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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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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