snaketest 0.0.4

Description:

snaketest 0.0.4

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.