[Bioperl-l] quick question

Jason Stajich jason at cgt.duhs.duke.edu
Fri Feb 20 15:10:25 EST 2004

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

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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