Add better functionality to the Tier system used by the Accession file. - Githubissues

datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

https://orthoevolution.readthedocs.io/en/master/

29 stars 4 forks source link

Add better functionality to the Tier system used by the Accession file. #105

Open grabear opened 6 years ago

grabear commented 6 years ago

For the master accession files, we can control the workflow by giving the end user access to priority labels that we define. For instance...

Our default set of tier labels:

Priority Levels:
- Higher priority genes are put through the pipeline first.
- Numerical ranges from 1 to infinity
  - 0 = Do not execute
  - 1 = High Priority
  - 100000000 = Low Priority
- Alternatively allow the user to create a YAML file
  - This allows for strings in the .csv files
  - For instance:
```
Opioid: 1
Alcohol: 2
Cocaine: 3
Opioid/Cocaine: 4
```
- String levels
  - "Skip" could actually skip over genes that don't need to be analyzed right away
  - "Isoform-1-Insert-Gene-Here" could be used for identifying isoforms
    - Isoform-0-HTR1A (the desired gene to analyze)
    - Isoform-1-HTR1A
```
 Isoform-0-HTR1A: 1
 Isoform-1-HTR1A:  "Skip"
```

This could also be very useful when we get to parsing updated HGNC files directly.