[Bioperl-l] quick question

[Shawn Hoon]

On Feb 20, 2004, at 12:10 PM, Jason Stajich wrote:

> if there is a clustalw header separating the concatenated alignments
> AlignIO is supposed to handle it.
>

Maybe I'm wrong, but there is no catch in the clustalw module to break 
if
one sees the header so it keeps going..
in anycase, i have committed a fix that seems to work.

thanks

shawn

> We might want to change the code below in AlignIO::clustalw to ignore
> blank lines...
>
>     my $first_line;
>     if( defined ($first_line  = $self->_readline )
>         && $first_line !~ /CLUSTAL/ ) {
>         $self->warn("trying to parse a file which does not start with 
> a CLUSTAL header");
>     }
>
> On Fri, 20 Feb 2004, Shawn Hoon wrote:
>
>> Anybody have a quick way of parsing concatenated clustalw files?
>> I could split the files up but wonder if anybody had a quick solution.
>> I don't think the AlignIO parse seems to handle this.
>>
>> shawn
>>
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>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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