version_tracker.md

January 8, 2024 ยท View on GitHub

V2.4.0

  • Restored a compatibility with Python versions > 3.7.1.
  • .pickle files, containing data neccasary for the work of the tool, were replaced with .json and .csv files to resolve compatibility issues.
  • Added prophage IDs across outputs to improve compatibility between files.
  • Fixed a bug with gff3 and bed files formats: prophage coordinates were shifted by 1 nucleotide upstream in versions phigaro <= 2.3.0.

V2.3.0

Added a --save-fasta option.

V2.2.6

Minor corrections. Docker & Singularity containers. What_the_phage implementation.

V2.2.5

A locate exception was added. So, if the user does not have this tool the configuration of Phigaro will not fail.

V2.2.4-1

Minor corrections and optional temporary files saving

V2.2.3

Code style: black. Output parameter corrections.

V2.2.2

This version is absent.

V2.2.1

! IMPORTANT !
Updated thresholds for abs and without_gc modes.

V2.2.0

New parameter: -m, --mode
Runs the tool at one of the available modes:

  1. basic - find phages using phage score and GC content.
  2. abs - find phages using phage score and GC content deviation.
  3. without_gc - find phages using phage score only.

V2.1.10

New output formats:

  • gff3;
  • bed.

New parameter: -d, --delete-shorts
Allows the tool to exclude sequences with length less 20 000 bp automatically.