All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
New common_sub_strings function. The previous version was implemented in pure python that was quite fast, but still a bottleneck in the code. Thanks to @louisabraham, we now have code based on pydivsufsort which provide bindings to libdivsufsort, a very fast suffix array construction algorithm written in c. As a consequence, the Assembly code is now much faster.
Poetry is now used for building pydna. I have removed the setup.py file. I also do not build Anaconda packages anymore, as conda-build got too slow to work with. I have plans to update the Bioconda recipe for the new version. As pydna is pure Python, anyone can make a conda package using grayskull for example.
Dseq and Dseqrecord now only take a circular argument (True or False) to indicate topology. Previously, linear was also
accepted. This was a little used feature (by me) that made the init methods of both classes slow and complex. As this
was a violation of zen#13 ("There should be one-- and preferably only one...") This change could break code,
hence the bump of major version number.
Code formatting with Black (also suggested by @louisabraham). I now use a git pre-commit hook for this, so formatting should be more standardized.
Removed cache for all but download and genbank. Several functions and methods could previously be cached, something that saw very little use. The cache for genbank and download remain as this reduces the load on Genbank servers and also speed things up.
Environment variable pydna_assembly_limit sets the execution time in seconds (default 10) for
the assemble_linear and assemble_circular methods. There might be a better way to find out if an assembly is likely to take long, usually when there are many paths through the assembly graph.
17:01 $ git log --oneline --graph v5.2.0..a03c2a06a20afef95415f5f1786df2f71e921fd0
* a03c2a06a2 (HEAD -> dev_bjorn, origin/dev_bjorn) only build on master
* c7ce8582fa uppd action
* ca4c969c28 fix tests and commented out unneeded code
* 6539a1f076 added this as probably needed for a future bioconda package
* c933ca5a7b added this as probably needed for a future bioconda package
* c32fc5c9be fastes dseq init in dsecrecord init
* 70ced77d24 added min_rotation from pydivsufsort
* 2cc4edbc68 (origin/black, black) ws
* 4888db36f3 all black
* 0bf9fbd993 formatted with black precommit hook
* 74e3e1c229 fromatted with black
* f78dcb2fdd uppd poetry.lock
* 769dc98d89 (mergeexp) merge
|\
| * d242459fc5 (speed_up_Dseqrecord) try to ignore prof dir
| * bef4f6800c (origin/speed_up_Dseqrecord) edit
| * e29ac49f8e prep for adding new dundermethods
| * 2acbc5033c prep for implementing __copy__ and __deepcopy__ methods
| * 9916a62c93 added pstats script
| * 0b41671c1c mod tests
| * 9f060a0dea ignore
| * cbd4773605 added back test for iterable
| * 9b93d8988c removed linear property
| * 798899569a profiling
| * 9b5e7a6c13 added back prof
| * b1a8771323 add back profilig dir
| * ae93cb340f added dep pydivsufsort
| * 6f3f39398a Remover 'linear' method for Dseq and Dseqrecord - passes modified tests
| * 694ea1b5d5 (smallest_rot) new faster common_sub_strings
* | c57f5cb3c5 try fix profining error
* | f82a5676d6 fix test
* | 9d18ed4c03 gitignore
|/
* 28d8e98fd8 separated doctests
* dacf9e1f3b whitespace
* 6513a0bf85 removed cruft
* c4a0265a12 removed profiling
* 3c11115871 try ignore
* 01999514c2 do not track profiling files
* 6eb2154fff reformatted code
* 4e08cb910d switched to array in smallest_rotation function and fixed a docstring
* 014b40e20d reorganized common_sub_strings
* 190541a51e fix pyproject.toml
* 4c9d27042f added pytest-profiling to env
* 733d83782a added profiling to run_test
* 1db40a1bc7 added experiment files
* 9ac4f4c6f2 added prof
* b867cd2039 removed old file
* 35f8eb03d1 added profiling
* 4b4bafb272 changed badge
* f496be825b url
* a16e7a004d uppdate
* 5190177811 removed python 2 code
* 76a5930791 set timeout from env var pydna_assembly_limit
* 3cf0bba9bc added assembly limit to default env vars
* cd76b4a123 added urls
* f4ef97dbc0 uppdated cheat sheet
* c0f111c67a changed target branch for pull req
* f0385b7981 New timeout for assembly
* 5252df3cf4 switched from wrapt-timeout-decorator
* 5d46b153e6 upd poetry deps
