snaketest 0.0.4

A small package to help test and prototype snakemake rules

snaketest

instalation:

pip install snaketest

runing

A small package to help test and prototype snakemake rules

from  snaketest import *

The idea is to make the prototype as copypasteable as possible Rou declare input and output by just initializing a snaketest class. You can just copy paste the content of the input, output, log, params...

input = snaketest(
    table='data/table.csv',
    genome='data/genome.fa',
    sample = expand('data/sample/{sample}.csv',sample=[1,2,3]) #there's even an expand function
)

You can even use wildcards in them

output = snaketest(
    csv='results/table_{chromosome}.csv',
)

But if you do you gotta create a wildcard SM which the other SM classes will refer to

wildcards = snaketest(
  chromosome="chrY"
)

Now you can fill the code using SM variables:

import pandas as pd
df = pd.read_csv(input.table)
df = df[df['chromosome']==wildcards.chromosome]

Because all variables are in the snakemake format, you can just test and copy paste withought needing to manually change anything.