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所以我正在尝试使用snakemake构建管道，但我在访问配置文件中字典“small_reference”中的值时遇到了一些问题。根据示例，我想使用不同的参考进行对齐。

配置文件：

samples: ['C130165', 'C014044p', 'C130166', 'C130157', 'C014040p', 'C014054b-1', 'C051198-A', 'C014042p', 'C052007W-C', 'C130167', 'C051198-B', 'C130157A', 'C130165A', 'C014038p', 'C052004-B', 'C051198-C', 'C052004-C', 'C130167', 'C052003-B', 'C130165', 'C052003-A', 'C052004-A', 'C052002-C', 'C130157', 'C052005-C', 'C130157W', 'C130167A', 'C130157A', 'C130166A', 'C052002-A', 'C130157N', 'C052006-B', 'C014063pW', 'C130157W', 'C130157N', 'C014054b-2', 'C052002-B', 'C130167A', 'C052006-C', 'C130166A', 'C052007W-B', 'C052003-C', 'C130165A', 'C014064bW', 'C052005-B', 'C130166', 'C052006-A', 'C052005-A']


reference: "/mnt/storage/refs/human_1kg/human_g1k_v37.fasta"

index: "/mnt/storage/refs/human_1kg/human_g1k_v37.fasta.fai"

dbsnp: "/mnt/storage/refs/human_1kg/dbsnp_137.b37.vcf"

small_reference: {
    C01: "/mnt/storage/projects/hiv_data/refs/BRCA/BRCA12_PALB2.fasta",
    Z01: "/mnt/storage/projects/hiv_data/refs/BRCA/BRCA12.fasta",
    C02: "/mnt/storage/projects/hiv_data/refs/STICKLERS/STICKERS_ext.fasta",
    C03: "/mnt/storage/projects/hiv_data/refs/TS/TS.fasta",
    C04: "/mnt/storage/projects/hiv_data/refs/STICKLERS/STICKERS.fasta",
    C05: "/mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.fasta",
    C07: "/mnt/storage/projects/hiv_data/refs/NEMO/NEMO.fasta",
    C08: "/mnt/storage/projects/hiv_data/refs/HNPCC/HNPCC.fasta",
    C09: "/mnt/storage/projects/hiv_data/refs/TAU/TAU.fasta",
    C10: "/mnt/storage/projects/hiv_data/refs/THYROID/THYROID.fasta",
    C12: "/mnt/storage/projects/hiv_data/refs/VWF/VWF.fasta",
    C13: "/mnt/storage/refs/human_1kg/human_g1k_v37.fasta",
    C17: "/mnt/storage/projects/hiv_data/refs/DICER_PALB2/DICER_PALB2.fasta",
    C18: "/mnt/storage/projects/hiv_data/refs/DICER_PALB2/DICER_PALB2.fasta",
}

baits: {
    C01: "/mnt/storage/projects/hiv_data/refs/BRCA/BRCA12_PALB2.bed",
    Z01: "/mnt/storage/projects/hiv_data/refs/BRCA/BRCA12_exons.bed",
    C02: "/mnt/storage/projects/hiv_data/refs/STICKLERS/STICKERS_ext.bed",
    C03: "/mnt/storage/projects/hiv_data/refs/TS/TS_exons.bed",
    C04: "/mnt/storage/projects/hiv_data/refs/STICKLERS/STICKERS.bed",
    C05: "/mnt/storage/projects/hiv_data/refs/PKD_GANAB/PKD.bed",
    C07: "/mnt/storage/projects/hiv_data/refs/NEMO/NEMO.bed",
    C08: "/mnt/storage/projects/hiv_data/refs/HNPCC/HNPCC.bed",
    C09: "/mnt/storage/projects/hiv_data/refs/TAU/TAU.bed",
    C10: "/mnt/storage/projects/hiv_data/refs/THYROID/THYROID_v2.bed",
    C12: "/mnt/storage/projects/hiv_data/refs/VWF/VWF.bed",
    C13: "/mnt/storage/refs/human_1kg/human_g1k_v37.bed",
    C17: "/mnt/storage/projects/hiv_data/refs/DICER_PALB2/DICER_PALB2.bed",
    C18: "/mnt/storage/projects/hiv_data/refs/DICER_PALB2/DICER_PALB2.bed",
}

根据样本的前 3 个字符，我想选择不同的参考。当 config["samples"] 只是一个字符串时，我编写了一个可以解决问题的函数。但现在我想考虑运行文件夹，所以我有一个样本列表。

工作功能：

def get_ref(wildcards):
    prefix = config["samples"][0:3]
    return config["small_reference"][prefix]

当我刚刚更改配置文件时，我首先遇到了这个错误Duplicate output file pattern in rule（所以在运行完整管道时）

测试规则：

rule test:
    input:
        fq = expand("{sample}.1.fq.gz", sample = config["samples"]),
        ref = get_ref
    shell:
        "echo {input.fq} {input.ref}"

现在运行测试规则时出现此错误：

InputFunctionException in line 17 of /mnt/storage/home/kimy/projects/automate_CP/scripts/Snakefile:
TypeError: unhashable type: 'list'
Wildcards:

示例：C014038p --> C01 --> /mnt/storage/projects/hiv_data/refs/BRCA/BRCA12_PALB2.fasta

如何根据管道正在分析的样本的前缀获得正确的“small_reference”？

4

1 回答 1

0

原来我的snakemake都错了，expand()是用来创建通配符的——>只在规则中指定它，而不是在每个规则中。
修改后的功能：

def get_ref(wildcards):
    prefix = wildcards.sample[0:3]
    return config["small_reference"][prefix]
于 2019-07-04T15:31:33.437 回答