我有一個包含多個目錄的目錄:/test/cond1//test/cond2//test/cond3//test/cond4/所有子目錄都有幾個不同的文件:cond1 : a1.txt, a2.txtcond2 : b1.txt, b2.txt, b3.txtcond3 : c1.txt, c2.txt, c4.txtcond4 : d1.txt,c2.txt, c4.txt, d2.txt我正在使用 Snakemake 運行命令,我需要通過 cond 獲取所有文件,并用空白分隔我嘗試這樣做:def get_motifs_tf(wildcards): file_list = sorted(glob.glob("tf_final/{wildcards.cond}/*.bed")) return " ".join(file_list)這是我的規則snakemakerule compute_combi_enrichment: """ For a given input, compute the enrichment in n-wise TF combinations using OLOGRAM-MODL. """ input: query = 'input/core_silencer/{cond}/core_silencer.bed', excl = "input/exclude_region_dhs.bed", genome = "input/mm9.chromsizes" params: trs = get_motifs_tf, minibatch_number = 16, minibatch_size = 10 # Modulate depending on available RAM threads: 8 # Do not use 16 threads to not vampirize all the cluster output: 'output/ologram_result/{cond}/00_ologram_stats.tsv', shell: """ set +u; source /gpfs/tagc/home/Apps/anaconda3/bin/activate dev; set -u gtftk ologram -z -c {input.genome} -p {input.query} --more-bed {params.trs} \ -o output/ologram_result/{wildcards.cell_line} --force-chrom-peak --force-chrom-more-bed \ -V 3 -k {threads} -mn {params.minibatch_number} -ms {params.minibatch_size} \ --more-bed-multiple-overlap --bed-excl {input.excl} --no-date \ --multiple-overlap-max-number-of-combinations 80 """在 --more-bed {params.trs} 中我預計會得到:/test/cond1/a1.txt /test/cond1/a2.txt然后/test/cond2/b1.txt /test/cond2/b2.txt /test/cond2/b3.txt等等...
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TA貢獻1942條經驗 獲得超3個贊
我解決了它:
函數中的通配符必須在 stp 中轉換并且不帶括號:
def get_motifs_tf(wildcards): file_list = sorted(glob.glob("tf_final/"+str(wildcards.cond)+"/*.bed")) return " ".join(file_list)
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