[Bioperl-l] Blast parsers missing functions

Kevin Brown Kevin.M.Brown at asu.edu
Thu Mar 22 11:25:21 EDT 2007


I was looking through the deobfuscator after creating a blast file
parser that failed on parsing a blast XML file due to a missing method
and I see there are actually quite a few missing.

Found in Bio::SearchIO::blast, but not Bio::SearchIO::blastxml or
Bio::SearchIO::blasttable
best_hit_only
check_all_hits
inclusion_threshold
max_significance
min_query_length
min_score
signif

I use the min_score in my parser so that blastall can be run with a high
E and later filtered, or refiltered for other things after the blast is
done.

It would be nice if all the blast parsers had most of these missing
functions to at least keep them consistent with each other for parsing
blast reports :)



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