pyroe v0.9.3

Fixes #39, which caused id-to-name to fail for files with multiple suffixes.

pyroe v0.9.2

fix: There was another bug upstream in pyranges (issue here) that breaks GTF/GFF parsing. This is a "hot fix" release that simply pins pyranges to 0.0.120 until the bug is fixed upstream in pyranges, or until a more reliable replacement can be found for GTF parsing and interval arithmetic for reference building.

pyroe v0.9.1

fix: There is a bug upstream in pyranges that precludes using
pandas >= 2.0. However, that restriction isn't in place for the pyranges dependencies. This release restricts pyroe to depend on a pandas < 2.0 until this is fixed upstream.

fix: The aliases for the make-spliced+intronic and make-spliced+unspliced subcommands were not working; this release fixes those aliases.

pyroe v0.9.0

fix: fix bug in make_splici_txome that could cause invalid program termination
improvement: silence expected deprecation warning due to pyranges

pyroe v0.8.1

What's Changed

• fix: update minimum pyranges version (to 0.0.120) and improve exception handling by @DongzeHE in #25

Full Changelog: v0.8.0...v0.8.1

pyroe v0.8.0

What's Changed

• feat: new predefined output_formats for load_fry function by @DongzeHE in #19
• fix: fix bugs in "try except" by @DongzeHE in #20
• Improve GTF parsing by @DongzeHE in #21
• fix: refine bed file formats by @DongzeHE in #23
• fix: ensure only proper fields are written to bed file by @rob-p in #24

Full Changelog: v0.7.1...v0.8.0

pyroe v0.7.1

Add aliases for make-splici and make-splcieu:

• make-spliced+intronic can be used as an alias for make-splici
• make-spliced+unspliced can be used as an alias for make-spliceu

pyroe v0.7.0

Added make-spliceu command.

pyroe v0.6.4

Rename gene_name_to_id.tsv output of make-splici to gene_id_to_name.tsv to match the actual order of the columns in the file.

pyroe v0.6.3

This release improves the robustness of GTF parsing, adds the --write-clean-gtf flag to the make-splici command, and adds an extra output (a gene-id to gene-name mapping) as the result of the make-splici command.

Full Changelog: v0.6.0...v0.6.3