[Bioperl-l] SimpleAlign object
Jason Stajich
jason at bioperl.org
Fri May 22 03:51:05 UTC 2009
I'm not sure what you *want* to print in "alignment" section? you have
the "actual alignment" as an object. It looks like you already got
that alignment object with get_aln() from your HSP- did you look at
the documentation for that method? You can also get the query/hit/
homology strings with methods called on the HSP object. The SearchIO
HOWTO describes this.
See Bio::SearchIO::Writer::TextResultWriter if you want to reformat a
blast report.
Or if you want to write it out in a Multiple alignment format (multi-
fasta, clustalw, phylip, etc) with Bio::AlignIO
You can use IO::String to write the sequence into a string instead of
to a file/STDOUT if you want to format things in your script
my $str = IO::String->new;
my $alnio = Bio::AlignIO->new(-format => 'clustalw', -fh => $str);
$alnio->write_aln($str);
The alignment formatted as a string is now in $str->string_ref so you
can access it from ${str->string_ref}
On May 21, 2009, at 8:38 PM, Mgavi Brathwaite wrote:
> Hello,
>
> I am parsing a blast report. My script is returning the following
> output to file:
>
> Name: 13414|HD
> Percent Identity: 100
> Alignment: Bio::SimpleAlign=HASH(0x40d0ac4)
> How do I access " Bio::SimpleAlign=HASH(0x40d0ac4)" actual alignment
> for this object?
>
> LomSpace
Jason Stajich
jason at bioperl.org
More information about the Bioperl-l
mailing list