New dseq - draft #441
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New dseq - draft #441
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…mplement_table, _complement_table, to_watson_table, to_crick_table, to_N, to_5tail_table, to_3tail_table, to_full_sequence, bp_dict
2. new Dseq.__init__ w same arguments as before, but data is now stored in Bio.Seq.Seq._data 3. altered Dseq.quick classmethod 4. watson, crick and ovhg are methods decorated with @Property 5. New method to_blunt_string with returns a the string of the watson strand if the underlying Dseq object was blunt. 6. Old __getitem__ replaced 7. New __repr__ method 8. new looped method 9. new __add__ method
… imports at the top. Some tests involved strands that did not anneal prefectly, these have been corrected.
…ytestrings 2. user method that removes U and leaves an empty site. 3. cast_to_ds_right, cast_to_ds_left methods, these are *not* fill_in methods as they do not rely on a polymerase. 4. New melt method, useful for USER cloning etc.. 5. reimplemented apply_cut method
… utils. This should fix U in primers
…XME indicating a large change in behaviour.
…e x and y has meaning in the new Dseq implementation. (line 1074) 2. The expected result in test_pcr_assembly_uracil should be AUUAggccggTTOO. 3. Removed numbers at start and end of some sequenses. This could be discussed. 4. Four instances of FIXME: The assert below fails in the Sanity check on line 770 in assembly2, but gives the expected result.
…he check for internal splits in init
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