在使用 Snakemake 变量在 R 脚本中时出错。

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英文:

Error when using Snakemake variable in R script

问题

The issue you're encountering is related to how you're trying to access the elements of the snakemake object in your R script. It seems like you're using HTML-encoded characters like " instead of the actual double quotes ".

To fix this, you should use double quotes directly when accessing elements of the snakemake object. For example:

Instead of:

  1. save(dds, snakemake@output[[2]])

Use:

  1. save(dds, snakemake@output[[2]])

Make sure you replace all instances of " with actual double quotes " in your R script where you access elements of the snakemake object. This should resolve the "object not found" error you're encountering.

英文:

I have got the following Snakemake rule:

  1. rule deseq2:
  2.     input:
  3.         salmon=expand("salmon/{sample}/quant.sf", sample=SAMPLES)
  4.     output:
  5.         xlsx="deseq2/deseq2_diff_trx.xlsx",
  6.         rdata="deseq2/dds.Rdata",
  7.     params:
  8.         map_with,
  9.         genome,
  10.         gtf,
  11.     log:
  12.         "logs/deseq2/deseq2.log"
  13.     conda:
  14.         "envs/deseq2.yml"
  15.     threads: config["resources"]["deseq2"]["cpu"]
  16.     resources: 
  17.         runtime=config["resources"]["deseq2"]["time"]
  18.     script:
  19.         "scripts/deseq2.R"

The part of that R script that the rule runs that gives an error is when I save a variable to a file name in the output section of the snakemake variable:

  1. save(dds, snakemake@output[[2]])
  1. Error in save(dds, snakemake@output[[2]]) : 
  2.   object ‘snakemake@output[[2]]’ not found

Earlier in the script I access the params part of the snakemake variable in a similar way, but without any errors:

  1. map.with <- snakemake@params[[1]]
  2. genome <- snakemake@params[[2]]
  3. gtf <- snakemake@params[[3]]

When I print the snakemake variable I get this (only partial,relevant output):

  1. An object of class "Snakemake"
  2. Slot "input":
  3. [[1]]
  4. [1] "salmon/Control-1/quant.sf"
  6. [[2]]
  7. [1] "salmon/Control-2/quant.sf"
  9. [[3]]
  10. [1] "salmon/Control-Hypoxia-1/quant.sf"
  12. [[4]]
  13. [1] "salmon/Control-Hypoxia-2/quant.sf"
  15. $salmon
  16. [1] "salmon/Control-1/quant.sf"         "salmon/Control-2/quant.sf"        
  17. [3] "salmon/Control-Hypoxia-1/quant.sf" "salmon/Control-Hypoxia-2/quant.sf"
  20. Slot "output":
  21. [[1]]
  22. [1] "deseq2/deseq2_diff_trx.xlsx"
  24. [[2]]
  25. [1] "deseq2/dds.Rdata"
  27. $xlsx
  28. [1] "deseq2/deseq2_diff_trx.xlsx"
  30. $rdata
  31. [1] "deseq2/dds.Rdata"
  34. Slot "params":
  35. [[1]]
  36. [1] "salmon"
  38. [[2]]
  39. [1] "hg38"
  41. [[3]]
  42. [1] "/home/user/Documents/references/gtf/hg38/gencode.v43.annotation.gtf"

I have also saved the work space to a file for debugging as suggest by the snakemake web site. When I load this into R I can do the following things:

  1. > snakemake@output[["rdata"]]
  2. [1] "deseq2/dds.Rdata"
  4. > snakemake@output[[2]]
  5. [1] "deseq2/dds.Rdata"

But when the above code is include in the proper script I get the object not found (see above) error.

What am I doing wrong?

答案1

得分: 1

  1. 未经测试，但我认为您想要的是：

save(dds, file = snakemake@output[[2]])

  2. 在您的代码中，`snakemake@output[[2]]` 出现为要保存的对象，而不是要保存到的文件。从`?save` 中相关的部分应该是：

用法:

  1.  save(..., list = character(),
  2.       file = stop("必须指定 'file'"),
  3.       ascii = FALSE, version = NULL, envir = parent.frame(),
  4.       compress = isTRUE(!ascii), compression_level,
  5.       eval.promises = TRUE, precheck = TRUE)
  6.  
  7.  save.image(file = ".RData", version = NULL, ascii = FALSE,
  8.             compress = !ascii, safe = TRUE)

参数:

  1.  ...: 要保存的对象的名称（作为符号或字符字符串）。
  3. list: 包含要保存的对象名称的字符向量。
  5. file: 一个可写的二进制模式连接或要保存数据的文件的名称（进行波浪线扩展时）。必须是 'save.image' 或 'version = 1' 的文件名。
  3. <details>
  4. <summary>英文:</summary>
  6. Not tested, but I think you want:

save(dds, file = snakemake@output[[2]])

  2. In your code, `snakemake@output[[2]]` appears as an object to be saved, not as the file to save to. The relevant bit from `?save` should be:

Usage:

  1.  save(..., list = character(),
  2.       file = stop(&quot;&#39;file&#39; must be specified&quot;),
  3.       ascii = FALSE, version = NULL, envir = parent.frame(),
  4.       compress = isTRUE(!ascii), compression_level,
  5.       eval.promises = TRUE, precheck = TRUE)
  6.  
  7.  save.image(file = &quot;.RData&quot;, version = NULL, ascii = FALSE,
  8.             compress = !ascii, safe = TRUE)

Arguments:

  1.  ...: the names of the objects to be saved (as symbols or character
  2.       strings).
  4. list: A character vector containing the names of objects to be
  5.       saved.
  7. file: a (writable binary-mode) connection or the name of the file
  8.       where the data will be saved (when tilde expansion is done).
  9.       Must be a file name for ‘save.image’ or ‘version = 1’.
  2. </details>

huangapple
  • 本文由 发表于 2023年6月26日 15:49:30
  • 转载请务必保留本文链接：https://go.coder-hub.com/76554595.html
  • python
  • r
  • snakemake
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