https://github.com/zkamvar/genotype_iterators

Examples of genotype iteration utilized in Bruvo's distance in poppr
https://github.com/zkamvar/genotype_iterators

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Examples of genotype iteration utilized in Bruvo's distance in poppr

• Host: GitHub
• URL: https://github.com/zkamvar/genotype_iterators
• Owner: zkamvar
• License: gpl-3.0
• Created: 2014-12-11T17:11:27.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2014-12-16T18:01:43.000Z (almost 10 years ago)
• Last Synced: 2024-06-12T18:23:44.670Z (5 months ago)
• Language: C
• Size: 109 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
## Genotype Iteration

This repository contains scripts I used to test implementation of Bruvo's 

distance in C.

It also contains a script called `genome_addition_filler.c`, which is a scirpt

that demonstrates the imputation method for the genome model for Bruvo's 

distance. It also demonstrates a generalization of the algorithm to be able to

create DNA models for genotypes of any ploidy. 

These are fully implemented in the [poppr R package](https://github.com/grunwaldlab/poppr)

## Running

You can test out `genome_addition_filler.c` by modifying the `test_DNA()` 

function and compiling it with gcc:

```

$ gcc genome_addition_filler.c -o gam

$ ./gam

```

Here is the output for triploids:

```

$ ./gam

CREATING TRIPLOID GENOTYPE MODEL

20 POSSIBLE COMBINATIONS

===============

GENOTYPE MODEL:	AAA

GENOTYPE MODEL:	AAC

GENOTYPE MODEL:	AAG

GENOTYPE MODEL:	AAT

GENOTYPE MODEL:	ACC

GENOTYPE MODEL:	ACG

GENOTYPE MODEL:	ACT

GENOTYPE MODEL:	AGG

GENOTYPE MODEL:	AGT

GENOTYPE MODEL:	ATT

GENOTYPE MODEL:	CCC

GENOTYPE MODEL:	CCG

GENOTYPE MODEL:	CCT

GENOTYPE MODEL:	CGG

GENOTYPE MODEL:	CGT

GENOTYPE MODEL:	CTT

GENOTYPE MODEL:	GGG

GENOTYPE MODEL:	GGT

GENOTYPE MODEL:	GTT

GENOTYPE MODEL:	TTT

```

If you wanted to specify a higher ploidy, that option is there, too:

```

$ ./gam 12 | head

CREATING DODECAPLOID GENOTYPE MODEL

455 POSSIBLE COMBINATIONS

===============

GENOTYPE MODEL:	AAAAAAAAAAAA

GENOTYPE MODEL:	AAAAAAAAAAAC

GENOTYPE MODEL:	AAAAAAAAAAAG

GENOTYPE MODEL:	AAAAAAAAAAAT

GENOTYPE MODEL:	AAAAAAAAAACC

GENOTYPE MODEL:	AAAAAAAAAACG

$ ./gam 12 | grep MODEL: | wc

     455    1365   13195

```