[Bioperl-l] parsing only the summary part of a blast report

Hilmar Lapp hlapp@gmx.net
Wed, 11 Oct 2000 11:12:12 +0200

> "Zhao, David [PRI]" wrote:
> Hi there,
> How can I parse the summary part of a blast report using bioperl
> modules? such as:

I'm almost sure you can't using Blast.pm. Maybe you can with BPlite
(development trunk only). I know that Blast.pm takes a signifant time to
parse long reports (i.e., with  hundreds of alignments), but we haven't
checked yet whether BPlite is significantly faster in such cases. I guess
you're asking because you bother about the time lost in parsing the
alignments, although you needed only the summary data which are already
present in the hit list.

BTW you can pass a significance threshold to Blast.pm, and although I'm
not sure I think it won't parse those alignments beyond the significance

Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727