[Bioperl-l] problem parsing WU-blast output

Joseph Fass joseph.fass at gmail.com
Wed Oct 24 14:56:55 EDT 2007


Has anyone else encountered a problem parsing wu-blast output with
Bio::SearchIO ?

The ->next_hit method first returns the "unfiltered+1" sequence; that is,
the plus strand representation of the query sequence that is listed (before
the minus strand) before the summary of hits and e-values.

Then, the next time the next_hit method is called, it returns the second hit
on the list.

The only caveat to my "bug" report here is that I was searching a database
that included the query sequence, so the first hit was identical to the
query (and maybe somehow retained the "unfiltered+1" tag?) ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


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