我正在使用一个名为snakemake的python-dsl,它看起来像这样:
from bx.intervals.cluster import ClusterTree
from epipp.config import system_prefix, include_prefix, config, expression_matrix
config["name"] = "correlate_chip_regions_and_rna_seq"
bin_sizes = {"H3K4me3": 1000, "PolII": 200, "H3K27me3": 200}
rule all:
input:
expand("data/{bin_size}_{modification}.bed", zip,
bin_size=bin_sizes.values(), modification=bin_sizes.keys())
rule get_gene_expression:
input:
expression_matrix
output:
"data/expression/series.csv"
run:
expression_matrix = pd.read_table(input[0])
expression_series = expression_matrix.sum(1).sort_values(ascending=False)
expression_series.to_csv(output[0], sep=" ")
我想对run:
块内的东西运行 yapf。
是否有可能让 yapf 忽略 python 中不存在的东西,比如rule
关键字等,只在文件的特定部分使用它?