I know we can't get around the problem of the IDs, since blast & blast -m8
give different IDs. But columns 5 and 6 (mismatches, gap openings) are
consistently different. Is search2table not trying to mimic -m8 exactly, or
is this a bug?
Apologies if this is due to using bioperl 1.4 and the PLS script from
1.5.0-RC1. That's what I have on hand.
> Note that if you just using BLAST you will find that the blast2table
> script that is included in the BLAST book (see the O'Reilly website
> for the book and download the code examples) will also generate this
> sort of thing for you and will be many times faster than SearchIO
I could steal that. But I was thinking that if NCBI changes the BLAST
format, bioperl may upgrade while the dead trees code won't.
- Amir Karger
Computational Biology Group
Bauer Center for Genomics Research
> There is also an equivalent hmmer_to_table and
> fastam9_to_table which are very fast re-formatters that don't
> actually use SearchIO since one is just trying to get the
> very simple
> data out.
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12/ >