* 436ae27381 removed cython notebook
* ce9a919e15 fix dep
* 2ce61667de fix deps
* 8be47b5463 stuff
* 75ea5dbee1 Merge branch 'dev_bjorn' of https://github.com/BjornFJohansson/pydna into dev_bjorn
|\
| * 5c2ec77539 Merge pull request #106 from BjornFJohansson/dependabot/pip/coverage-7.2.2
| |\
| | * b15fd0cbb4 Bump coverage from 7.2.1 to 7.2.2
* | | 8e529ff1c7 remove cashing for some functions
|/ /
* / 8dd2ca19a0 bugfix: hardcoded strand set to 1
|/
* dacb024944 updated poetry.lock
* a3c3791917 fix
* 74d3850352 Merge pull request #94 from BjornFJohansson/dependabot/pip/ipython-8.10.0
|\
| * 66f20aa195 (origin/dependabot/pip/ipython-8.10.0) Bump ipython from 8.9.0 to 8.10.0
* | 30d109bbb2 Merge pull request #95 from BjornFJohansson/dependabot/pip/biopython-1.81
|\ \
| * | bd0ef21a96 Bump biopython from 1.80 to 1.81
| |/
* | 879c81ccf7 Merge pull request #96 from BjornFJohansson/dependabot/pip/pyqt5-5.15.9
|\ \
| * | 5482b0788f Bump pyqt5 from 5.15.8 to 5.15.9
| |/
* | 813ac07394 fix gel image test
* | 63de396a5f fix gel examples
* | 1eb18bc709 new example w gel
|/
* c6d1fbda8c fix link
* ffda81e24e Merge branch 'master' of https://github.com/BjornFJohansson/pydna
|\
| * f8896ab27f Update README.md
* | 546f357997 Merge branch 'dev_bjorn'
|\ \
| |/
|/|
| * 98b6eaa55f improve example
| * 186dbff025 bugfix for slicing genbankrecords
| * 10e79ccaba fix table
* | c45913bee0 Merge branch 'dev_bjorn'
|\|
| * 593b1f4dfb simplify readme
| * 9800fdf2bb whitespace
| * 9276a054fa start to make a better figure for amplicon
| * 0cb741bf84 better example with pcr
* | a6fda7a276 Merge branch 'dev_bjorn'
|\|
| * c1ec911a22 fix example
| * 5b53ffc9ff fix raw link
* | 77f2121d76 Merge branch 'dev_bjorn'
|/
* fbcdb0bea4 fix link
* b9ada45f20 (origin/poetry, LouisAbraham/poetry, poetry) new readme
07:26 $ git log --oneline --graph v5.2.0..a16e7a004da1292f33db5a9a48f19c61b415dff6
* a16e7a004d (HEAD -> dev_bjorn, origin/dev_bjorn) uppdate
* 5190177811 removed python 2 code
* 76a5930791 set timeout from env var pydna_assembly_limit
* 3cf0bba9bc added assembly limit to default env vars
* cd76b4a123 added urls
* f4ef97dbc0 uppdated cheat sheet
* c0f111c67a changed target branch for pull req
* f0385b7981 New timeout for assembly
* 5252df3cf4 switched from wrapt-timeout-decorator
* 5d46b153e6 upd poetry deps
* 436ae27381 removed cython notebook
* ce9a919e15 fix dep
* 2ce61667de fix deps
* 8be47b5463 stuff
* 75ea5dbee1 Merge branch 'dev_bjorn' of https://github.com/BjornFJohansson/pydna into dev_bjorn
|\
| * 5c2ec77539 Merge pull request #106 from BjornFJohansson/dependabot/pip/coverage-7.2.2
| |\
| | * b15fd0cbb4 Bump coverage from 7.2.1 to 7.2.2
* | | 8e529ff1c7 remove cashing for some functions
|/ /
* / 8dd2ca19a0 bugfix: hardcoded strand set to 1
|/
* dacb024944 (origin/master, master) updated poetry.lock
* a3c3791917 fix
* 74d3850352 Merge pull request #94 from BjornFJohansson/dependabot/pip/ipython-8.10.0
|\
| * 66f20aa195 (origin/dependabot/pip/ipython-8.10.0) Bump ipython from 8.9.0 to 8.10.0
* | 30d109bbb2 Merge pull request #95 from BjornFJohansson/dependabot/pip/biopython-1.81
|\ \
| * | bd0ef21a96 Bump biopython from 1.80 to 1.81
| |/
* | 879c81ccf7 Merge pull request #96 from BjornFJohansson/dependabot/pip/pyqt5-5.15.9
|\ \
| * | 5482b0788f Bump pyqt5 from 5.15.8 to 5.15.9
| |/
* | 813ac07394 fix gel image test
* | 63de396a5f fix gel examples
* | 1eb18bc709 new example w gel
|/
* c6d1fbda8c fix link
* ffda81e24e Merge branch 'master' of https://github.com/BjornFJohansson/pydna
|\
| * f8896ab27f Update README.md
* | 546f357997 Merge branch 'dev_bjorn'
|\ \
| |/
|/|
| * 98b6eaa55f improve example
| * 186dbff025 bugfix for slicing genbankrecords
| * 10e79ccaba fix table
* | c45913bee0 Merge branch 'dev_bjorn'
|\|
| * 593b1f4dfb simplify readme
| * 9800fdf2bb whitespace
| * 9276a054fa start to make a better figure for amplicon
| * 0cb741bf84 better example with pcr
* | a6fda7a276 Merge branch 'dev_bjorn'
|\|
| * c1ec911a22 fix example
| * 5b53ffc9ff fix raw link
* | 77f2121d76 Merge branch 'dev_bjorn'
|/
* fbcdb0bea4 fix link
* b9ada45f20 (origin/poetry, poetry) new readme
(END)
- New gel module
- New module myprimers_gdoc for storing primers in a google doc
- New module fakeseq for making DNA ladders.
