我正在使用bcftools consensus
从vcf文件中提取单体型。给定输入文件:
A.sorted.bam
B.sorted.bam
将创建以下输出文件:
A.hap1.fna
A.hap2.fna
B.hap1.fna
B.hap2.fna
我目前有两条规则来做到这一点。它们在输出文件和shell命令中仅有数字1和2的区别。代码:
rule consensus1:
input:
vcf="variants/phased.vcf.gz",
tbi="variants/phased.vcf.gz.tbi",
bam="alignments/{sample}.sorted.bam"
output:
"haplotypes/{sample}.hap1.fna"
params:
sample="{sample}"
shell:
"bcftools consensus -i -s {params.sample} -H 1 -f {reference_file} {input.vcf} > {output}"
rule consensus2:
input:
vcf="variants/phased.vcf.gz",
tbi="variants/phased.vcf.gz.tbi",
bam="alignments/{sample}.sorted.bam"
output:
"haplotypes/{sample}.hap2.fna"
params:
sample="{sample}"
shell:
"bcftools consensus -i -s {params.sample} -H 2 -f {reference_file} {input.vcf} > {output}"
虽然这段代码可以工作,但似乎应该有一种更好、更有pythonic风格的方法,只使用一条规则就可以做到这一点。有没有可能把它压缩成一条规则,或者我目前的方法是最好的方法?
发布于 2018-04-02 11:19:40
对rule all
中的单倍型1和2使用通配符。See here了解有关通过rule all
添加目标的更多信息
reference_file = "ref.txt"
rule all:
input:
expand("haplotypes/{sample}.hap{hap_no}.fna",
sample=["A", "B"], hap_no=["1", "2"])
rule consensus1:
input:
vcf="variants/phased.vcf.gz",
tbi="variants/phased.vcf.gz.tbi",
bam="alignments/{sample}.sorted.bam"
output:
"haplotypes/{sample}.hap{hap_no}.fna"
params:
sample="{sample}",
hap_no="{hap_no}"
shell:
"bcftools consensus -i -s {params.sample} -H {params.hap_no} \
-f {reference_file} {input.vcf} > {output}"
https://stackoverflow.com/questions/49604782
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