[Bioperl-l] SearchIO HOWTO

[Bernd Web]

Hi,

On http://www.bioperl.org/wiki/HOWTO:SearchIO there is a great HOWTO
parse your BLAST report.
In the Table of methods, the third line from the bottom is:
"HSP  alignment  Not available in this report  Bio::SimpleAlign object  "

Would it not be good to add the get_aln method ( $hsp->get_aln) ?

The line in "Using the methods"
my $alignment_as_string = $alnIO->write_aln($aln);

may be confusing: $alignment_as_string will be "1" on success and the
alignment is printed to STDIO. Should IO::String be introduced here
too set up a string filehandle?


Best regards,
Bernd