[Bioperl-l] Bio::AlignIO::Mase

[Jason Stajich]

Hi Tristan - 

This regular expression is to is to strip everything that isn't a letter, . or -  
the [^] means match everything EXCEPT what follows.  I guess if numeric values are valid in these type of alignments you would just add \d (instead of 0-9)  

So you are asking for the parser to not strip out frameshift info from a MASE parser? 

This doesn't have anything to do with the chunk pattern or size set with $/ AFAIK.

On Jun 8, 2011, at 7:45 AM, Tristan Lefebure wrote:

> Hi there,
> 
> I have some weird alignments with some numerical code stored 
> within the sequence strings (eg. frameshift genewise code). 
> Most AlignIO module I have tried eat them without any 
> trouble except for Bio::AlignIO::Mase.
> 
> The following patch seems to do the trick:
> 
> diff -u mase.pm mase_mod.pm
> --- mase.pm     2011-06-08 14:08:58.558033996 +0200
> +++ mase_mod.pm 2011-06-08 14:09:20.388066014 +0200
> @@ -109,7 +109,7 @@
> 
>        while( $entry = $self->_readline) {
>            $entry =~ /^;/ && last;
> -           $entry =~ s/[^A-Za-z\.\-]//g;
> +           $entry =~ s/[^A-Za-z0-9\.\-]//g;
>            $seq .= $entry;
>        }
>        if( $end == -1) {
> 
> But I am left with the feeling that I don't really 
> understand why this works (which I don't quite like before 
> pushing a patch...)
> 
> Why doing a s///g instead of a simple m//, and why doing 
> '/[^' and not '/^['... Is that linked to that fact that $/ 
> was modified to read chunks of files? BTW where is $/ set? I 
> searched in Bio::Root::IO but didn't find it... 
> 
> Oh so many questions...
> 
> Thanks!
> 
> --
> Tristan
> 
> 
> 
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