Minor corrections. Docker & Singularity containers. What_the_phage implementation.
A locate exception was added. So, if the user does not have this tool the configuration of Phigaro will not fail.
Minor corrections and optional temporary files saving
Code style: black. Output parameter corrections.
This version is absent.
! IMPORTANT !
Updated thresholds for abs and without_gc modes.
New parameter:
-m, --mode
Runs the tool at one of the available modes:
- basic - find phages using phage score and GC content.
- abs - find phages using phage score and GC content deviation.
- without_gc - find phages using phage score only.
New output formats:
- gff3;
- bed.
New parameter:
-d, --delete-shorts
Allows the tool to exclude sequences with length less 20 000 bp automatically.