- New module ladders containing DNA molecular weight markers.
- Changes to myprimer module.
3.1.3 - 2020-10-10
- added .sorted_features method for SeqRecord
- added a new lcs (longest common substring) method for SeqRecord and DseqRecord
- changed format for changelog
- biopython 1.78 in requirements.txt
- fix to scripts/check_my_primers.py
3.1.2 - 2020-09-28
- Bugfix release. There was a bug in stamping genbank files with cSEGUID.
3.1.1 - 2020-09-25
- Bugfix release. There was a bug in locating features in certain circular assemblies.
- Added a test: "test_marker_replacement_on_plasmid" in test_module_assembly.py to test for this.
3.1.0 - 2020-09-16
- Changed to src layout for the package. Changed how melting temperature is calculated.
- Changes to tests, added a conftest.py. Updated for comatibility with biopython 1.7.8.
- Removed mysequences.py
- Reformatted code with BLACK
- Use github actions for building and testing
3.0.2a1 - 2019-07-23
- .upper() and .lower() methods for Dseq and Dseqrecord classes. Improved slicing
3.0.1 - 2019-05-28
- Many changes and improvements, especially for the Assembly class.
3.0.0 - 2019-05-17
2.0.3 - 2017-12-14
- pcr function now takes an amplicon. This way an amplicon can easily be rerun after modification of primers or template
2.0.3a0 - 2017-12-03
2.0.2 - 2017-08-26
2.0.2 - 2017-08-26
2.0.1 - 2017-08-24
2.0.0 - 2017-06-23
- First release of 2.0.0. This version adds changes in the alpha versions
2.0.0a4 - 2017-05-05
-Fixed bug in _multiply_circular
2.0.0a3 - 2017-04-04
- added the all module, from pydna.all import *, now imports a set of useful pydna modules into the main namespace.
- Finer control over cache, genbank download is now on by default. Bug fix in assembly_fragments function that created too long primer tails.
2.0.0a2 - ---
- removed setting functions for cache in _init and the delete_cache function for simplicity
- removed these functions
- pydna.design.print_primer_pair
- pydna.design.cloning_primers
- pydna.design.integration_primers
- pydna.design.assembly_primers
2.0.0a0 - 2017-03-15
- alpha release, removed imports in init
- This version breaks compatibility.
1.2.0 - 2017-03-10
- New and simpler primer design api, especially for gibson assembly primers. See docstrings
- Dseqrecord.find method that allows finding subsequences "over the edge" of circular sequences.
1.1.5 - 2016-12-16
- added message for Dseqrecord write
1.1.4 - 2016-12-15
- split some files into more logical and smaller chunks.
- The Primer class is now the same in primer design and amplify modules
- less modules are imported in init.py
- pydna.getcache returns the pydna_cache environment variable
- pydna.cached sets pydna_cache to "cached"
- pydna.nocache sets pydna_cache to "nocache"
- pydna.refresh sets pydna_cache to "refresh"
- Many of the Classes have new repr methods compatible with the Jupyter notebook.
- One Jupyter notebook is now run as a part of the test suite using pytest/nbval
- pydna.parse_primers now return a list of Primer class objects
- pydna.read_primer now a Primer class object
- pydna.read_url and pydna.parse_url removed, since they are too risky.
- it is better to use pydna.download_text in combination with read or parse. this way, the intermediate text can be inspected and genbankfixer can be applied if necessary
1.1.1 - 2016-11-20
- New module genbankfixer for salvaging broken genbank files (pydna.gbtext_clean).
- New pydna.readprimer function (shortcut for reading to Biopython.SeqRecord).
- Tests merged to pytest.
- read_url function
- parse_url function
- download_text function
- New key function for cache of Assemblies.
1.0.2 - 2016-10-08
- Python 3 only!
