What's new?
* **Compose your own mutation model:** the class Model now lets you create your own mutation model and use it with the generative functions of the HaploDX framework.
python
import HaploDynamics.Framework as fmx
Start your simulation
model = fmx.Model("tutorial")
Initialize the genomic landscape
model.initiate_landscape(reference = 1.245)
Design your own genomic landscape with any allele frequency model
model.extend_landscape(*(fmx.Model.standard_schema(20) for _ in range(6)))
Population and LD parameters
strength = 1
population = 0.1
Npop = 1000
chrom = "1"
Generate the simulation in a VCF file
model.generate_vcf(strength,population,Npop,chrom)
* **Improvements:**
* [Documentation for the Framework module](docs/source/framework-doc.md) polished;
* Various typos and clumsy phrasing have been corrected in the [documentation](documentation);
* Loading bar appreance changed:
shell
$ python myscript.py
Model.generate_vcf: |████████████████████| 100%
time (sec.): 0.7510931491851807
max. mem (MB): 0.11163139343261719
cur. mem (MB): 0.0834970474243164
* **New functionalities:**
* [HaploDynamics.Framework.Model.initiate_landscape](docs/source/framework-doc.mdhaplodynamicsframeworkmodelinitiate_landscape) added;
* [HaploDynamics.Framework.Model.extend_landscape](docs/source/framework-doc.mdhaplodynamicsframeworkmodelextend_landscape) added;
* [HaploDynamics.Framework.Model.standard_schema](docs/source/framework-doc.mdhaplodynamicsframeworkmodelstandard_schema) added;
* [HaploDynamics.Framework.Model.genotype_schema](docs/source/framework-doc.mdhaplodynamicsframeworkmodelgenotype_schema) added;
* [HaploDynamics.Framework.Model.linkage_disequilibrium](docs/source/framework-doc.mdhaplodynamicsframeworkmodellinkage_disequilibrium) added;
* [HaploDynamics.Framework.Model.cond_genotype_schema](docs/source/framework-doc.mdhaplodynamicsframeworkmodelcond_genotype_schema) added;