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 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