CDScompare 0.3.0rc6

Small fixes for the all pairing mode.

• Fixed reporting of unpaired loci in all mode.
• Restricted all mode to comparisons between exactly two GFF files.
• Updated documentation accordingly.

Installation:

pip install cdscompare==0.3.0rc6

docker pull ghcr.io/johgi/cdscompare:0.3.0rc6

CDScompare 0.3.0rc5

This release candidate was prepared for the revised manuscript submission.

Main changes

• Added safer handling of sequence identifiers between compared GFF3 files (automatic 'chr' prefix harmonization) when appropriate.
• Added explicit error reporting when no common seqids are found between the two input annotations.

Installation

pip install cdscompare==0.3.0rc5

Docker / GHCR

docker pull ghcr.io/johgi/cdscompare:0.3.0rc5
docker run --rm ghcr.io/johgi/cdscompare:0.3.0rc5 -v

Release candidate corresponding to the manuscript submission

Installation:

• PyPI: pip install cdscompare==0.3.0rc4
• Docker: docker pull ghcr.io/johgi/cdscompare:0.3.0rc4
• Apptainer: apptainer pull docker://ghcr.io/johgi/cdscompare:0.3.0rc4

v0.2.0

Last update from Vetea for his internship

v0.1.0

Features

Old v2.0.0

• different chromosomes gestion
• distinction between 'Exon-Intron' ('EI') and 'Reading Frame' ('RF') mismatches
• results now indicate chromosome, EI and RF non-correspondance zones, and EI and RF mismatches
• simplified locus comparison through intervals operations
• script split into different files
• reduced complexity of 'get_gff_borders', 'annotation_sort', and 'annotation_match' functions

Old v3.0.0

• Better name ! (CDScompR : "CDS Comparison with Reading frames")

Bug fix

Old v2.0.0

• fixed length computation of locus annotation intervals
• fixed comparison of reverse-strand loci

Old v3.0.0

• fixed error message not appearing for orphan CDS (with no previous mRNA) in get_gff_borders()
• fixed and completed the documentation

Other

Old v2.0.0

• dropped 'debug' mode and cleaned 'verbose' mode

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Note

• v1.0.0 (deleted tag) was attached to the commit 3e432ff (11/06/2024)
• v2.0.0 (deleted tag) was attached to the commit 39676ff (27/06/2024)
• v3.0.0 (deleted tag) was attached to the commit bfce512 (04/07/2024)