CHANGES.md

Release notes

v0.3.3

Date: 2022-02-28

Bug fixes:

• fixed a couple functions returning an error instance instead of raising
• fetch_mrna link fixed

v0.3.2

Date: 2022-02-01

Bug fixes:

• fixed error in is_contained
• tutorial updates

v0.3.1

Date : 2021-11-15

API changes:

• bioframe.sort_bedframe does not append columns or modify their dtypes.

v0.3.0

Date : 2021-08-31

Conceptual changes:

• we formulated strict definitions for genomic intervals, dataframes, and their various properties. All bioframe functions are expected to follow to these definitions tightly.

API changes:

• reorganize modules:

  • ops - operations on genomic interval dataframes
  • extras - miscellaneous operations, most involving genomic sequences and gene annotations
  • vis - visualizations of genomic interval dataframes
  • core.arrops - operations on genomic interval arrays
  • core.checks - tests for definitions of genomic interval dataframes
  • core.construction - construction and sanitation of genomic interval dataframes
  • core.specs - specifications for the implementation of genomic intervals in pandas.dataframes (i.e. column names, datatypes, etc)
  • core.stringops - operations on genomic interval strings
  • io.fileops - I/O on common file formats for genomic data
  • io.schemas - schemas for standard tabular formats for genomic data storage
  • io.resources - interfaces to popular online genomic data resources

• new functions: extras.pair_by_distance, ops.sort_bedframe, ops.assign_view, dataframe constructors

• existing functions:

  • expand: take negative values and fractional values
  • overlap: change default suffixes, keep_order=True
  • subtract: add return_index and keep_order

• enable pd.NA for missing values, typecasting

New data:

• add schemas for bedpe, gap, UCSCmRNA, pgsnp
• add tables with curated detailed genome assembly information

Bugfixes:

• None?..

Miscellaneous:

• speed up frac_gc is faster now
• drop support for Python 3.6, add support for 3.9

v0.2.0

Date : 2020-12-02

API changes

• read_chromsizes and fetch_chromsizes: add new as_bed parameter.
• read_chromsizes and fetch_chromsizes: revert to filtering chromosome names by default, but clearly expose filter_chroms kwarg.

Bug fixes

• Fixed bioframe.split
• Restored frac_genome_coverage

v0.1.0

Date : 2020-09-23

First beta release.

What's new

• New extensive dataframe genomic interval arithmetic toolsuite.
• Improved region handling and region querying functions.
• Documentation!

Maintenance

• Dropped Python 2 support
• Refactoring of various genome operations and resources.
• Improved testing and linting