xPore v2.0
Summary
xPore v2.0 is a major release that implements the following changes:
- xPore now has 3 main running modes that replace the scripts in earlier versions:
- xpore dataprep
- xpore diffmod
- xpore postprocessing
- Checking the version is now supported by
xpore -v
- Changes in the
xpore dataprep
command as follows:- the pyensembl package is no longer required and supported to map transcriptome to genome coordinates. Please use the --genome flag and provide the GTF file (
--gtf_path_or_url
) and transcriptome FASTA file (--transcript_fasta_paths_or_urls
) if you would like to work with genomic coordinates. - The option
--summary
is no longer needed and was removed. - xpore dataprep will no longer produce 'N' in k-mers.
- the pyensembl package is no longer required and supported to map transcriptome to genome coordinates. Please use the --genome flag and provide the GTF file (
- The documentation was updated to include these changes.
xPore is still compatible with dataprep files generated with xPore v1.0.
What's Changed
- gtf option, fastdataprep, and dataprep intermediate file removal by @yuukiiwa in #48
- Update README.md by @jonathangoeke in #49
- remove pyensembl requirement and solve Arabidopsis bug by @yuukiiwa in #57
- replace if statement with KeyError in g2t mapping, add post-processing option, and add xpore wrapper by @yuukiiwa in #58
Full Changelog: v0.5.6...v2.0