[Seqinr-forum] inconsistent behaviour of the getAnnot() function

[Jean lobry]

At 17:25 +0000 17/03/10, Coghlan, Avril wrote:
>Dear all,
>
>I've been using the getAnnot() function to retrieve annotations for
>UniProt sequences.
>
>For each query, I've been asking for a set of UniProt sequences. I've
>then been retrieving the annotations for each set of sequences using
>getAnnot().
>
>I noticed that usually getAnnot() returns the annotations for a set of
>sequences in the form of a list variable, where each element of the list
>variable is a vector containing the annotations for a particular
>sequence.
>
>However, sometimes getAnnot() returns the annotations for a set of
>sequences in the form of a matrix variable, where each column of the
>matrix variable contains the annotations for one sequence.
>
>I've included the R code for two examples below, one where getAnnot()
>returns the annotations in a matrix variable (Example 1 below), and one
>where getAnnot() returns the annotations in a list variable (Example 2
>below).
>
>I am a bit confused why getAnnot() does not always return the
>annotations in the same sort of data structure (eg. always as a list
>variable).
>I'm wondering could this possibly be due to a bug in getAnnot()?
>
>Kind regards,
>Avril
>
>Avril Coghlan
>University College Cork
>Ireland
>

Hi Avril,

thanks for the nice bug repport. I have just commited a fix, will
be available on R-forge (revision >= 1742) in a day or two and
then in release 2.0-9 (not yet schedulded but this clearly desserves
a new release).

Best,

Z.
-- 
Pr. Jean R. Lobry (Dr. phil. hab.)
Head of Laboratoire de Police Scientifique de Lyon
Institut National de Police Scientifique
31 av. F. Roosevelt, F-69134 ECULLY CEDEX
Allo: +33 (0)4 72 86 89 60
e-mail: jean.lobry at interieur.gouv.fr