Format Overview For Developers

Format overview

Python implementation

Linkml generates a datamodel file with all classes: https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py

Tools

Started development of a tool called pmotools. Python implementation can be found here: https://github.com/PlasmoGenEpi/pmotools-python/tree/develop

From GEM meeting

adding header with info on each field
adding version to header
random access ability

---
title: "Format Overview For Developers"
---

```{r setup, echo=FALSE}
source("../common.R")

#' Check sharing and unqiue values between two vectors
#'
#' @param vectorA the first vector
#' @param vectorB the second vector
#'
#' @returns a list with 4 vectors, "only_in_vectorA" unique to vectorA, "only_in_vectorB" unique to vectorB, "shared_samples" shared between both vectorA and vectorB, "all" all values by combinng vectorA and vectorB 
set_decompose <- function(vectorA, vectorB){
  ret = list()
  # Find unique and shared samples
  ret[["only_in_vectorA"]] <- setdiff(vectorA, vectorB)  # Samples only in vectorA
  ret[["only_in_vectorB"]] <- setdiff(vectorB, vectorA)  # Samples only in vectorB
  ret[["shared_samples"]] <- intersect(vectorA, vectorB) # Samples shared between vectorA and vectorB
  ret[["all"]] <- union(vectorA, vectorB) # All samples between vectorA and vectorB
  return(ret)
}
```


# Format overview 

:::{.column-screen}

```{r, echo=FALSE, results="asis"}
cat(readr::read_lines("portable_microhaplotype_object.schema.dot.svg", skip = 6), sep = "\n")
```
<!-- ![](portable_microhaplotype_object.schema.dot.svg) -->

:::


# Python implementation 

Linkml generates a datamodel file with all classes: <https://github.com/PlasmoGenEpi/portable-micorhaplotype-object/blob/main/src/plasmo_tar_amp_schema/datamodel/plasmo_tar_amp_schema.py>


# Tools  

Started development of a tool called pmotools. Python implementation can be found here: <https://github.com/PlasmoGenEpi/pmotools-python/tree/develop>




# From GEM meeting

- [ ] adding header with info on each field 
- [x] adding version to header   
- [ ] random access ability