GaoxiangLi/VCF_Exercise

VCF file simple exercise

#Simple VCF exercise:

Shawn Li

function:sort keyvalue in the VCF file

Python version:3.68
No other libiary needed.

How to use:

1.Download and unzip

2.input command line at root file path:

              python vcf --sort 
              --key KEY_NAME 
              --filename FILENAME
              --saved_path SAVED_PATH 
              --order AES OR DES
              --h  call for help 

3.Sorted file will be created at: ./data/SortByKEY_NAME.vcf

              filename: default as small_demo.vcf
              order:default as AES
              saved_path default as ./data/

              Simple example: python vcf --sort --key BaseQRankSum
              Simple example: python vcf --sort --key BaseRankSum --filename small_demo.vcf --svaed_path ./result/ --order AES

Notice:

1.Some Keys cannot be used since some data mistakes Example: At 441 line, AC values 1,1. So this cannot be convert to float and used to sort.

2.For the missing value, float 0.0 is used to replace "." (NONE cannot be used to sort)

3.TimSort algorithm is used. It's a stable sort which I think should be important for research to get a stable result.