[Bioperl-l] Newbie alert: Aligning and printing first position

Diego M. Vadell dvadell at clustering.com.ar
Thu Mar 31 08:59:46 EDT 2011


Hi Roy,

  Thanks!! I can't beleive I didn't see that method in the documentation. 
Thank you very much. It worked perfectly.

Cheers,
 -- Diego

On Wednesday, March 30, 2011 12:43:35 pm Roy Chaudhuri wrote:
> Hi Diego,
> 
> Column refers to the position in the alignment, not the individual
> sequence. location_from_column therefore gives the position in the
> individual sequence that corresponds to the requested column (you get
> undef since there is a gap in the first column of the alignment for
> seq1). If I understand correctly, you want the reverse, the position in
> the alignment that corresponds to the first position in your sequence.
> For that you need the opposite function, column_from_residue_number:
> 
> my $loc=$seq->column_from_residue_number(1);
> 
> $loc will now contain 8 (not 7), since position 1 of your sequence is in
> column 8 of the alignment.
> 
> Hope this helps,
> Roy.
> 
> On 30/03/2011 15:51, Diego M. Vadell wrote:
> > Hi list,
> > 
> >      I have an alignment ( done with Bio::Tools::Run::Alignment::Clustalw
> >      )
> > 
> > that I can see ( printing $aln->match_line() along with the sequences ):
> >          ********* .:                                   (match_line)
> > 
> > .......TDDSFDTDVSSS.........[...].............   ($seq1)
> > SDKIIHLTDDSFDTDVLKADGA[...]EFLDANLA   ($seq2)
> > 
> >      It looks right ( that "[...]" is mine, it's larger ). Now I want to
> >      get
> > 
> > the position of the match ( the first "T" ), which should be "7". I
> > thought I needed to use something like:
> > 
> > my $seq = $aln->get_seq_by_pos(1);
> > my $loc = $seq->location_from_column(1);
> > say $loc;
> > 
> > And $loc would be 7, but it's undef. If I try to iterate from 1 to 10, I
> > start getting Bio::Location::Simple objects at the 8th place. So, should
> > I loop untill I location_from_column() gives me an object? Is it another
> > way of finding the position of the match?
> > 
> > As you can see, I'm just starting with bioinformatics. Any pointer will
> > be appreciated.
> > 
> > Thanks in advance,
> > 
> >   -- Diego
> > 
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l


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