[Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output

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http://bugzilla.open-bio.org/show_bug.cgi?id=2476





------- Comment #18 from maj at fortinbras.us  2008-11-30 00:15 EST -------
Created an attachment (id=1129)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1129&action=view)
subseq() defaults to "non-native" calls; see comments

I call a 'native' call one that is made with full understanding of the new
LocatableSeq functionality (with flexible start coordinate and ignoring of gaps
in length and subseq calculations). A non-native call is one that expects the
length of the sequence to be the absolute number of characters (gaps n all),
the sequence to always start at '1', and all characters to be returned. In a
non-native call, the mapping functionality should still work, but no frameshift
detection is done. Non-native subseq() will still throw if start is <0 or end >
length($lseq->seq).


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