我有一个 snakemake 文件,其中包含连接示例表中列出的文件的规则。示例表如下所示:
sample unit fq1 fq2
A lane1 A.l1.1.R1.txt A.l1.1.R2.txt
A lane1 A.l1.2.R1.txt A.l1.2.R2.txt
A lane2 A.l2.R1.txt A.l2.R2.txt
B lane1 B.l1.R1.txt B.l1.R2.txt
B lane2 B.l2.R1.txt B.l2.R2.txt
我的目标是合并来自同一样本和同一单元的 fq1 文件并将它们放入 {sample}/fastq/ 中,并将样本上的结果文件( {sample}/fastq 中的文件)合并到 {sample}/bam/ 中
对于 {sample}/fastq 来说,它运行正常,但对于 {sample}/bam,{sample}/fastq 中列出的所有文件(不考虑样本)将在 {sample}/bam 中连接。有什么办法可以解决这个问题吗?
import pandas as pd
shell.executable("bash")
configfile: "config.yaml"
# open samplesheet
units = pd.read_table(config["units"], dtype=str)
# set df index
units=units.set_index(["sample","unit"])
rule all:
input:
expand("{sample}/bam/{sample}_bam.txt",
sample=units.index.get_level_values('sample').unique().values),
# functions to return information in the samplesheet
def get_fastq_r1(wildcards):
return units.loc[(wildcards.sample, wildcards.unit), ["fq1"]].dropna().values.flatten()
def get_fastq_r2(wildcards):
return units.loc[(wildcards.sample, wildcards.unit), ["fq2"]].dropna().values.flatten()
# merge files from the same sample and unit
rule merge_fastq_lane:
input:
r1 = get_fastq_r1,
r2 = get_fastq_r2
output:
r1_o = "{sample}/fastq/{sample}_{unit}_merge_R1.fastq",
r2_o = "{sample}/fastq/{sample}_{unit}_merge_R2.fastq"
message:
"Merge fastq from the same sample and lane"
shell:
"""
cat {input.r1} > {output.r1_o}
cat {input.r2} > {output.r2_o}
"""
# merge files from the same sample
rule align_lane:
input:
r1 = expand("{sample}/fastq/{sample}_{unit}_merge_R1.fastq",
unit=units.index.get_level_values('unit').unique().values,
sample=units.index.get_level_values('sample').unique().values),
r2 = expand("{sample}/fastq/{sample}_{unit}_merge_R2.fastq",
unit=units.index.get_level_values('unit').unique().values,
sample=units.index.get_level_values('sample').unique().values)
output:
bam = "{sample}/bam/{sample}_bam.txt"
message:
"Align lane with bwa mem"
shell:
"""
cat {input.r1} {input.r2} > {output.bam}
"""
在您的规则中align_lane
,您的输入列出了所有可能的样本。由于您sample
在输出中使用通配符,我猜您想在输入中使用它。在扩展函数中使用通配符的方法是将括号加倍。所以我想你的规则应该是这样的(如果我理解正确的话):
rule align_lane:
input:
r1 = expand("{{sample}}/fastq/{{sample}}_{unit}_merge_R1.fastq",
unit=units.index.get_level_values('unit').unique().values),
r2 = expand("{{sample}}/fastq/{{sample}}_{unit}_merge_R2.fastq",
unit=units.index.get_level_values('unit').unique().values)
output:
bam = "{sample}/bam/{sample}_bam.txt"
message:
"Align lane with bwa mem"
shell:
"""
cat {input.r1} {input.r2} > {output.bam}
"""