be happy to send you a little
>> >"show bug" script
>> >I wrote, along with the small data file I use to feed it.
>> >
>> >I would be interested in knowing if the bug does not occur on
>> >your system.
>> >
>> >Thanks,
>> >
>> >Rich
>> >
>> >-------------------------------------------------------
>> >Richard LeDuc
>> >Research Programmer
>> >Bioinformatics Unit
>> >W.M. Keck Center for Comparative and Functional Genomics
>> >Biotechnology Center
>> >University of Illinois at Urbana-Champaign
>> >
>> >
>> >_______________________________________________
>> >Bioperl-l mailing list
>> >Bioperl-l@bioperl.org
>> >http://bioperl.org/mailman/listinfo/bioperl-l
>> >
>
>-------------------------------------------------------
>Richard LeDuc
>Research Programmer
>Bioinformatics Unit
>W.M. Keck Center for Comparative and Functional Genomics
>Biotechnology Center
>University of Illinois at Urbana-Champaign
>
>