- pydna.open_cache -> pydna.open_cache_folder; opens the cache folder in the file browser
- logging level is not "info" added the possiblity to specify a text file containing primers and a path to the ApE plasmid editor (http://biologylabs.utah.edu/jorgensen/wayned/ape/) These settings can be made in the pydna.ini file that is located in the "user_config_dir" specified on each platform by the appdirs module. on linux it is in ~/.config/pydna
- Bugfix: invisible gel bands in the gel module.
1.0.1 - 2016-03-10
- Bugfix: for errors in IPython import if IPython is too old ( < 4.0)
- Bugfix: Large genbank records were not downloaded completely.
1.0.0 - -
- Gel simulation added
0.9.3 - 2015-06-03
- Shelve does not work under MacOS under certain conditions.
- This release tries to solve this by not specifying file extensions for the cache files. Two functions are added, pydna.
0.9.2 - 2015-05-28
- pydna_data_dir is encoded to a string in init.py instead of unicode. The Popen module does not accept environment variables that are not strings.
0.9.1 - 2015-05-26
- fixed critical error in the calculation of seguid and cseguid checksums
0.9.0 - 2015-05-26
- seguid and cseguid are now url safe so they can be part of urls and file names.
- Dseqrecord.locus is an alias of Dseqrecord.name
- Dseqrecord.accession is an alias of Dseqrecord.id
- Dseqrecord.definition is an alias of Dseqrecord.description
- changed how circular assembly products are identified to use cseguid.
- removed proxy handling when proxy not set in download module.
- added CHANGELOG.md, currently empty.
- environment variable datadir is now pydna_data_dir.
- removed environmental variable pydna_dna_dir.
- if Dseqrecord is initiated with a name property that is longer than 16 characters, it is truncated to 16 chars and a warning is issued.
- Default Dseqrecord name property is "na".
- Default Dseqrecord id property is "-".
- Default Dseqrecord description property is "@".
- Dseqrecord eq and ne methods defined.
- Dseqrecord.write now overwrites an old sequence with the same
- filename if the primary sequence is the same.
- Dseqrecord.read now only looks in current working directory.
- fixed ipynb_import test code.
0.8.4 - 2015-04-17
- Bugfix for parsing text files with unicode characters.
0.8.3 - -
0.8.2 - -
0.8.1 - 2015-03-07
- Bugfix for windows. The data directory was not created.
- Mapping reads added.
- First public release with the changes from 0.7.0 and 0.7.1.
- Added a Pretty_str class to beautify output of strings in the IPython shell.
- Short linkers can be incorporated in PCR primers in the assembly_primers function.
-
Caching to speed up Amplify, Assembly, download and the
-
Desqrecord synced method. The data is stored in four shelf files in the users application directory.
-
amplify.shelf
-
assembly.shelf
-
genbank.shelf
-
synced.shelf
-
The location is os specific.
-
See the documentation of appdirs https://pypi.python.org/pypi/appdirs/1.4.0
- new function nopcr.
- bugfix: cutting an amplicon object now preserves features
- Changed requirement for NetworkX to 1.8.1
- The pcr function and Anneal class can now deal with primers with ambiguous codons like R = A or G. In the resulting PCR product, the ambiguous nucleotides are preserved in the tails i.e. the primer part not annealing. The annealing part will have the sequence corresponding to the template.
- Dseqrecord.add_feature can now take a string or some other sequence as input. The assembly primers function can now produce primers for a circular assembly.
-
Dseqrecord gained three new methods:
-
isorf() method returning True or False.
-
List_features() method returns a list of all features as a formatted ASCII table.
-
Extract_feature() extracts a feature in the form os a new Dseqrecord object.
-
Changes to how the primer_design functions work, especially assembly primers.
- Fixed a bug in the Dseqrecord synced method and removed the utils synced function.
- Bugfixes and improvements in documentation.
- Changes to how the amplify and assembly modules work the Amplicon and Assembly classes are now subclasses of Dseqrecord.
- bugfix: changed the handling of compound features to fit with the new version of BioPython (1.62) which is now a requirement.
- bugfix: changed the SeqFeatures added to PCR products in the
- amplify module to a dict of list of strings instead of a dict of strings.
- Changed the code in amplify.Amplicon to handle features spanning the origin of circular sequences.
- Changed the behaviour of the find method of the Dseq object to find substrings that span the origin. Slicing for circular Dseq objects now works slightly different.
- Changed the setup.py script to permit installation of the source installer without access to a c compiler.
-
Cleaned up some docstrings
-
Renamed Drecord -> Dseqrecord to be more consistent with
-
Dseq and Biopython Seq/SeqRecord.
-
Changed name of keyword argument for read and parse.
-
ds=True returns Dseqrecord(s) while ds=False returns SeqRecords.
- pydna created from Python-dna.