Pygtftk

Bug Fixes

* Argparse was part of the dependencies. However, argparse is part of Python 3.
Thus, this caused pygtftk to come with an older version of argparse...

* Fixed gene sorting in tss_dict to ensure reproducible result.

* Fixed a problem with retrieve() when used from interpreter (45).

* The load_gtf() function (C API) no raise an error if a GFF3 is passed
with .gtf extension.

API Changes

* Input BED file in bed3 format are now converted to bed6 automatically.

* The select_by_numeric() function has been renamed eval_numeric()

* It is now possible to use numpy array of booleans to index the GTF (i.e.
using the indexing function).

* the prepare_gffutils_db() function allows one to create a db for
gffutils while selecting features and attributes.

Code changes

* The argformatter module was refactored. Development of FormattedFile(argparse.FileType)
that test for file extension and content (at least for bed).

* The BED conversion is now performed using the print_bed() C function .

New Features

Bug Fixes

* Fix a critical bug in get_sequence that affected get_feat_seq and get_tx_seq.

* Select_by_key now throw an error when no key/val are available.

* No more function with mutable objects as default arguments.

* Fix temporary file deletion.

API Changes

* Refactored arg_formatter by creating a single type (ranged_num)
to test for numeric inputs.

* Refactored all plugins so that there is no more reference to
unused arguments (tmp_dir, verbosity...).

Code changes

* No more reference to PY2.

* Added several test to get_tx_seq and get_feat_seq.

* Added several script to manipulate fasta files (see 'tools' folder).
For pygtftk dev.

* Added 'extra_require' slot in setup().

* The get-feature-seq program now relies on bedtools (not on internal C code).
This may change in the future as a a more
flexible C interface is available.

New Features

* Added --list-bigwigs to profile (to display the content of a coverage file).

* Added a novel dataset (mini_real_10M) derived from mini_real and containing
10 Mb of chr1.

* The configuration directory now supports several subdirectories named based
on a hash string computed from path to the gtftk program.

Bug Fixes

* Convergent and divergent return coordinate (e.g. dist_to_divergent)
in integer not float...

API Changes

* pygtftk is no more compatible with python 2. This decision aims at
integrating last plotnine versions (starting from 0.5.1) that
depends on matplotlib 3.0.0 which strictly depends on py3k.

New Features

* Added an example for col_from_tab in presentation.rst

* Added a dataset mini_real_coding_pot.tab.

* Working on travis now.

* gtftk configuration directory now contains several subdirectories whose
names are computed based on gtftk program location.

* Added a -d argument to gtftk program. This argument returns gtftk
configuration directory.

* All tests should be independent of the directory.

* Added test to count_key_values.

Bug Fixes

* Fixed a bug in add_attr_from_file. The arg has_header led to empty result.

* Fixed a bug in select_by_reg_exp. The match method was used instead of search method...

* Fixed an error in count_key_values.

API Changes

New Features

* Several changes in doc to make it compliant with readthedoc.

Bug Fixes

API Changes

New Features

* Several changes in setup.py and requirements_develops.txt to makes it
compliant with Pypi and buildable with manylinux.

Bug Fixes

API Changes

New Features

* Several changes in setup.py and requirements_develops.txt to makes it compliant
with Pypi and buildable with manylinux.