博文
snakemake 学习笔记3
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目标
这次, 我要实现这个路程图.
目标介绍
第一: 生成1.txt , 2.txt, 3.txt
第二: 向每个文件中加入”add a”字符, 命名为:1_add_a.txt, 2_add_a.txt, 3_add_a.txt
第三: 向文件中增加”add b”, 命名为:1_add_a_add_b.txt, 2_add_a_add_b.txt, 3_add_a_add_b.txt
第四: 向文件中增加”add c”, 命名为: 1_add_a_add_b_add_c.txt, 2_add_a_add_b_add_c.txt, 3_add_a_add_b_add_c.txt
第五: 将1_add_a_add_b.txt, 2_add_a_add_b.txt, 1_add_a_add_b_add_c.txt, 2_add_a_add_b_add_c.txt, 3_add_a_add_b_add_c.txt 合并为hebing.txt文件
1. 生成三个文件
(snake_test) [dengfei@localhost ex4]$ ls *txt 1.txt 2.txt 3.txt (snake_test) [dengfei@localhost ex4]$ cat *txt this is 1.txt this is 2.txt this is 3.txt
2. 在每个文件中增加”add a”
对应的Snakefile内容如下:
rule adda:
input: "{file}.txt"
output: "{file}_add_a.txt"
shell: "cat {input} |xargs echo add a >{output}"预览一下命令:snakemake -np {1,2,3}_add_a.txt
注意: 这里要把生成的文件{1,2,3}_add_a.txt写出来, 命令才可以运行.
(snake_test) [dengfei@localhost ex4]$ snakemake -np {1,2,3}_add_a.txt
Building DAG of jobs...
Job counts:
count jobs
3 adda
3
[Tue Apr 2 21:09:19 2019]
rule adda:
input: 3.txt
output: 3_add_a.txt
jobid: 2
wildcards: file=3
cat 3.txt |xargs echo add a >3_add_a.txt
[Tue Apr 2 21:09:19 2019]
rule adda:
input: 2.txt
output: 2_add_a.txt
jobid: 0
wildcards: file=2
cat 2.txt |xargs echo add a >2_add_a.txt
[Tue Apr 2 21:09:19 2019]
rule adda:
input: 1.txt
output: 1_add_a.txt
jobid: 1
wildcards: file=1
cat 1.txt |xargs echo add a >1_add_a.txt
Job counts:
count jobs
3 adda
3
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.执行命令:
snakemake {1,2,3}_add_a.txtBuilding DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 3 adda 3 [Tue Apr 2 21:11:09 2019] rule adda: input: 3.txt output: 3_add_a.txt jobid: 0 wildcards: file=3 [Tue Apr 2 21:11:09 2019] Finished job 0. 1 of 3 steps (33%) done [Tue Apr 2 21:11:09 2019] rule adda: input: 1.txt output: 1_add_a.txt jobid: 1 wildcards: file=1 [Tue Apr 2 21:11:09 2019] Finished job 1. 2 of 3 steps (67%) done [Tue Apr 2 21:11:09 2019] rule adda: input: 2.txt output: 2_add_a.txt jobid: 2 wildcards: file=2 [Tue Apr 2 21:11:09 2019] Finished job 2. 3 of 3 steps (100%) done Complete log: /home/dengfei/test/snakemake/ex4/.snakemake/log/2019-04-02T211109.153566.snakemake.log
查看*add_a.txt文件:
(snake_test) [dengfei@localhost ex4]$ ls *add_a.txt 1_add_a.txt 2_add_a.txt 3_add_a.txt (snake_test) [dengfei@localhost ex4]$ cat *add_a.txt add a this is 1.txt add a this is 2.txt add a this is 3.txt
搞定.
3. 在每个文件中增加”add b”
对应的Snakefile内容如下:
rule adda:
input: "{file}.txt"
output: "{file}_add_a.txt"
shell: "cat {input} |xargs echo add a >{output}"
rule addb:
input:
"{file}_add_a.txt"
output:
"{file}_add_a_add_b.txt"
shell:
"cat {input} | xargs echo add b >{output}"预览一下命令:snakemake -np {1,2,3}_add_a_add_b.txt
(snake_test) [dengfei@localhost ex4]$ snakemake {1,2,3}_add_a_add_b.txt
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
3 addb
3
[Tue Apr 2 21:13:57 2019]
rule addb:
input: 2_add_a.txt
output: 2_add_a_add_b.txt
jobid: 0
wildcards: file=2
[Tue Apr 2 21:13:57 2019]
Finished job 0.
