0.7.5 - 2023-07-10
Note: 0.7.4 had a minor bug with pyreference.cfg defaults
- #10 - GTFs can contain multiple gene versions per symbol
- #11 - Can now choose how representative transcript is resolved. Can use MANE tags
- #12 - Handle cdot biotype fixes
- #13 - Don't duplicate Gene objects (Reduces memory + cpu time)
0.7.3 - 2023-07-06
- Fix gene.representative_transcript dying with "AttributeError: module 'sys' has no attribute 'maxint'" in Python3
0.7.2 - 2022-11-21
- New Gene properties 'description', 'summary', 'map_location' and 'biotype'
- Support for Fasta reference genomes that use contigs for sequence names (eg NCBI)
- We now use cdot JSON.gz files
0.6.3 - 2022-01-12
- Fixed bug where pyreference_biotype.py crashed due to args not matching method signature
0.6.2 - 2022-01-12
- Include pyreference_biotype.py script in PyPi distribution
- Removed individual graphs, improved appearance of stacked bar graph
- Fixes for pyreference_biotype, pin HTSeq version to stop crash
0.6 - 2021-11-05
- Handle Ensembl specific GTFs
- Support for GFF3
- Store gene/transcript versions
- Store HGNC, description, cDNA_match (refseq transcript/genome alignment gaps)
- Store URL (where GTF/GFF was downloaded from eg RefSeq/Ensembl FTP site)
- Fix for deprecated BioPython code
0.5 - 2020-02-24
- Fixed Python 3.7 issue - ConfigParser mandatory arguments
0.4 - 2019-10-31
- Fix Python3 issues
- Use PySam instead of PyFasta (performance issues at high chromosome coordinates)
0.3 - 2018-01-26
- Store GTF/GFF path and md5sum in JSON
- TSS uses representative transcript start rather than most 3' transcript start
0.2 - 2018-01-25
- Be able to retrieve multiple genes at a time via list
- Option to decompress Gzip in memory to get around server shared filesystem issues
- Removed non-standard chromosomes
0.1 - 2018-01-24
- Initial commit. Created project, extracted existing code from SACGF bioinformatics repo
- Wrote GTF to JSON converter and loader