[Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Apr 19 23:52:53 EDT 2008


------- Comment #4 from cjfields at uiuc.edu  2008-04-19 23:52 EST -------
This is due to the way that GenericHSP::frame is implemented, which returns an
array of query/subject frame under list context.  Doing so bumps everything
else post frame in the columns back (and drops the last off).  

Unfortunately, this is inconsistent with the way that strand(), start(), end(),
and other HSPI methods are implemented (which expect 'hit'/'subject' and an
optional additional argument for setting the frame).  I'll go about trying to
change this for more consistency.

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