snakemake
如何連接不同的rule
我在stackoverflow中問了一個問題, 獲得了答案, 對snakemake的理解也加深了一成.
經驗所得
- 每一個
snakemake
的rule都要有input
,output
, 裏面的內容交叉的地方, 是確定不同rule的依賴, 比如rule1的輸出文件(output)b.bed, b.bim, b.fam
, 如果作爲rule2的輸入文件(input), 那麼rule1和rule2就可以關聯了. rule all
是定義最後的輸出文件, 比如rule2的最後輸出文件是c.raw
, 那麼也寫爲c.raw
即可.
測試文件
這裏, 有兩個plink的文件,a.map
和a.ped
, 內容如下:
(base) [dengfei@localhost plink-test]$ cat a.map
1 snp1 0 1
1 snp2 0 2
1 snp3 0 3
(base) [dengfei@localhost plink-test]$ cat a.ped
1 1 0 0 1 0 1 1 2 2 1 1
1 2 0 0 2 0 2 2 0 0 2 1
1 3 1 2 1 2 0 0 1 2 2 1
2 1 0 0 1 0 1 1 2 2 0 0
2 2 0 0 2 2 2 2 2 2 0 0
2 3 1 2 1 2 1 1 2 2 1 1
1. 將plink
文件變爲二進制bfile
格式
正常plink方式:
plink --file a --out b
結果:
(base) [dengfei@localhost plink-test]$ plink --file a --out b
PLINK v1.90b6.5 64-bit (13 Sep 2018) www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to b.log.
Options in effect:
--file a
--out b
63985 MB RAM detected; reserving 31992 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3 variants, 6 people).
--file: b.bed + b.bim + b.fam written.
2. 將bfile
變爲raw
格式
plink --bfile b --out c --recodeA
結果:
(base) [dengfei@localhost plink-test]$ plink --bfile b --out c --recodeA
PLINK v1.90b6.5 64-bit (13 Sep 2018) www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3
Note: --recodeA flag deprecated. Use 'recode A ...'.
Logging to c.log.
Options in effect:
--bfile b
--out c
--recode A
63985 MB RAM detected; reserving 31992 MB for main workspace.
3 variants loaded from .bim file.
6 people (4 males, 2 females) loaded from .fam.
3 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 4 founders and 2 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.777778.
3 variants and 6 people pass filters and QC.
Among remaining phenotypes, 3 are cases and 0 are controls. (3 phenotypes are
missing.)
--recode A to c.raw ... done.
3. 使用snakemake進行連接
命名爲: plink.smk
rule all:
input:
"c.log","c.raw"
rule bfile:
input:
"a.map","a.ped"
output:
"b.bed","b.bim","b.fam"
params:
a1 = "a",
a2 = "b"
shell:
"plink --file {params.a1} --out {params.a2}"
rule cfile:
input:
"b.bed","b.bim","b.fam"
output:
"c.log", "c.raw"
params:
aa1 = "b",
aa2 = "c"
shell:
"plink --bfile {params.aa1} --out {params.aa2} --recodeA"
命令解析:
- 1, rule all定義最終的輸出文件, 這裏fule cfile輸出的是
c.log
和c.raw
, 因此rule all中的input也寫爲c.log
和c.raw
- 2, rule bfile, 這裏的input是
a.map
和a.ped
, output是b.bed
,b.bim
,b.fam
, 這三個文件也要寫, 因爲是下一個rule的input文件, 建立依賴關係. - 3, rule cfile中建立input, 是上一個rule bfile的輸出, 這樣就建立的依賴
- 4, rule cfile中的output, 對應的是rule all的input, 這樣三個就建立好了依賴關係.
4. 查看流程圖
運行命令:
snakemake -s plink.smk
查看流程圖:
snakemake --dag -s plink.smk |dot -Tpdf >a.pdf
歡迎關注我的公衆號
相關閱讀: