qapa v1.3.3

Fixes a bug when calling qapa quant (see #44) that was introduced in the previous release.

qapa v1.3.2

This maintenance release contains some improvements to logging messages and exception handling. No new features have been added.

• Added more logging messages for debugging. Use --debug flag to print more verbose messages to help with troubleshooting.
• Added more error checking
• Added environment.yml to setup qapa virtual environment
• Added Github Actions workflow for continuous integration
• Update Python minimum requirement to 3.8

qapa v1.3.1

Some bug fixes and maintenance updates. More unit tests added.

Bug fixes:

• Minor bug introduced in v1.3.0 that broke the handling of genePred files obtained via the UCSC MySQL command (#28).
• Incompatibility issues between fasta sub-module and newer versions of BioPython (#40)

qapa v1.3.0

This release contains new functionality and improvements to the build and fasta sub-modules. The main highlight is support for PolyASite version 2 that should benefit users of human and mouse libraries. The quant sub-module is unchanged from previous versions.

Pre-compiled libraries for hg38 and mm10 are available for download below.

• hg38 sources: GENCODE V31 Basic, GENCODE Poly(A), PolyASite V2, and Ensembl Genes V97
• mm10 sources: GENCODE VM22 Basic, GENCODE Poly(A), PolyASite V2, and Ensembl Genes V97.

Changes:

• Python 2 is no longer supported in this release (https://www.python.org/doc/sunset-python-2/). The last working version with Python 2 is v1.2.3.
• Add support for PolyASite version 2 (gets auto-detected). (#22)
• Replace log messaging with logging framework
• Add --debug option for increasing verbosity of log messages
• Add parallel processing to some stages of build that should help improve runtime. Can be controlled using --cores option (defaults to using all available cores).
• Deprecate -H option for custom genePred files as they are now auto-detected.
• Deprecate --dist5 option for merging 5’ ends. This option was never actually used.
• More unit tests
• Fix bug in fasta sub-module where duplicate sequences were not being properly detected based on identifier.

qapa v1.2.3

This release fixes a bug that occurs when input files contain quoting characters that are default in read.table() (#15). Quoting characters are now disabled using quote=NULL.

qapa v1.2.2

This release contains a few bug fixes and updates:

• Fix bug for dealing with an edge case where UTR is at the chromosome boundary (#10)
• Add a warning if chromosome contains underscores, which are not supported and will be skipped
• Update legacy support for python 2. Moving forward, python 3 is recommended and support for python 2 will eventually be dropped.
• A new suite of unit tests have also been added. They currently only cover some components and are non-exhaustive.

Known issues:

• Possible incompatibility with recent changes in data.table v1.12.2 (#13)

qapa v1.2.1

• Add check for improperly formatted BED files

qapa v1.2.0

This release adds some new features for the build step:

• Support for other species (#2, #4), but need to supply your own poly(A) site annotation, if desired. Can use the option --species to specify a species, otherwise unk is used.
• Support for custom genePred files converted by gtfToGenePred using option -H.
• Skip annotation step using option -N.

qapa v1.1.1

This is a minor release that fixes a small bug introduced in v1.1.0.

This release and the pre-compiled 3' UTR libraries are also available on Zenodo.

Installation

See README for installing any pre-requisites.

To install this specific version:

tar -xzvf qapa-1.1.1.tar.gz
cd qapa-1.1.1
python setup.py install

qapa v1.0.0

This is the first release