[Bioperl-l] is the Bio::Align::AlignI doc right?
cjfields at illinois.edu
Thu Feb 25 08:24:17 EST 2010
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 ;>
On Feb 25, 2010, at 6:35 AM, Ben Bimber wrote:
> below is a Bio::Align::AlignI example found here:
> Title : column_from_residue_number
> Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber)
> 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
> 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
More information about the Bioperl-l