1 of 3 steps (33%) done
[Tue Apr 2 21:13:57 2019]
rule addb:
input: 1_add_a.txt
output: 1_add_a_add_b.txt
jobid: 1
wildcards: file=1
[Tue Apr 2 21:13:57 2019]
Finished job 1.
2 of 3 steps (67%) done
[Tue Apr 2 21:13:57 2019]
rule addb:
input: 3_add_a.txt
output: 3_add_a_add_b.txt
jobid: 2
wildcards: file=3
[Tue Apr 2 21:13:57 2019]
Finished job 2.
3 of 3 steps (100%) done
Complete log: /home/dengfei/test/snakemake/ex4/.snakemake/log/2019-04-02T211357.666661.snakemake.log执行命令:
snakemake {1,2,3}_add_a_add_b.txt查看流程图
命令:
snakemake --dag {1,2,3}_add_a_add_b.txt |dot -Tpdf >a.pdf这里生成的a.pdf如下:
4. 在每个文件中增加”add c”
Snakemake命令:
rule adda:
input: "{file}.txt"
output: "{file}_add_a.txt"
shell: "cat {input} |xargs echo add a >{output}"
rule addb:
input:
"{file}_add_a.txt"
output:
"{file}_add_a_add_b.txt"
shell:
"cat {input} | xargs echo add b >{output}"
rule addc:
input:
"{file}_add_a_add_b.txt"
output:
"{file}_add_a_add_b_add_c.txt"
shell:
"cat {input} | xargs echo add c >{output}"流程图:
命令:
snakemake --dag {1,2,3}_add_a_add_b_add_c.txt |dot -Tpdf >a1.pdf
5. 将文件合并
rule adda:
input: "{file}.txt"
output: "{file}_add_a.txt"
shell: "cat {input} |xargs echo add a >{output}"
rule addb:
input:
"{file}_add_a.txt"
output:
"{file}_add_a_add_b.txt"
shell:
"cat {input} | xargs echo add b >{output}"
rule addc:
input:
"{file}_add_a_add_b.txt"
output:
"{file}_add_a_add_b_add_c.txt"
shell:
"cat {input} | xargs echo add c >{output}"
rule hebing:
input:
a=expand("{file}_add_a_add_b_add_c.txt",file=["1","2","3"]),
b=expand("{file}_add_a_add_b.txt",file=["1","2"])
output:"hebing.txt"
shell:"cat {input.a} {input.b} >{output}"执行命令:
snakemake hebing.txt
执行结果:
Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 3 addc 1 hebing 4 [Tue Apr 2 21:21:04 2019] rule addc: input: 1_add_a_add_b.txt output: 1_add_a_add_b_add_c.txt jobid: 1 wildcards: file=1 [Tue Apr 2 21:21:04 2019] Finished job 1. 1 of 4 steps (25%) done [Tue Apr 2 21:21:04 2019] rule addc: input: 3_add_a_add_b.txt output: 3_add_a_add_b_add_c.txt jobid: 3 wildcards: file=3 [Tue Apr 2 21:21:04 2019] Finished job 3. 2 of 4 steps (50%) done [Tue Apr 2 21:21:04 2019] rule addc: input: 2_add_a_add_b.txt output: 2_add_a_add_b_add_c.txt jobid: 2 wildcards: file=2 [Tue Apr 2 21:21:04 2019] Finished job 2. 3 of 4 steps (75%) done [Tue Apr 2 21:21:04 2019] rule hebing: input: 1_add_a_add_b_add_c.txt, 2_add_a_add_b_add_c.txt, 3_add_a_add_b_add_c.txt, 1_add_a_add_b.txt, 2_add_a_add_b.txt output: hebing.txt jobid: 0 [Tue Apr 2 21:21:04 2019] Finished job 0. 4 of 4 steps (100%) done Complete log: /home/dengfei/test/snakemake/ex4/.snakemake/log/2019-04-02T212104.719887.snakemake.log
流程图:
搞定
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