我有下面的bash脚本,我想将其转换为snakefile:
mmseqs rbh flye_db megahit_db flye_megahit_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
mmseqs rbh flye_db metaspades_db flye_metaspades_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
mmseqs rbh megahit_db metaspades_db megahit_metaspades_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
我已经想出了以下方法,但我想知道是否有一种方法可以使用regex或expand来进一步改进代码:
rule mmseq2_compare:
input:
mm1=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="flye"),
mm2=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="megahit"),
mm3=expand(os.path.join(RESULTS_DIR, "annotation/mmseq2/{assembler}_db"), assembler="metaspades_hybrid")
output:
mo1=os.path.join(RESULTS_DIR, "annotation/mmseq2/flye_megahit_rbh"),
mo2=os.path.join(RESULTS_DIR, "annotation/mmseq2/flye_metaspades_hybrid_rbh"),
mo3=os.path.join(RESULTS_DIR, "annotation/mmseq2/megahit_metaspades_hybrid_rbh")
log: os.path.join(RESULTS_DIR, "annotation/mmseq2/compare.mmseq2.log")
conda: "cd-hit.yml"
shell:
"""
(date &&\
mmseqs rbh {input.mm1} {input.mm2} {output.mo1} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
mmseqs rbh {input.mm1} {input.mm3} {output.mo2} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
mmseqs rbh {input.mm2} {input.mm3} {output.mo3} --min-seq-id 0.9 mmseq2_tmp --threads 12 &&\
date) &> >(tee {log})
"""
有了3个汇编程序(flye、megahit和metaspades_hybrid),有没有办法消除冗余,尤其是在“shell”中
谢谢大家!
干运行输出
Building DAG of jobs...
Job counts:
count jobs
1 all
1 mmseq_compare
2
[Thu Mar 26 12:25:14 2020]
rule mmseq_compare:
input: results/annotation/mmseq2/flye_db, results/annotation/mmseq2/megahit_db
output: results/annotation/mmseq2/flye_megahit_rbh
jobid: 1
wildcards: assembler1=flye, assembler2=megahit
mmseqs rbh results/annotation/mmseq2/flye_db results/annotation/mmseq2/megahit_db results/annotation/mmseq2/flye_megahit_rbh --min-seq-id 0.9 mmseq2_tmp --threads 12
[Thu Mar 26 12:25:14 2020]
localrule all:
input: results/annotation/mmseq2/flye_megahit_rbh, results/annotation/mmseq2/flye_metaspades_hybrid_rbh, results/annotation/mmseq2/megahit_metaspades_hybrid_rbh
jobid: 0
Job counts:
count jobs
1 all
1 mmseq_compare
2
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.```
首先,在输入中不需要
expand
。如果您希望创建具有相同模式的文件名列表,则需要执行此操作接下来,只要您已经在路径中使用了Unix类型的斜杠,就可以将
RESULTS_DIR
添加到f字符串中以提高可读性(但不要忘记将通配符的大括号加倍)最后,不需要将脚本管道与&&;:这就是Snakemake的设计目的
我的重写脚本版本:
我已经排除了
date
和日志记录。我的解决方案有一个限制,即比较的执行顺序是未定义的:在这种情况下,您需要重新考虑日志记录策略相关问题 更多 >
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