HaploDynamics beta 0.4

• minor changes;
• updated link to tutorial.

HaploDynamics beta 0.4

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.

  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 polished;
  • Various typos and clumsy phrasing have been corrected in the documentation;
  • Loading bar appreance changed:

    $ 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 added;
  • HaploDynamics.Framework.Model.extend_landscape added;
  • HaploDynamics.Framework.Model.standard_schema added;
  • HaploDynamics.Framework.Model.genotype_schema added;
  • HaploDynamics.Framework.Model.linkage_disequilibrium added;
  • HaploDynamics.Framework.Model.cond_genotype_schema added;

HaploDynamics beta 0.3

Updated setup.py (the file was missing a module).

HaploDynamics beta 0.3

Documentation was completed. The class "Model" was added.

HaploDynamics beta 0.2

v0.2-beta.4

Delete future.note

HaploDynamics beta 0.2

Added more information in the documentation. Started developing the module "HaploDynamics.Framework" toward multiprocessing.

HaploDynamics beta 0.2

DOI added.

HaploDynamics beta 0.2

v0.2-beta.1

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HaploDynamics beta 0.2

Pip install working. Framework module created.

HaploDynamics beta 0.1

v0.1-beta.9

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