Releases: Tharos-ux/wisp
Releases · Tharos-ux/wisp
v0.1.1 - Cohesive build
This release is about being cohesive in function usage, imports, and parallelism.
Parallelism was added to prediction, each read in the sample file spawns a concurrent process.
Also, some cleaning and bugfix was performed along the way.
Upgrades :
- Added multithreading support to prediction
- Moved predict loop to dedicated module
- Added scripts to plot graphs from results
Fixes :
- Removed bug where read threshold inferior to 10kb would crash the software
- Removed bug where building database would fail if a specie had only fragments of length inferior to threshold
v0.1.0 - Core features release
Fully functional release, featuring :
- Reference genome gathering
- Database creation
- Model creation
- Sample creation
- Sample prediction
Lightweight implementation of the original software on master branch, with only core features, redesigned to be more flexible, accepting letters over a wider alphabet.
No tools for downstream analysis provided. Only outputs a report in .json format per sample.
Available commands :
usage: wisp [-h] [-l] {build,predict} ...
Bacteria family identification tool.
Subcommands:
{build,predict} Available subcommands
build Creates the database from the specified set of files.
predict Creates the samples and evaluates them.
Global Arguments:
-h, --help show this help message and exit
-l, --locals Display locals on error.
usage: wisp build [-h] [-p PARAMETERS] database_name input_folder
positional arguments:
database_name Name for database
input_folder Input folder containig reference genomes
options:
-h, --help show this help message and exit
-p PARAMETERS, --parameters PARAMETERS
Specifies a parameter file
usage: wisp predict [-h] [-p PARAMETERS] database_name input_folder output_folder
positional arguments:
database_name Name for database
input_folder Input folder containig unknown genomes
output_folder Input folder containig reference genomes
options:
-h, --help show this help message and exit
-p PARAMETERS, --parameters PARAMETERS
Specifies a parameter file