[Bioperl-l] is the Bio::Align::AlignI doc right?

[Mauricio Herrera Cuadra]

You should use our online documentation once you upgrade:

http://doc.bioperl.org/

Here is the updated POD in the 1.6.1 release:

http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Align/AlignI.html#POD32

Mauricio.

On 2/25/10 7:24 AM, Chris Fields wrote:
> Yes, but this has been long corrected on main trunk and the latest CPAN code (1.6.1).  v.1.2.3 is very old, very very very old.  Dinosaurs and perl 5.6.1-old.  You should update, even if you are using ensembl's perl API ;>
>
> chris
>
> On Feb 25, 2010, at 6:35 AM, Ben Bimber wrote:
>
>> below is a Bio::Align::AlignI example found here:
>>
>> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Align/AlignI.pm#column_from_residue_number
>>
>>
>> Title   : column_from_residue_number
>> Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
>> Function:
>>
>>            This function gives the position in the alignment
>>            (i.e. column number) of the given residue number in the
>>            sequence with the given name. For example, for the
>>            alignment
>>
>>              Seq1/91-97 AC..DEF.GH
>>              Seq2/24-30 ACGG.RTY..
>>              Seq3/43-51 AC.DDEFGHI
>>
>>            column_from_residue_number( "Seq1", 94 ) returns 5.
>>            column_from_residue_number( "Seq2", 25 ) returns 2.
>>            column_from_residue_number( "Seq3", 50 ) returns 9.
>>
>>
>> Perhaps I am simply misunderstanding the method, but shouldnt the first
>> example return 6, not 5?
>>
>> E is the 94th residue.  It is in the 6th column.  Am I missing something?
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>