Started fixing incorrect DP in pairwise2
Added unit tests.
Fixed tabs.
Fixed a couple of typos in comments. PEP8 formatting
Thank Bryan Lunt as a contributor (Bio.pairwise2 work)
Fix BgzfWriter's tell method (reported by Petra Kubincová)
Bio.trie fix for with_prefix
Test for Bio.trie with_prefix bug reported by Kenvin Wu
Thank Jeffrey Chang in news (Bio.trie with_prefix fix)
Cope when eprimer3 reports oligo without sequence
Test case where eprimer3 reports oligo without sequence
Increase Bio.trie MAX_KEY_LENGTH and check if exceeded
Test BgzfWriter tell method works (see recent fix)
Added a PendingDeprecationWarning to Bio.Motif. Added a paragraph to NEWS to announce the new Bio.motifs module
Upgrading obsolete code to deprecated code
SearchIO hmmer3-text: Don't overload the hit_list variable with different datatypes

No functional change, just a rename of a variable to make the code less confusing

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
SearchIO: Add optionalcascade getter/setter to allow Hit objects without HSPs

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
SearchIO hmmer3-text: HSP entries can be empty for valid hits

This should fix bug #3400 and still needs a test

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Fix stray comma
ElementTree deprecated getchildren in Python 2.7