changelog

version

date

comment

2.0.3 2017-12-14 ---

2.0.3a1 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 --- ----

2.0.0a1 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.

0.8.0 2015-02-06 Mapping reads added.

0.7.2 2014-11-21 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.

0.7.1 not public Short linkers can be incorporated in PCR primers in the

assembly_primers function.

0.7.0 not public 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

0.6.6 new function nopcr.

0.6.5 2014-07-31 bugfix: cutting an amplicon object now preserves features

Changed requirement for NetworkX to 1.8.1

0.6.4 2014-07-09 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.

0.6.3 2014-07-06 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.

0.6.2 2014-06-13 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.

0.6.1 2014-04-25 Fixed a bug in the Dseqrecord synced method and removed the

utils synced function.

0.6.0 2014-04-18 Bugfixes and improvements in documentation.

0.5.0 2013-12-16 Changes to how the amplify and assembly modules work

the Amplicon and Assembly classes are now subclasses of Dseqrecord.

0.2.2 2013-11-05 bugfix: changed the handling of compound features

to fit with the new version of BioPython (1.62) which is now a requirement.

0.2.1 2013-08-18 ---

0.1.8 2013-06-02 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.

0.1.7 2013-05-29 Changed the code in amplify.Amplicon to handle features

spanning the origin of circular sequences.

0.1.6 2013-04-22 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.

0.1.5 2013-04-18 Changed the setup.py script to permit installation

of the source installer without access to a c compiler.

0.1.4 2013-04-10 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.

0.1.3 2013-04-09 pydna created from Python-dna. ======= ========== ==========================================================================================