New dseq manu bjorn rebased#484

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manulera wants to merge 90 commits intomasterfrom

new_dseq_manu_bjorn_rebased

Commits on Nov 11, 2025

updated seq class: use base class slicing, added full_sequence property

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Added override of Bio.Restriction.FormattedSeq._table

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Added dicts and tables _ambiguous_dna_complement, _keys, _values, _complement_table, _complement_table, to_watson_table, to_crick_table, to_N, to_5tail_table, to_3tail_table, to_full_sequence, bp_dict

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1. import inspect module, tables and dicts from utils module

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Dseq + empty string now returns the Dseq obj unchanged. collected all imports at the top. Some tests involved strands that did not anneal prefectly, these have been corrected.

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1. A new CircularString class. Work in progress, should be natively bytestrings

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_annealing_positions new implementation using _iupac_compl_regex from utils. This should fix U in primers

BjornFJohansson
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fixed fill_left and fill_right and a FIXME

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fixed initiation

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deleted

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anneal_from_left function and more regexes and tables

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updated test for USER cloning

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moved all imports to the beginning. Changed some tests. There is a FIXME indicating a large change in behaviour.

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removed if __name__ == __main__

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removed main test and moved imports to the top

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1. Exchanged xxxx and yyyy to 1111 and 2222 respectively. This because x and y has meaning in the new Dseq implementation. (line 1074)

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Updated docstrings in Dseq class for clarity, work in progress

BjornFJohansson
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fix doctests

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removed main chunk

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moved import

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removed reference to .length property

BjornFJohansson
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removed reference to .length property

BjornFJohansson
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removed code regarding the alphabet, not in the alphabet module

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broke out the __repr__ code to a function for clarity, reintroduced the check for internal splits in init

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alphabet related code in src/pydna/alphabet.py

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mostly comments

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Commented out code to be removed.

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CircularString -> CircularBytes (a byte string version).

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Only check for start of error message.

BjornFJohansson
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Clearer names for some dicts

BjornFJohansson
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Replaced numbers 1111 and 2222 with bbbb and rrrr, respectively. Numbers do not work with new

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Added tests.

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Moved imports to top. removed main block

BjornFJohansson
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remove empty file `master`
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refactor to simplify + address #452
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Commented out unused code.

BjornFJohansson
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Added a stub for the new user_assembly_design function.

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more details in test_USERcloning.py

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Added back apply_cut based on processing with translation tables.

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better code comment

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These slices behave differently with the new simplified Dseq.__getitem__. I would like to define the behaviour like this and add more tests

BjornFJohansson
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code clarification

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alphabet defitition now in docstring

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strip data before setting ._data property

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instead of testing for identity we test if seq_u and seq_v anneal

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test for feeding Dseq with watson/crick having leading whitespace

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Changed how dscode_to_watson_table and dscode_to_crick_table are built to avoid duplicate symbols in the translation tables. This is important for the dscode for U/A ($) and A/U (%).

BjornFJohansson
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Improved implementation of looped method with bugfixes. More tests needed.

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1. Modified __add__ to accept single stranded sequences. This is necessary for the new implementation of the pydna.assembly2.assemble function, for primers etc. placeholder now used to check for ba…

BjornFJohansson
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1. reimplemented a part of the assemble function to be able to deal with PCR and avoid shuffling of features.

BjornFJohansson
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Fixed tests regarding looped. More tests are needed.

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Numbered feature types in test misc -> misc1..misc18. Two tests still failing.

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spelling error

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Edited out Dseq.from_string method and switched to Dseq.quick in Dseqrecord.__init__

BjornFJohansson
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fixed tests switching Dseq.from_string to Dseq.quick

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better Dseq.__str__ docstring

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added a find method to the CircularBytes class.

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docsstring for get_parts function.

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Commented out test_cas9(), since this tests an obsolete feature.

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Commented out obsolete cas9 method.

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Bugfix!

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watson_ovhg is a property

BjornFJohansson
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Mostly better docstrings, interactive examples and comments.

BjornFJohansson
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moved big regexes to alphabet and expressed them in terms of dscode alphabet letters

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docstring stubs for factory functions

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copied tests from Dseq4 branch

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all melt tests pass

BjornFJohansson
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fixed the range test so that two of the melt tests pass

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fix looped and add docstring to overridden pcr linear assembly function
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Commits on Nov 15, 2025

Commits on Dec 4, 2025

switch from namedtuple to dataclass

manulera
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BjornFJohansson
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remove FIXMEs

manulera
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BjornFJohansson
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add getitem to DseqParts dataclass

manulera
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BjornFJohansson
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Commits on Dec 10, 2025