Genomedata 1.7.3

This release fixes a few issues with Genomedata dependencies, namely with "path.py" (now named "path") and "numpy". Both packages deprecated names of equivalent functions or constants and the equivalents have been used in their stead. As a result Path.py/path now has an updated minimum requirement while numpy should be backwards compatible with the 1.0 series release.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• replace deprecated .isdir and .isfile path API uses with is_dir and is_file from version 16.12 onwards
• add numpy 2.0 compatibilty

Known Bugs:
To see all known bugs head to the issue tracker

Genomedata 1.7.2

This release fixes a few minor Python interface inconsistencies between using bigWig files and Genomedata archives and moves the minimum supported Python version to 3.9 to stay in line with future PyTables compatibility.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• required Python is now >=3.9
• fixed consistency in array shape output when track indexing on bigWig files

Known Bugs
To see all known bugs head to the issue tracker

Genomedata 1.7.1

This release fixes a few minor Python interface inconsistencies between using bigWig files and Genomedata archives. Summary statistics on a bigWig file are now always an array of a single element. Debug string representation for chromosomes when using bigWig files has also been added.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• fix array dimensionality consistency for summary statistics on bigWig files
• add debug representation for chromosomes for bigWig files

Known Bugs
To see all known bugs head to the issue tracker

Genomedata 1.7.0

This release adds the ability to use the Python API with bigWig files. Simply replace opening a Genomedata archive with a bigWig file and the interface should work nearly identically. For details, see the interface differences between bigWig and the Genomedata archives in the documentation.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• adapted existing python interface to open bigWig files

Known Bugs
To see all known bugs head to the issue tracker

Genomedata 1.6.0

This release addresses long standing issues with builds and legacy Python support. Genomedata will now only support a minimum Python version of 3.7. Future releases will be easier to install and support. With the release of wheel builds, development tools and libraries are no longer necessary for Genomedata to be installed. It is still recommended that users install with Bioconda.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• required Python is now >=3.7
• genomedata-load-data: changed to a python script with a c-extension

Known Bugs
To see all known bugs head to the issue tracker

Genomedata 1.5.0

This release addresses loading in sequence data where chromosome names do not have a UCSC-style name. In these cases, we have added the ability to give a tab-delimited file with a commented header (denoted with '#') to map between naming styles. This is the format used by NCBI and their assembly reports. Here is an example of an assembly report for hg38 from NCBI. You may choose what chromosome naming style you wish based on the given tab-delimited files. By default, chromosome names will attempt to map to UCSC-style names when given a tab-delimited file.

Genomedata is available on Bioconda. With Bioconda installed, to install Genomedata run 'conda install genomedata'. Genomedata can still be installed through older methods using "pip", see the Installation instructions for details.

Here is a full list of changes made since the last announcement here:

Enhancements:

• genomedata-load-seq: add chromosome name mapping based on assembly reports

Bug Fixes:

• genomedata-load-data: fix bad error message when loading process fails

Known Bugs
To see all known bugs head to the issue tracker